Here is a list of all class members with links to the classes they belong to:

- s -

• SALT_COMPONENTS_REMOVED : CDPL::Chem::ChEMBLStandardizer
• sampleAngleToleranceRanges() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings
• sampleHeteroAtomHydrogens() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings
• save() : CDPL::ConfGen::FragmentLibrary , CDPL::ConfGen::TorsionLibrary
• saveState() : CDPL::Vis::CairoRenderer2D , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D
• Scalar13QuaternionTernary() : CDPL::Math::Scalar13QuaternionTernary< E1, E2, E3, F >
• Scalar1GridBinary() : CDPL::Math::Scalar1GridBinary< E1, E2, F >
• Scalar1MatrixBinary() : CDPL::Math::Scalar1MatrixBinary< E1, E2, F >
• Scalar1QuaternionBinary1() : CDPL::Math::Scalar1QuaternionBinary1< E1, E2, F >
• Scalar1QuaternionBinary2() : CDPL::Math::Scalar1QuaternionBinary2< E1, E2, F >
• Scalar1VectorBinary() : CDPL::Math::Scalar1VectorBinary< E1, E2, F >
• Scalar2GridBinary() : CDPL::Math::Scalar2GridBinary< E1, E2, F >
• Scalar2MatrixBinary() : CDPL::Math::Scalar2MatrixBinary< E1, E2, F >
• Scalar2QuaternionBinary1() : CDPL::Math::Scalar2QuaternionBinary1< E1, E2, F >
• Scalar2QuaternionBinary2() : CDPL::Math::Scalar2QuaternionBinary2< E1, E2, F >
• Scalar2VectorBinary() : CDPL::Math::Scalar2VectorBinary< E1, E2, F >
• Scalar3QuaternionTernary() : CDPL::Math::Scalar3QuaternionTernary< E1, E2, E3, F >
• ScalarGrid() : CDPL::Math::ScalarGrid< T >
• ScalarMatrix() : CDPL::Math::ScalarMatrix< T >
• ScalarVector() : CDPL::Math::ScalarVector< T >
• scale() : CDPL::Vis::Rectangle2D
• SCALE1 : CDPL::Biomol::PDBData
• SCALE2 : CDPL::Biomol::PDBData
• SCALE3 : CDPL::Biomol::PDBData
• ScalingMatrix() : CDPL::Math::ScalingMatrix< T >
• ScoreCombinationFunction : CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator
• scoresDiminishedByAtomDensity() : CDPL::GRAIL::GRAILDataSetGenerator
• scoresNormalized() : CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator
• ScoringFunction : CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator , CDPL::Pharm::ScreeningProcessor , CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::ScreeningSettings
• ScreeningMode : CDPL::Shape::ScreeningSettings
• ScreeningProcessor() : CDPL::Pharm::ScreeningProcessor , CDPL::Shape::ScreeningProcessor
• ScreeningSettings() : CDPL::Shape::ScreeningSettings
• SDFMolecularGraphWriter() : CDPL::Chem::SDFMolecularGraphWriter
• SDFMoleculeReader() : CDPL::Chem::SDFMoleculeReader
• searchDB() : CDPL::Pharm::ScreeningProcessor
• SearchHit() : CDPL::Pharm::ScreeningProcessor::SearchHit
• seekBestAlignments() : CDPL::Pharm::ScreeningProcessor
• selected() : CDPL::ConfGen::RMSDConformerSelector
• SelfType : CDPL::Math::ComplexTraits< T > , CDPL::Math::InitListMatrix< T > , CDPL::Math::InitListVector< T > , CDPL::Math::ScalarTraits< T >
• SEMI_SPLIT : CDPL::Descr::MoleculeAutoCorr2DDescriptorCalculator
• SEQADV : CDPL::Biomol::PDBData
• SEQRES : CDPL::Biomol::PDBData
• set() : CDPL::Biomol::ResidueDictionary , CDPL::Chem::AtomDictionary , CDPL::ConfGen::FragmentLibrary , CDPL::ConfGen::TorsionLibrary , CDPL::ForceField::MMFF94AngleBendingParameterTable , CDPL::ForceField::MMFF94AromaticAtomTypeDefinitionTable , CDPL::ForceField::MMFF94AtomTypePropertyTable , CDPL::ForceField::MMFF94BondChargeIncrementTable , CDPL::ForceField::MMFF94BondStretchingParameterTable , CDPL::ForceField::MMFF94BondStretchingRuleParameterTable , CDPL::ForceField::MMFF94DefaultStretchBendParameterTable , CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable , CDPL::ForceField::MMFF94HeavyToHydrogenAtomTypeMap , CDPL::ForceField::MMFF94OutOfPlaneBendingParameterTable , CDPL::ForceField::MMFF94PartialBondChargeIncrementTable , CDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMap , CDPL::ForceField::MMFF94StretchBendParameterTable , CDPL::ForceField::MMFF94SymbolicAtomTypePatternTable , CDPL::ForceField::MMFF94SymbolicToNumericAtomTypeMap , CDPL::ForceField::MMFF94TorsionParameterTable , CDPL::ForceField::MMFF94VanDerWaalsParameterTable , CDPL::ForceField::UFFAtomTypePropertyTable , CDPL::Math::Quaternion< T > , CDPL::Math::QuaternionReference< Q > , CDPL::Math::RotationMatrix< T > , CDPL::Math::ScalingMatrix< T > , CDPL::Math::TranslationMatrix< T > , CDPL::Math::VectorQuaternionAdapter< V >
• setAbortCallback() : CDPL::ConfGen::ConformerGenerator , CDPL::ConfGen::FragmentAssembler , CDPL::ConfGen::FragmentConformerGenerator , CDPL::ConfGen::FragmentLibraryGenerator , CDPL::ConfGen::RMSDConformerSelector , CDPL::ConfGen::StructureGenerator , CDPL::ConfGen::TorsionDriver
• setAcceptorAngleScoringFunction() : CDPL::Pharm::HBondingInteractionScore , CDPL::Pharm::XBondingInteractionScore
• setAHDAngleScoringFunction() : CDPL::Pharm::HBondingInteractionScore
• setAlignedColorSelfOverlap() : CDPL::Shape::AlignmentResult
• setAlignedSelfOverlap() : CDPL::Shape::AlignmentResult
• setAlignedShapeIndex() : CDPL::Shape::AlignmentResult
• setAlignmentMode() : CDPL::Shape::ScreeningSettings
• setAlpha() : CDPL::Vis::Color
• setAngleBendingFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setAngleBendingParameterTable() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94InteractionParameterizer
• setAngleScoringFunction() : CDPL::Pharm::CationPiInteractionScore , CDPL::Pharm::OrthogonalPiPiInteractionScore , CDPL::Pharm::ParallelPiPiInteractionScore
• setAromaticAtomTypeDefinitionTable() : CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94InteractionParameterizer
• setAromaticRingSetFunction() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94BondTyper , CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94TorsionInteractionParameterizer
• setAtom2DCoordinatesFunction() : CDPL::Chem::BondStereoFlagCalculator
• setAtom3DCoordinatesCheckFunction() : CDPL::Chem::Hydrogen3DCoordinatesCalculator
• setAtom3DCoordinatesFunction() : CDPL::Chem::Hydrogen3DCoordinatesCalculator , CDPL::Chem::SurfaceAtomExtractor , CDPL::Descr::MoleculeAutoCorr3DDescriptorCalculator , CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::GRAIL::AtomDensityGridCalculator , CDPL::GRAIL::BuriednessGridCalculator , CDPL::GRAIL::BuriednessScore , CDPL::Pharm::FeatureGenerator , CDPL::Pharm::PharmacophoreGenerator
• setAtomChargeFunction() : CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer
• setAtomDescriptorFunction() : CDPL::Descr::PathFingerprintGenerator
• setAtomHardness() : CDPL::Shape::GaussianShapeGenerator
• setAtomHashSeedFunction() : CDPL::Chem::HashCodeCalculator
• setAtomIdentifierFunction() : CDPL::Descr::CircularFingerprintGenerator
• setAtomMatchExpressionFunction() : CDPL::Chem::SubstructureSearch
• setAtomPairWeightFunction() : CDPL::Descr::AutoCorrelation2DVectorCalculator , CDPL::Descr::MoleculeAutoCorr2DDescriptorCalculator , CDPL::Descr::MoleculeAutoCorr3DDescriptorCalculator , CDPL::Descr::MoleculeRDFDescriptorCalculator
• setAtomPredicate() : CDPL::Chem::StereoisomerGenerator
• setAtomPropertyFlags() : CDPL::Chem::AutomorphismGroupSearch , CDPL::Chem::CanonicalNumberingCalculator , CDPL::Chem::SymmetryClassCalculator
• setAtomRadius() : CDPL::Shape::GaussianShapeGenerator
• setAtomTypeFunction() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94BondTyper , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer , CDPL::ForceField::MMFF94TorsionInteractionParameterizer , CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer
• setAtomTypePropertyTable() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94BondTyper , CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer , CDPL::ForceField::MMFF94TorsionInteractionParameterizer
• setAtomWeightFunction() : CDPL::Descr::BCUTDescriptorCalculator , CDPL::Descr::BurdenMatrixGenerator
• setAXBAngleScoringFunction() : CDPL::Pharm::XBondingInteractionScore
• setBegin() : CDPL::Vis::Line2D
• setBeginToLineSegIntersection() : CDPL::Vis::Line2D
• setBeta() : CDPL::ForceField::MMFF94VanDerWaalsParameterTable
• setBlue() : CDPL::Vis::Color
• setBold() : CDPL::Vis::Font
• setBondAtom1Type() : CDPL::ConfGen::TorsionCategory
• setBondAtom2Type() : CDPL::ConfGen::TorsionCategory
• setBondChargeIncrementTable() : CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94InteractionParameterizer
• setBondDescriptorFunction() : CDPL::Descr::PathFingerprintGenerator
• setBondHashSeedFunction() : CDPL::Chem::HashCodeCalculator
• setBondIdentifierFunction() : CDPL::Descr::CircularFingerprintGenerator
• setBondMatchExpressionFunction() : CDPL::Chem::SubstructureSearch
• setBondPredicate() : CDPL::Chem::StereoisomerGenerator
• setBondPropertyFlags() : CDPL::Chem::AutomorphismGroupSearch , CDPL::Chem::CanonicalNumberingCalculator , CDPL::Chem::SymmetryClassCalculator
• setBondStretchingFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setBondStretchingParameterTable() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94InteractionParameterizer
• setBondStretchingRuleParameterTable() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94InteractionParameterizer
• setBondTypeIndexFunction() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94TorsionInteractionParameterizer
• setBounds() : CDPL::Vis::Rectangle2D
• setBoxSize() : CDPL::ConfGen::DGStructureGeneratorSettings
• setBrush() : CDPL::Vis::CairoRenderer2D , CDPL::Vis::EllipsePrimitive2D , CDPL::Vis::PathPrimitive2D , CDPL::Vis::PolygonPrimitive2D , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D
• setCallbackFunction() : CDPL::Chem::TautomerGenerator
• setCapStyle() : CDPL::Vis::Pen
• setChainHydrophobicityThreshold() : CDPL::Pharm::HydrophobicFeatureGenerator
• setChargeCountWindow() : CDPL::Chem::ResonanceStructureGenerator
• setCleanupFunction() : CDPL::Util::ObjectPool< T > , CDPL::Util::ObjectStack< T >
• setClipPath() : CDPL::Vis::CairoRenderer2D , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D
• setColor() : CDPL::Shape::GaussianShape::Element , CDPL::Vis::Brush , CDPL::Vis::Pen
• setColorFeatureType() : CDPL::Shape::ScreeningSettings
• setColorFilterFunction() : CDPL::Shape::ExactGaussianShapeOverlapFunction , CDPL::Shape::FastGaussianShapeOverlapFunction , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::GaussianShapeOverlapFunction
• setColorMatchFunction() : CDPL::Shape::ExactGaussianShapeOverlapFunction , CDPL::Shape::FastGaussianShapeOverlapFunction , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::GaussianShapeOverlapFunction
• setColorOverlap() : CDPL::Shape::AlignmentResult
• setConfiguration() : CDPL::Chem::StereoDescriptor
• setConformers() : CDPL::ConfGen::ConformerGenerator , CDPL::ConfGen::FragmentConformerGenerator
• setConstraintFunction() : CDPL::Pharm::InteractionAnalyzer
• setConvergenceCheckCycleSize() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings
• setCoordinates() : CDPL::ConfGen::StructureGenerator
• setCoordinatesTransform() : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• setCoreEnvironmentRadius() : CDPL::Pharm::InteractionPharmacophoreGenerator
• setCustomSetupFunction() : CDPL::Chem::TautomerGenerator
• setCycleStepCountFactor() : CDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >
• setDampingFactor() : CDPL::MolProp::PEOESigmaChargeCalculator
• setData() : CDPL::Chem::StringDataBlockEntry
• setDataMode() : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• setDataWriter() : CDPL::Pharm::FileScreeningHitCollector
• setDBAccessor() : CDPL::Pharm::ScreeningProcessor
• setDefaultStretchBendParameterTable() : CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer
• setDensityCombinationFunction() : CDPL::GRAIL::AtomDensityGridCalculator
• setDensityFunction() : CDPL::GRAIL::AtomDensityGridCalculator
• setDescription() : CDPL::Base::DataFormat
• setDGModeForceFieldType() : CDPL::ConfGen::StructureGeneratorSettings
• setDielectricConstant() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings , CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer , CDPL::ForceField::MMFF94InteractionParameterizer
• setDistanceCutoff() : CDPL::GRAIL::AtomDensityGridCalculator , CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunction
• setDistanceExponent() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings , CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer , CDPL::ForceField::MMFF94InteractionParameterizer
• setDistanceScoringFunction() : CDPL::Pharm::CationPiInteractionScore , CDPL::Pharm::FeatureDistanceScore , CDPL::Pharm::HBondingInteractionScore , CDPL::Pharm::OrthogonalPiPiInteractionScore , CDPL::Pharm::ParallelPiPiInteractionScore , CDPL::Pharm::XBondingInteractionScore
• setElectronContrib() : CDPL::Chem::ElectronSystem
• setElectrostaticFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setElement() : CDPL::Util::Array< ValueType >
• setEnabledInteractionTypes() : CDPL::ForceField::MMFF94EnergyCalculator< ValueType > , CDPL::ForceField::MMFF94GradientCalculator< ValueType >
• setEnabledReactionRoles() : CDPL::Chem::ReactionSubstructureSearch
• setEnd() : CDPL::Vis::Line2D
• setEndToLineSegIntersection() : CDPL::Vis::Line2D
• setEnergy() : CDPL::ConfGen::ConformerData
• setEnergyWindow() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings , CDPL::ConfGen::TorsionDriverSettings
• setEntity3DCoordinatesFunction() : CDPL::Chem::SpatialEntityAlignment< T > , CDPL::Descr::AutoCorrelation3DVectorCalculator< T > , CDPL::Descr::RDFCodeCalculator< T >
• setEntityMatchFunction() : CDPL::Chem::SpatialEntityAlignment< T > , CDPL::Chem::TopologicalEntityAlignment< T >
• setEntityPairMatchFunction() : CDPL::Chem::SpatialEntityAlignment< T > , CDPL::Chem::TopologicalEntityAlignment< T >
• setEntityPairWeightFunction() : CDPL::Descr::AutoCorrelation3DVectorCalculator< T > , CDPL::Descr::RDFCodeCalculator< T >
• setEntityWeightFunction() : CDPL::Chem::SpatialEntityAlignment< T >
• setEntries() : CDPL::Util::Map< Key, Value, AllowDefValues, KeyCompFunc > , CDPL::Util::MultiMap< Key, Value, AllowDefValues, KeyCompFunc >
• setEntry() : CDPL::Util::Map< Key, Value, AllowDefValues, KeyCompFunc > , CDPL::Util::MultiMap< Key, Value, AllowDefValues, KeyCompFunc >
• setEnvironmentAtomDensityGridName() : CDPL::GRAIL::GRAILDataSetGenerator
• setExponent() : CDPL::ForceField::MMFF94VanDerWaalsParameterTable
• setFactorB() : CDPL::ForceField::MMFF94VanDerWaalsParameterTable
• setFactorDAEPS() : CDPL::ForceField::MMFF94VanDerWaalsParameterTable
• setFactorDARAD() : CDPL::ForceField::MMFF94VanDerWaalsParameterTable
• setFamily() : CDPL::Vis::Font
• setFeature3DCoordinatesFunction() : CDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator
• setFeatureBits() : CDPL::Descr::CircularFingerprintGenerator
• setFeatureGenerator() : CDPL::Pharm::PharmacophoreGenerator
• setFeatureGeometry() : CDPL::Pharm::AromaticFeatureGenerator , CDPL::Pharm::HydrophobicAtomFeatureGenerator , CDPL::Pharm::HydrophobicFeatureGenerator
• setFeatureGeometryMatchWeight() : CDPL::Pharm::PharmacophoreFitScore
• setFeatureHardness() : CDPL::Shape::GaussianShapeGenerator
• setFeatureMatchCountWeight() : CDPL::Pharm::PharmacophoreFitScore
• setFeaturePairWeightFunction() : CDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator
• setFeaturePositionMatchWeight() : CDPL::Pharm::PharmacophoreFitScore
• setFeatureRadius() : CDPL::Shape::GaussianShapeGenerator
• setFeatureSelectionPredicate() : CDPL::GRAIL::FeatureInteractionScoreGridCalculator
• setFeatureTolerance() : CDPL::Pharm::AromaticFeatureGenerator , CDPL::Pharm::HydrophobicAtomFeatureGenerator , CDPL::Pharm::HydrophobicFeatureGenerator
• setFeatureType() : CDPL::Pharm::AromaticFeatureGenerator , CDPL::Pharm::HydrophobicAtomFeatureGenerator , CDPL::Pharm::HydrophobicFeatureGenerator
• setFileExtension() : CDPL::Base::DataFormat
• setFillRule() : CDPL::Vis::Path2D
• setFilterFunction() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer , CDPL::ForceField::MMFF94TorsionInteractionParameterizer , CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer
• setFixedAtomMask() : CDPL::ForceField::MMFF94GradientCalculator< ValueType >
• setFixedPitch() : CDPL::Vis::Font
• setFont() : CDPL::Vis::CairoFontMetrics , CDPL::Vis::CairoRenderer2D , CDPL::Vis::FontMetrics , CDPL::Vis::QtFontMetrics , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D , CDPL::Vis::TextLabelPrimitive2D
• setFontMetrics() : CDPL::Vis::ReactionView2D , CDPL::Vis::StructureView2D , CDPL::Vis::View2D
• setForceFieldType() : CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings
• setForceFieldTypeStochastic() : CDPL::ConfGen::ConformerGeneratorSettings
• setForceFieldTypeSystematic() : CDPL::ConfGen::ConformerGeneratorSettings
• setFormalAtomChargeDefinitionTable() : CDPL::ForceField::MMFF94InteractionParameterizer
• setFormalChargeDefinitionTable() : CDPL::ForceField::MMFF94ChargeCalculator
• setFoundMappingCallback() : CDPL::Chem::AutomorphismGroupSearch
• setFragmentFilterFunction() : CDPL::Chem::FragmentGenerator
• setFragmentLibrary() : CDPL::ConfGen::FragmentLibraryGenerator
• setFragmentModeForceFieldType() : CDPL::ConfGen::StructureGeneratorSettings
• setGenerationMode() : CDPL::ConfGen::StructureGeneratorSettings
• setGeneric() : CDPL::Chem::FragmentGenerator::ExcludePattern
• setGeometryMatchFunction() : CDPL::Pharm::SpatialFeatureMapping
• setGreen() : CDPL::Vis::Color
• setGridName() : CDPL::GRAIL::GRAILDataSetGenerator
• setGridOversize() : CDPL::Chem::SurfaceAtomExtractor
• setGridParamsForBoundingBox() : CDPL::GRAIL::GRAILDataSetGenerator
• setGridStepSize() : CDPL::Chem::SurfaceAtomExtractor , CDPL::GRAIL::GRAILDataSetGenerator
• setGridTransform() : CDPL::GRAIL::GRAILDataSetGenerator
• setGridXSize() : CDPL::GRAIL::GRAILDataSetGenerator
• setGridYSize() : CDPL::GRAIL::GRAILDataSetGenerator
• setGridZSize() : CDPL::GRAIL::GRAILDataSetGenerator
• setGroupHydrophobicityThreshold() : CDPL::Pharm::HydrophobicFeatureGenerator
• setHardness() : CDPL::Shape::GaussianShape::Element
• setHashCode() : CDPL::ConfGen::FragmentLibraryEntry
• setHeader() : CDPL::Chem::StringDataBlockEntry
• setHeavyToHydrogenAtomTypeMap() : CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94InteractionParameterizer
• setHeight() : CDPL::Vis::EllipsePrimitive2D
• setHitCallback() : CDPL::Pharm::ScreeningProcessor , CDPL::Shape::ScreeningProcessor
• setHitReportMode() : CDPL::Pharm::ScreeningProcessor
• setHydrogenCountFunction() : CDPL::Chem::CanonicalNumberingCalculator
• setHydrophobicityThreshold() : CDPL::Pharm::HydrophobicAtomFeatureGenerator
• setID() : CDPL::Chem::FragmentGenerator::FragmentationRule , CDPL::Chem::MatchConstraint
• setInitFunction() : CDPL::Util::ObjectPool< T > , CDPL::Util::ObjectStack< T >
• setItalic() : CDPL::Vis::Font
• setJoinStyle() : CDPL::Vis::Pen
• setLearningRateDecrement() : CDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >
• setLineStyle() : CDPL::Vis::Pen
• setLogMessageCallback() : CDPL::ConfGen::ConformerGenerator , CDPL::ConfGen::FragmentAssembler , CDPL::ConfGen::FragmentConformerGenerator , CDPL::ConfGen::FragmentLibraryGenerator , CDPL::ConfGen::StructureGenerator , CDPL::ConfGen::TorsionDriver
• setMacrocycleRotorBondCountThreshold() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings
• setMatchPattern() : CDPL::Chem::FragmentGenerator::ExcludePattern , CDPL::Chem::FragmentGenerator::FragmentationRule , CDPL::ConfGen::TorsionCategory , CDPL::ConfGen::TorsionRule
• setMatchPatternString() : CDPL::ConfGen::TorsionCategory , CDPL::ConfGen::TorsionRule
• setMax() : CDPL::Vis::Rectangle2D
• setMaxAROrientationDeviation() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMaxDistance() : CDPL::Descr::AutoCorrelation2DVectorCalculator , CDPL::Descr::MoleculeAutoCorr2DDescriptorCalculator
• setMaxHBAInteractionDirAngle() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMaxHBAOrientationDeviation() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMaxHBDInteractionDirDeviation() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMaxNumGeneratedStructures() : CDPL::Chem::ResonanceStructureGenerator
• setMaxNumMappings() : CDPL::Chem::AutomorphismGroupSearch , CDPL::Chem::CommonConnectedSubstructureSearch , CDPL::Chem::MaxCommonAtomSubstructureSearch , CDPL::Chem::MaxCommonBondSubstructureSearch , CDPL::Chem::ReactionSubstructureSearch , CDPL::Chem::SubstructureSearch
• setMaxNumOmittedFeatures() : CDPL::Pharm::ScreeningProcessor
• setMaxNumOptimizationIterations() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::ScreeningSettings
• setMaxNumOutputConformers() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings
• setMaxNumRefinementIterations() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings
• setMaxNumSampledConformers() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings , CDPL::ConfGen::StructureGeneratorSettings
• setMaxNumSymmetryMappings() : CDPL::ConfGen::RMSDConformerSelector
• setMaxOrder() : CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunction
• setMaxPathLength() : CDPL::Descr::PathFingerprintGenerator
• setMaxPoolSize() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings
• setMaxRandomTranslation() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator
• setMaxRotatableBondCount() : CDPL::ConfGen::ConformerGeneratorSettings
• setMaxSize() : CDPL::Util::ObjectPool< T > , CDPL::Util::ObjectStack< T >
• setMaxXBAInteractionDirDeviation() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMaxXBDInteractionDirDeviation() : CDPL::Pharm::FeatureGeometryMatchFunctor
• setMimeType() : CDPL::Base::DataFormat
• setMin() : CDPL::Vis::Rectangle2D
• setMinNumSampledConformers() : CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings
• setMinPathLength() : CDPL::Descr::PathFingerprintGenerator
• setMinRingSize() : CDPL::Chem::StereoisomerGenerator
• setMinRMSD() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings , CDPL::ConfGen::RMSDConformerSelector
• setMinSubstructureSize() : CDPL::Chem::CommonConnectedSubstructureSearch , CDPL::Chem::MaxCommonAtomSubstructureSearch , CDPL::Chem::MaxCommonBondSubstructureSearch
• setMinSurfaceAccessibility() : CDPL::Chem::SurfaceAtomExtractor
• setMinTopologicalMappingSize() : CDPL::Chem::SpatialEntityAlignment< T >
• setMinVdWSurfaceDistance() : CDPL::GRAIL::BuriednessGridCalculator , CDPL::GRAIL::BuriednessScore
• setMode() : CDPL::Chem::TautomerGenerator , CDPL::Descr::MoleculeAutoCorr2DDescriptorCalculator
• setMolecularGraphMatchExpressionFunction() : CDPL::Chem::SubstructureSearch
• setMultiRecordFormat() : CDPL::Base::DataFormat
• setName() : CDPL::Base::DataFormat , CDPL::Base::LookupKey , CDPL::ConfGen::TorsionCategory
• setNitrogenEnumerationMode() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentAssemblerSettings
• setNumBits() : CDPL::Descr::PathFingerprintGenerator
• setNumCycles() : CDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >
• setNumericAtomTypeFunction() : CDPL::ForceField::MMFF94ChargeCalculator
• setNumIterations() : CDPL::Descr::CircularFingerprintGenerator , CDPL::MolProp::PEOESigmaChargeCalculator
• setNumRandomStarts() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator , CDPL::Shape::ScreeningSettings
• setNumSteps() : CDPL::Descr::AutoCorrelation3DVectorCalculator< T > , CDPL::Descr::MoleculeAutoCorr3DDescriptorCalculator , CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator , CDPL::Descr::RDFCodeCalculator< T >
• setNumTestPoints() : CDPL::Chem::SurfaceAtomExtractor
• setNumTestRays() : CDPL::GRAIL::BuriednessGridCalculator , CDPL::GRAIL::BuriednessScore
• setOptimizationStopGradient() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::ScreeningSettings
• setOutOfPlaneBendingFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setOutOfPlaneBendingParameterTable() : CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer
• setOverlap() : CDPL::Shape::AlignmentResult
• setOverlapFunction() : CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment
• setOverlined() : CDPL::Vis::Font
• setParameter() : CDPL::Base::ControlParameterContainer
• setParameterAtomTypeMap() : CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL::ForceField::MMFF94TorsionInteractionParameterizer
• setParameterSet() : CDPL::ForceField::MMFF94InteractionParameterizer
• setParent() : CDPL::Base::ControlParameterContainer
• setPartialBondChargeIncrementTable() : CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94InteractionParameterizer
• setPen() : CDPL::Vis::CairoRenderer2D , CDPL::Vis::EllipsePrimitive2D , CDPL::Vis::LinePrimitive2D , CDPL::Vis::LineSegmentListPrimitive2D , CDPL::Vis::PathPrimitive2D , CDPL::Vis::PointListPrimitive2D , CDPL::Vis::PolygonPrimitive2D , CDPL::Vis::PolylinePrimitive2D , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D , CDPL::Vis::TextLabelPrimitive2D
• setPharmacophoreGenerator() : CDPL::Shape::GaussianShapeGenerator
• setPharmacophoreProcessingFunction() : CDPL::GRAIL::GRAILDataSetGenerator
• setPoints() : CDPL::Vis::Line2D
• setPosition() : CDPL::Shape::GaussianShape::Element , CDPL::Vis::EllipsePrimitive2D , CDPL::Vis::TextLabelPrimitive2D
• setPositionMatchFunction() : CDPL::Pharm::SpatialFeatureMapping
• setPrimaryToParameterAtomTypeMap() : CDPL::ForceField::MMFF94InteractionParameterizer
• setProbeRadius() : CDPL::Chem::SurfaceAtomExtractor , CDPL::GRAIL::BuriednessGridCalculator , CDPL::GRAIL::BuriednessScore
• setProgressCallback() : CDPL::Pharm::ScreeningProcessor
• setProperty() : CDPL::Base::PropertyContainer
• setQuery() : CDPL::Chem::CommonConnectedSubstructureSearch , CDPL::Chem::MaxCommonAtomSubstructureSearch , CDPL::Chem::MaxCommonBondSubstructureSearch , CDPL::Chem::ReactionSubstructureSearch , CDPL::Chem::SubstructureSearch
• setRadius() : CDPL::Shape::GaussianShape::Element
• setRadiusIncrement() : CDPL::Descr::AutoCorrelation3DVectorCalculator< T > , CDPL::Descr::MoleculeAutoCorr3DDescriptorCalculator , CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator , CDPL::Descr::RDFCodeCalculator< T >
• setRadiusScalingFactor() : CDPL::Shape::FastGaussianShapeOverlapFunction
• setRandomSeed() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator , CDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >
• setReaction() : CDPL::Vis::ReactionView2D
• setReactionPattern() : CDPL::Chem::Reactor
• setRecord() : CDPL::Biomol::PDBData
• setRecordIndex() : CDPL::Base::DataReader< T > , CDPL::Pharm::PSDMoleculeReader , CDPL::Pharm::PSDPharmacophoreReader , CDPL::Util::CompoundDataReader< DataType > , CDPL::Util::CompressedDataReader< ReaderImpl, DecompStream, DataType > , CDPL::Util::FileDataReader< ReaderImpl, DataType > , CDPL::Util::MultiFormatDataReader< DataType > , CDPL::Util::StreamDataReader< DataType, ReaderImpl >
• setRed() : CDPL::Vis::Color
• setReference() : CDPL::Shape::GaussianShapeAlignmentStartGenerator , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator
• setReferenceAngle() : CDPL::ForceField::MMFF94AngleBendingInteraction , CDPL::ForceField::MMFF94StretchBendInteraction
• setReferenceColorSelfOverlap() : CDPL::Shape::AlignmentResult
• setReferenceLength() : CDPL::ForceField::ElasticPotential , CDPL::ForceField::MMFF94BondStretchingInteraction
• setReferenceLength1() : CDPL::ForceField::MMFF94StretchBendInteraction
• setReferenceLength2() : CDPL::ForceField::MMFF94StretchBendInteraction
• setReferenceSelfOverlap() : CDPL::Shape::AlignmentResult
• setReferenceShapeIndex() : CDPL::Shape::AlignmentResult
• setReferenceShapeSetIndex() : CDPL::Shape::AlignmentResult
• setRefinementStopGradient() : CDPL::ConfGen::FragmentConformerGeneratorSettings
• setRefinementTolerance() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings
• setRelation() : CDPL::Chem::MatchConstraint
• setRelative() : CDPL::Vis::SizeSpecification
• setResultCompareFunction() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment
• setResultSelectionMode() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment
• setRGBA() : CDPL::Vis::Color
• setRingHydrophobicityThreshold() : CDPL::Pharm::HydrophobicFeatureGenerator
• setRuleID() : CDPL::Chem::FragmentGenerator::ExcludePattern
• setSamplingMode() : CDPL::ConfGen::ConformerGeneratorSettings
• setScalingFactor() : CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator , CDPL::Descr::RDFCodeCalculator< T >
• setScore() : CDPL::Shape::AlignmentResult
• setScoreCombinationFunction() : CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator
• setScoreCutoff() : CDPL::Shape::ScreeningSettings
• setScoringFunction() : CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator , CDPL::Pharm::ScreeningProcessor , CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::ScreeningSettings
• setScreeningMode() : CDPL::Shape::ScreeningSettings
• setShape() : CDPL::Shape::GaussianShapeFunction
• setShapeFunction() : CDPL::Shape::ExactGaussianShapeOverlapFunction , CDPL::Shape::FastGaussianShapeOverlapFunction , CDPL::Shape::GaussianShapeOverlapFunction
• setSize() : CDPL::Vis::Font
• setSmallRingSystemSamplingFactor() : CDPL::ConfGen::FragmentConformerGeneratorSettings
• setSMILES() : CDPL::ConfGen::FragmentLibraryEntry
• setSmoothingFactor() : CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator , CDPL::Descr::RDFCodeCalculator< T >
• setStartGenerator() : CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunctionAlignment
• setStartLearningRate() : CDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >
• setStartRadius() : CDPL::Descr::AutoCorrelation3DVectorCalculator< T > , CDPL::Descr::MoleculeAutoCorr3DDescriptorCalculator , CDPL::Descr::MoleculeRDFDescriptorCalculator , CDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculator , CDPL::Descr::PharmacophoreRDFDescriptorCalculator , CDPL::Descr::RDFCodeCalculator< T >
• setStretchBendFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setStretchBendParameterTable() : CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer
• setStrikedOut() : CDPL::Vis::Font
• setStructure() : CDPL::Vis::StructureView2D
• setStyle() : CDPL::Vis::Brush
• setSymbolicAtomTypeFunction() : CDPL::ForceField::MMFF94ChargeCalculator
• setSymbolicAtomTypePatternTable() : CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94InteractionParameterizer
• setSymbolicToNumericAtomTypeMap() : CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94InteractionParameterizer
• setSymmetryThreshold() : CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator
• setText() : CDPL::Vis::TextLabelPrimitive2D
• setTimeout() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettings , CDPL::ConfGen::StructureGeneratorSettings
• setTimeoutCallback() : CDPL::ConfGen::ConformerGenerator , CDPL::ConfGen::FragmentAssembler , CDPL::ConfGen::FragmentConformerGenerator , CDPL::ConfGen::FragmentLibraryGenerator , CDPL::ConfGen::StructureGenerator , CDPL::ConfGen::TorsionDriver
• setTopAlignmentConstraintFunction() : CDPL::Chem::SpatialEntityAlignment< T >
• setTopologicalDistanceFunction() : CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer , CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer
• setTorsionFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setTorsionLibrary() : CDPL::ConfGen::TorsionRuleMatcher
• setTorsionParameterTable() : CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94TorsionInteractionParameterizer
• setTransform() : CDPL::Shape::AlignmentResult , CDPL::Vis::CairoRenderer2D , CDPL::Vis::QtRenderer2D , CDPL::Vis::Renderer2D
• setType() : CDPL::Chem::MatchConstraintList
• setTypeMatchFunction() : CDPL::Pharm::SpatialFeatureMapping
• setUnderlined() : CDPL::Vis::Font
• setup() : CDPL::Chem::CIPConfigurationLabeler , CDPL::Chem::Hydrogen3DCoordinatesCalculator , CDPL::Chem::PatternBasedTautomerizationRule , CDPL::Chem::StereoisomerGenerator , CDPL::Chem::TautomerizationRule , CDPL::ConfGen::DGConstraintGenerator , CDPL::ConfGen::DGStructureGenerator , CDPL::ConfGen::RMSDConformerSelector , CDPL::ConfGen::TorsionDriver , CDPL::ForceField::MMFF94EnergyCalculator< ValueType > , CDPL::ForceField::MMFF94GradientCalculator< ValueType > , CDPL::Math::BFGSMinimizer< VA, VT, FVT >
• setupAligned() : CDPL::Shape::GaussianShapeAlignmentStartGenerator , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator
• setupReference() : CDPL::Shape::GaussianShapeAlignmentStartGenerator , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::PrincipalAxesAlignmentStartGenerator
• setValue() : CDPL::Chem::MatchConstraint , CDPL::Vis::SizeSpecification
• setVanDerWaalsFilterFunction() : CDPL::ForceField::MMFF94InteractionParameterizer
• setVanDerWaalsParameterTable() : CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer
• setWidth() : CDPL::Vis::EllipsePrimitive2D , CDPL::Vis::Pen
• setXStepSize() : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• setXYData() : CDPL::Math::MLRModel< T >
• setYStepSize() : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• setZStepSize() : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• SHAPE_CENTROID : CDPL::Shape::ScreeningSettings
• ShapeTverskyScore() : CDPL::Shape::ShapeTverskyScore
• SharedObjectPointer : CDPL::Util::ObjectPool< T >
• SharedPointer : CDPL::Base::ControlParameterList , CDPL::Base::DataInputHandler< T > , CDPL::Base::DataOutputHandler< T > , CDPL::Base::DataReader< T > , CDPL::Base::DataWriter< T > , CDPL::Biomol::HierarchyView , CDPL::Biomol::PDBData , CDPL::Biomol::ResidueDictionary , CDPL::Biomol::ResidueList , CDPL::Chem::ANDMatchExpressionList< ObjType1, ObjType2 > , CDPL::Chem::ANDMatchExpressionList< ObjType, void > , CDPL::Chem::AromaticRingSet , CDPL::Chem::AromaticSSSRSubset , CDPL::Chem::AromaticSubstructure , CDPL::Chem::AtomBondMapping , CDPL::Chem::AtomConfigurationMatchExpression , CDPL::Chem::AtomDictionary , CDPL::Chem::AtomEnvironmentMatchExpression , CDPL::Chem::AtomMapping , CDPL::Chem::AtomSSSRRingSizeMatchExpression< MatchFunc > , CDPL::Chem::AtomTypeMatchExpression , CDPL::Chem::AutomorphismGroupSearch , CDPL::Chem::BasicMolecule , CDPL::Chem::BasicReaction , CDPL::Chem::BemisMurckoAnalyzer , CDPL::Chem::BondConfigurationMatchExpression , CDPL::Chem::BondDirectionMatchExpression , CDPL::Chem::BondMapping , CDPL::Chem::BondReactionCenterStatusMatchExpression , CDPL::Chem::BondSubstituentDirectionMatchExpression , CDPL::Chem::BRICSFragmentGenerator , CDPL::Chem::ChEMBLStandardizer , CDPL::Chem::CIPConfigurationLabeler , CDPL::Chem::CommonConnectedSubstructureSearch , CDPL::Chem::CompleteRingSet , CDPL::Chem::ComponentSet , CDPL::Chem::ConnectedSubstructureSet , CDPL::Chem::CyclicSubstructure , CDPL::Chem::DefaultMultiConfMoleculeInputProcessor , CDPL::Chem::ElectronSystem , CDPL::Chem::ElectronSystemList , CDPL::Chem::Entity3DMapping , CDPL::Chem::Fragment , CDPL::Chem::FragmentGenerator , CDPL::Chem::FragmentList , CDPL::Chem::MatchConstraintList , CDPL::Chem::MatchExpression< ObjType1, ObjType2 > , CDPL::Chem::MatchExpression< ObjType, void > , CDPL::Chem::MatchExpressionList< ObjType1, ObjType2 > , CDPL::Chem::MaxCommonAtomSubstructureSearch , CDPL::Chem::MaxCommonBondSubstructureSearch , CDPL::Chem::MolecularGraph , CDPL::Chem::MolecularGraphComponentGroupingMatchExpression , CDPL::Chem::Molecule , CDPL::Chem::MultiConfMoleculeInputProcessor , CDPL::Chem::NOTMatchExpression< ObjType1, ObjType2 > , CDPL::Chem::NOTMatchExpression< ObjType, void > , CDPL::Chem::ORMatchExpressionList< ObjType1, ObjType2 > , CDPL::Chem::ORMatchExpressionList< ObjType, void > , CDPL::Chem::PatternAtomTyper , CDPL::Chem::PatternBasedTautomerizationRule , CDPL::Chem::PiElectronSystemList , CDPL::Chem::PropertyMatchExpression< ValueType, MatchFunc, ObjType1, ObjType2 > , CDPL::Chem::PropertyMatchExpression< ValueType, MatchFunc, ObjType, void > , CDPL::Chem::ProtonationStateStandardizer , CDPL::Chem::Reaction , CDPL::Chem::ReactionAtomMappingMatchExpression , CDPL::Chem::ReactionComponentGroupingMatchExpression , CDPL::Chem::RECAPFragmentGenerator , CDPL::Chem::ResonanceStructureGenerator , CDPL::Chem::SmallestSetOfSmallestRings , CDPL::Chem::StereoisomerGenerator , CDPL::Chem::StringDataBlock , CDPL::Chem::SubstructureHistogramCalculator , CDPL::Chem::SubstructureSearch , CDPL::Chem::TautomerGenerator , CDPL::Chem::TautomerizationRule , CDPL::ConfGen::CanonicalFragment , CDPL::ConfGen::ConformerData , CDPL::ConfGen::FragmentLibrary , CDPL::ConfGen::FragmentLibraryEntry , CDPL::ConfGen::TorsionLibrary , CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer , CDPL::ForceField::MMFF94AngleBendingParameterTable , CDPL::ForceField::MMFF94AromaticAtomTypeDefinitionTable , CDPL::ForceField::MMFF94AromaticSSSRSubset , CDPL::ForceField::MMFF94AtomTypePropertyTable , CDPL::ForceField::MMFF94AtomTyper , CDPL::ForceField::MMFF94BondChargeIncrementTable , CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer , CDPL::ForceField::MMFF94BondStretchingParameterTable , CDPL::ForceField::MMFF94BondStretchingRuleParameterTable , CDPL::ForceField::MMFF94ChargeCalculator , CDPL::ForceField::MMFF94DefaultStretchBendParameterTable , CDPL::ForceField::MMFF94ElectrostaticInteractionParameterizer , CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable , CDPL::ForceField::MMFF94HeavyToHydrogenAtomTypeMap , CDPL::ForceField::MMFF94InteractionData , CDPL::ForceField::MMFF94InteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL::ForceField::MMFF94OutOfPlaneBendingParameterTable , CDPL::ForceField::MMFF94PartialBondChargeIncrementTable , CDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMap , CDPL::ForceField::MMFF94StretchBendInteractionParameterizer , CDPL::ForceField::MMFF94StretchBendParameterTable , CDPL::ForceField::MMFF94SymbolicAtomTypePatternTable , CDPL::ForceField::MMFF94SymbolicToNumericAtomTypeMap , CDPL::ForceField::MMFF94TorsionInteractionParameterizer , CDPL::ForceField::MMFF94TorsionParameterTable , CDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizer , CDPL::ForceField::MMFF94VanDerWaalsParameterTable , CDPL::ForceField::UFFAtomTypePropertyTable , CDPL::GRAIL::AtomDensityGridCalculator , CDPL::GRAIL::BuriednessGridCalculator , CDPL::GRAIL::FeatureInteractionScoreGridCalculator , CDPL::GRAIL::GRAILDataSetGenerator , CDPL::GRAIL::GRAILDescriptorCalculator , CDPL::GRAIL::GRAILXDescriptorCalculator , CDPL::Grid::AttributedGrid , CDPL::Grid::RegularGrid< T, CVT > , CDPL::Grid::RegularGridSet< T, CVT > , CDPL::Grid::SpatialGrid< T, CVT > , CDPL::Math::BoundedMatrix< T, M, N > , CDPL::Math::BoundedVector< T, N > , CDPL::Math::CMatrix< T, M, N > , CDPL::Math::CVector< T, N > , CDPL::Math::Grid< T, A > , CDPL::Math::Matrix< T, A > , CDPL::Math::RegularSpatialGrid< T, C, GD, XF > , CDPL::Math::SparseMatrix< T, A > , CDPL::Math::SparseVector< T, A > , CDPL::Math::Vector< T, A > , CDPL::Math::VectorArray< V > , CDPL::MolProp::ElementHistogram , CDPL::MolProp::HBondAcceptorAtomTyper , CDPL::MolProp::HBondDonorAtomTyper , CDPL::MolProp::MassComposition , CDPL::MolProp::MHMOPiChargeCalculator , CDPL::MolProp::PEOESigmaChargeCalculator , CDPL::Pharm::BasicPharmacophore , CDPL::Pharm::CationPiInteractionScore , CDPL::Pharm::FeatureContainer , CDPL::Pharm::FeatureDistanceScore , CDPL::Pharm::FeatureGenerator , CDPL::Pharm::FeatureInteractionScore , CDPL::Pharm::FeatureInteractionScoreCombiner , CDPL::Pharm::FeatureMapping , CDPL::Pharm::FeatureSet , CDPL::Pharm::FeatureTypeHistogram , CDPL::Pharm::HBondingInteractionScore , CDPL::Pharm::HydrophobicAtomFeatureGenerator , CDPL::Pharm::HydrophobicFeatureGenerator , CDPL::Pharm::HydrophobicInteractionScore , CDPL::Pharm::IonicInteractionScore , CDPL::Pharm::OrthogonalPiPiInteractionScore , CDPL::Pharm::ParallelPiPiInteractionScore , CDPL::Pharm::PatternBasedFeatureGenerator , CDPL::Pharm::Pharmacophore , CDPL::Pharm::PharmacophoreGenerator , CDPL::Pharm::PSDScreeningDBAccessor , CDPL::Pharm::PSDScreeningDBCreator , CDPL::Pharm::ScreeningDBAccessor , CDPL::Pharm::ScreeningDBCreator , CDPL::Pharm::ScreeningProcessor , CDPL::Pharm::XBondingInteractionScore , CDPL::Shape::ExactGaussianShapeOverlapFunction , CDPL::Shape::FastGaussianShapeAlignment , CDPL::Shape::FastGaussianShapeOverlapFunction , CDPL::Shape::GaussianShape , CDPL::Shape::GaussianShapeAlignment , CDPL::Shape::GaussianShapeFunction , CDPL::Shape::GaussianShapeFunctionAlignment , CDPL::Shape::GaussianShapeGenerator , CDPL::Shape::GaussianShapeOverlapFunction , CDPL::Shape::GaussianShapeSet , CDPL::Shape::ScreeningProcessor , CDPL::Util::Array< ValueType > , CDPL::Util::CompoundDataReader< DataType > , CDPL::Util::IndirectArray< ValueType, PointerType, NullPointerCheck > , CDPL::Util::Map< Key, Value, AllowDefValues, KeyCompFunc > , CDPL::Util::MultiFormatDataReader< DataType > , CDPL::Util::MultiFormatDataWriter< DataType > , CDPL::Util::MultiMap< Key, Value, AllowDefValues, KeyCompFunc > , CDPL::Vis::ClipPathPrimitive2D , CDPL::Vis::ColorTable , CDPL::Vis::EllipsePrimitive2D , CDPL::Vis::GraphicsPrimitive2D , CDPL::Vis::LinePrimitive2D , CDPL::Vis::LineSegmentListPrimitive2D , CDPL::Vis::PathPrimitive2D , CDPL::Vis::PointListPrimitive2D , CDPL::Vis::PolygonPrimitive2D , CDPL::Vis::PolylinePrimitive2D , CDPL::Vis::ReactionView2D , CDPL::Vis::StructureView2D , CDPL::Vis::TextLabelPrimitive2D
• SHEET : CDPL::Biomol::PDBData
• singleConformerSearch() : CDPL::Shape::ScreeningSettings
• SITE : CDPL::Biomol::PDBData
• Size : CDPL::Math::CVector< T, N >
• size() : CDPL::Util::Array< ValueType >
• Size1 : CDPL::Math::CMatrix< T, M, N >
• Size2 : CDPL::Math::CMatrix< T, M, N >
• SizeError() : CDPL::Base::SizeError
• SizeSpecification() : CDPL::Vis::SizeSpecification
• SizeType : CDPL::ForceField::GradientVectorTraits< GV > , CDPL::ForceField::GradientVectorTraits< Math::VectorArray< V > > , CDPL::ForceField::GradientVectorTraits< std::vector< V > > , CDPL::Math::BoundedMatrix< T, M, N > , CDPL::Math::BoundedVector< T, N > , CDPL::Math::CMatrix< T, M, N > , CDPL::Math::CrossProductMatrixFromVector< V > , CDPL::Math::CVector< T, N > , CDPL::Math::DiagonalMatrixFromVector< V > , CDPL::Math::Grid< T, A > , CDPL::Math::GridBinary1< E1, E2, F > , CDPL::Math::GridBooleanBinaryFunctor< G1, G2 > , CDPL::Math::GridEquality< G1, G2 > , CDPL::Math::GridReference< G > , CDPL::Math::GridToleranceEquality< G1, G2, T > , CDPL::Math::GridUnary< E, F > , CDPL::Math::HomogenousCoordsAdapter< V > , CDPL::Math::IdentityMatrix< T > , CDPL::Math::InitListMatrix< T > , CDPL::Math::InitListVector< T > , CDPL::Math::Matrix1VectorBinary< E1, E2, F > , CDPL::Math::Matrix2VectorBinary< E1, E2, F > , CDPL::Math::Matrix< T, A > , CDPL::Math::MatrixBinary1< E1, E2, F > , CDPL::Math::MatrixBinary2< E1, E2, F > , CDPL::Math::MatrixBinaryFunctor< M1, M2 > , CDPL::Math::MatrixBooleanBinaryFunctor< M1, M2 > , CDPL::Math::MatrixColumn< M > , CDPL::Math::MatrixEquality< M1, M2 > , CDPL::Math::MatrixProduct< M1, M2 > , CDPL::Math::MatrixRange< M > , CDPL::Math::MatrixReference< M > , CDPL::Math::MatrixRow< M > , CDPL::Math::MatrixSlice< M > , CDPL::Math::MatrixToleranceEquality< M1, M2, T > , CDPL::Math::MatrixTranspose< M > , CDPL::Math::MatrixUnary< E, F > , CDPL::Math::MatrixVectorBinaryFunctor< M, V > , CDPL::Math::MatrixVectorProduct< M, V > , CDPL::Math::MinimizerVariableArrayTraits< A > , CDPL::Math::MinimizerVariableArrayTraits< std::vector< V > > , CDPL::Math::MinimizerVariableArrayTraits< VectorArray< V > > , CDPL::Math::MLRModel< T > , CDPL::Math::QuaternionVectorAdapter< Q > , CDPL::Math::QuaternionVectorBinary< E1, E2, F > , CDPL::Math::QuaternionVectorBinaryFunctor< Q, V > , CDPL::Math::QuaternionVectorRotation< Q, V > , CDPL::Math::Range< S > , CDPL::Math::RegularSpatialGrid< T, C, GD, XF > , CDPL::Math::RotationMatrix< T > , CDPL::Math::Scalar1GridBinary< E1, E2, F > , CDPL::Math::Scalar1MatrixBinary< E1, E2, F > , CDPL::Math::Scalar1VectorBinary< E1, E2, F > , CDPL::Math::Scalar2GridBinary< E1, E2, F > , CDPL::Math::Scalar2MatrixBinary< E1, E2, F > , CDPL::Math::Scalar2VectorBinary< E1, E2, F > , CDPL::Math::Scalar3GridBooleanTernaryFunctor< G1, G2, T > , CDPL::Math::Scalar3MatrixBooleanTernaryFunctor< M1, M2, T > , CDPL::Math::Scalar3VectorBooleanTernaryFunctor< V1, V2, T > , CDPL::Math::ScalarGrid< T > , CDPL::Math::ScalarMatrix< T > , CDPL::Math::ScalarVector< T > , CDPL::Math::ScalingMatrix< T > , CDPL::Math::Slice< S, D > , CDPL::Math::SparseContainerElement< C, K > , CDPL::Math::SparseMatrix< T, A > , CDPL::Math::SparseVector< T, A > , CDPL::Math::TranslationMatrix< T > , CDPL::Math::TriangularAdapter< M, Tri > , CDPL::Math::UnitVector< T > , CDPL::Math::Vector< T, A > , CDPL::Math::VectorBinary1< E1, E2, F > , CDPL::Math::VectorBinary2< E1, E2, F > , CDPL::Math::VectorBooleanBinaryFunctor< V1, V2 > , CDPL::Math::VectorEquality< V1, V2 > , CDPL::Math::VectorIteratorTraits< E > , CDPL::Math::VectorIteratorTraits< const E > , CDPL::Math::VectorMatrixBinary< E1, E2, F > , CDPL::Math::VectorMatrixProduct< V, M > , CDPL::Math::VectorMatrixUnary< E, F > , CDPL::Math::VectorMatrixUnaryFunctor< V > , CDPL::Math::VectorRange< V > , CDPL::Math::VectorReference< V > , CDPL::Math::VectorScalarUnaryFunctor< V > , CDPL::Math::VectorSlice< V > , CDPL::Math::VectorToleranceEquality< V1, V2, T > , CDPL::Math::VectorUnary< E, F > , CDPL::Math::ZeroGrid< T > , CDPL::Math::ZeroMatrix< T > , CDPL::Math::ZeroVector< T > , CDPL::Util::Array< ValueType >
• skip() : CDPL::Base::DataReader< T > , CDPL::Pharm::PSDMoleculeReader , CDPL::Pharm::PSDPharmacophoreReader , CDPL::Util::CompoundDataReader< DataType > , CDPL::Util::CompressedDataReader< ReaderImpl, DecompStream, DataType > , CDPL::Util::FileDataReader< ReaderImpl, DataType > , CDPL::Util::MultiFormatDataReader< DataType > , CDPL::Util::StreamDataReader< DataType, ReaderImpl >
• Slice() : CDPL::Math::Slice< S, D >
• SliceType : CDPL::Math::MatrixSlice< M > , CDPL::Math::VectorSlice< V >
• SMALL_SET_DENSE : CDPL::ConfGen::ConformerGeneratorSettings
• SMALL_SET_DIVERSE : CDPL::ConfGen::ConformerGeneratorSettings
• SmallestSetOfSmallestRings() : CDPL::Chem::SmallestSetOfSmallestRings
• SMARTSMolecularGraphWriter() : CDPL::Chem::SMARTSMolecularGraphWriter
• SMARTSMoleculeReader() : CDPL::Chem::SMARTSMoleculeReader
• SMARTSReactionReader() : CDPL::Chem::SMARTSReactionReader
• SMARTSReactionWriter() : CDPL::Chem::SMARTSReactionWriter
• SMILESMolecularGraphWriter() : CDPL::Chem::SMILESMolecularGraphWriter
• SMILESMoleculeReader() : CDPL::Chem::SMILESMoleculeReader
• SMILESReactionReader() : CDPL::Chem::SMILESReactionReader
• SMILESReactionWriter() : CDPL::Chem::SMILESReactionWriter
• SOLID_LINE : CDPL::Vis::Pen
• SOLID_PATTERN : CDPL::Vis::Brush
• SOLVENT_COMPONENTS_REMOVED : CDPL::Chem::ChEMBLStandardizer
• SOURCE : CDPL::Biomol::PDBData
• sp1GeometryViolationsMinimized() : CDPL::Chem::ResonanceStructureGenerator
• SparseContainerElement() : CDPL::Math::SparseContainerElement< C, K >
• SparseMatrix() : CDPL::Math::SparseMatrix< T, A >
• SparseVector() : CDPL::Math::SparseVector< T, A >
• SpatialEntityAlignment() : CDPL::Chem::SpatialEntityAlignment< T >
• SpatialFeatureMapping() : CDPL::Pharm::SpatialFeatureMapping
• specifiedCentersIncluded() : CDPL::Chem::StereoisomerGenerator
• SPLIT : CDPL::Biomol::PDBData
• splitBondsIncluded() : CDPL::Chem::FragmentGenerator
• SPRSDE : CDPL::Biomol::PDBData
• sqrt() : CDPL::Math::ComplexTraits< T > , CDPL::Math::ScalarTraits< T >
• SQUARE_CAP : CDPL::Vis::Pen
• SSBOND : CDPL::Biomol::PDBData
• SSizeType : CDPL::Math::RegularSpatialGrid< T, C, GD, XF >
• standardize() : CDPL::Chem::ChEMBLStandardizer , CDPL::Chem::ProtonationStateStandardizer
• STATIC_H_DONORS : CDPL::Pharm::DefaultPharmacophoreGenerator
• Status : CDPL::Math::BFGSMinimizer< VA, VT, FVT >
• StereoCenterData : CDPL::ConfGen::DGConstraintGenerator
• stereochemistryRegarded() : CDPL::Chem::TautomerGenerator
• StereoDescriptor() : CDPL::Chem::StereoDescriptor
• StereoDescriptorArray : CDPL::Chem::StereoisomerGenerator
• stopAtFirstMatchingRule() : CDPL::ConfGen::TorsionRuleMatcher
• stopSearch() : CDPL::Chem::AutomorphismGroupSearch , CDPL::Chem::SubstructureSearch
• StorageType : CDPL::Util::Array< ValueType >
• storeEnvironmentAtomDensityGrid() : CDPL::GRAIL::GRAILDataSetGenerator
• StreamDataReader() : CDPL::Util::StreamDataReader< DataType, ReaderImpl >
• strictForceFieldParameterization() : CDPL::ConfGen::ConformerGeneratorSettings , CDPL::ConfGen::FragmentConformerGeneratorSettings , CDPL::ConfGen::StructureGeneratorSettings , CDPL::ConfGen::TorsionDriverSettings
• StringDataBlockEntry() : CDPL::Chem::StringDataBlockEntry
• stripHydrogens() : CDPL::Chem::BemisMurckoAnalyzer
• STRUCTURE_2D_CORRECTED : CDPL::Chem::ChEMBLStandardizer
• STRUCTURE_ID : CDPL::Biomol::PDBData
• STRUCTURE_NORMALIZED : CDPL::Chem::ChEMBLStandardizer
• StructureGenerator() : CDPL::ConfGen::StructureGenerator
• StructureGeneratorSettings() : CDPL::ConfGen::StructureGeneratorSettings
• StructureRetrievalFunction : CDPL::Biomol::ResidueDictionary::Entry
• StructureView2D() : CDPL::Vis::StructureView2D
• Style : CDPL::Vis::Brush
• sub() : CDPL::Math::MinimizerVariableArrayTraits< A > , CDPL::Math::MinimizerVariableArrayTraits< std::vector< V > > , CDPL::Math::MinimizerVariableArrayTraits< VectorArray< V > >
• SubstructureHistogramCalculator() : CDPL::Chem::SubstructureHistogramCalculator
• SubstructureSearch() : CDPL::Chem::SubstructureSearch
• SUCCESS : CDPL::Math::BFGSMinimizer< VA, VT, FVT >
• SulfenicAcidTautomerization() : CDPL::Chem::SulfenicAcidTautomerization
• SurfaceAtomExtractor() : CDPL::Chem::SurfaceAtomExtractor
• SVGMolecularGraphWriter() : CDPL::Vis::SVGMolecularGraphWriter
• SVGReactionWriter() : CDPL::Vis::SVGReactionWriter
• swap() : CDPL::Base::Any , CDPL::Base::PropertyContainer , CDPL::Chem::ElectronSystem , CDPL::Chem::Fragment , CDPL::ConfGen::ConformerData , CDPL::ConfGen::TorsionCategory , CDPL::ConfGen::TorsionRule , CDPL::ForceField::MMFF94InteractionData , CDPL::Math::BoundedMatrix< T, M, N > , CDPL::Math::BoundedVector< T, N > , CDPL::Math::CMatrix< T, M, N > , CDPL::Math::CVector< T, N > , CDPL::Math::Grid< T, A > , CDPL::Math::GridReference< G > , CDPL::Math::HomogenousCoordsAdapter< V > , CDPL::Math::IdentityMatrix< T > , CDPL::Math::Matrix< T, A > , CDPL::Math::MatrixColumn< M > , CDPL::Math::MatrixRange< M > , CDPL::Math::MatrixReference< M > , CDPL::Math::MatrixRow< M > , CDPL::Math::MatrixSlice< M > , CDPL::Math::MatrixTranspose< M > , CDPL::Math::Quaternion< T > , CDPL::Math::QuaternionReference< Q > , CDPL::Math::QuaternionVectorAdapter< Q > , CDPL::Math::Range< S > , CDPL::Math::RealQuaternion< T > , CDPL::Math::RegularSpatialGrid< T, C, GD, XF > , CDPL::Math::RotationMatrix< T > , CDPL::Math::ScalarGrid< T > , CDPL::Math::ScalarMatrix< T > , CDPL::Math::ScalarVector< T > , CDPL::Math::ScalingMatrix< T > , CDPL::Math::Slice< S, D > , CDPL::Math::SparseMatrix< T, A > , CDPL::Math::SparseVector< T, A > , CDPL::Math::TranslationMatrix< T > , CDPL::Math::UnitVector< T > , CDPL::Math::Vector< T, A > , CDPL::Math::VectorQuaternionAdapter< V > , CDPL::Math::VectorRange< V > , CDPL::Math::VectorReference< V > , CDPL::Math::VectorSlice< V > , CDPL::Math::ZeroGrid< T > , CDPL::Math::ZeroMatrix< T > , CDPL::Math::ZeroVector< T > , CDPL::Util::Array< ValueType > , CDPL::Util::Map< Key, Value, AllowDefValues, KeyCompFunc > , CDPL::Util::MultiMap< Key, Value, AllowDefValues, KeyCompFunc >
• swapComponentRoles() : CDPL::Chem::BasicReaction , CDPL::Chem::Reaction
• swapPoints() : CDPL::Vis::Line2D
• symmetricCentersIncluded() : CDPL::Chem::StereoisomerGenerator
• SymmetryClassCalculator() : CDPL::Chem::SymmetryClassCalculator