- s -

• 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.CairoBackend.CairoRenderer2D , CDPL.Vis.QtBackend.QtRenderer2D , CDPL.Vis.Renderer2D
• scale() : CDPL.Vis.Rectangle2D
• scoresDiminishedByAtomDensity() : CDPL.GRAIL.GRAILDataSetGenerator
• scoresNormalized() : CDPL.GRAIL.FeatureInteractionScoreGridCalculator , CDPL.GRAIL.GRAILDataSetGenerator
• searchDB() : CDPL.Pharm.ScreeningProcessor
• seek() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2IStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipIStream
• seekBestAlignments() : CDPL.Pharm.ScreeningProcessor
• seekr() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2IStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipIStream
• seekw() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2OStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipOStream
• selected() : CDPL.ConfGen.RMSDConformerSelector
• 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.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DRealQuaternion , CDPL.Math.DRotationMatrix , CDPL.Math.DScalingMatrix , CDPL.Math.DTranslationMatrix , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FRealQuaternion , CDPL.Math.FRotationMatrix , CDPL.Math.FScalingMatrix , CDPL.Math.FTranslationMatrix , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LRealQuaternion , CDPL.Math.LRotationMatrix , CDPL.Math.LScalingMatrix , CDPL.Math.LTranslationMatrix , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULRealQuaternion , CDPL.Math.ULRotationMatrix , CDPL.Math.ULScalingMatrix , CDPL.Math.ULTranslationMatrix , CDPL.Math.ULVectorQuaternionAdapter , CDPL.Util.BitSet
• 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
• setAtom1ID() : CDPL.Chem.PatternBasedTautomerizationRule.BondOrderChange
• setAtom2DCoordinatesFunction() : CDPL.Chem.BondStereoFlagCalculator
• setAtom2ID() : CDPL.Chem.PatternBasedTautomerizationRule.BondOrderChange
• 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.CairoBackend.CairoRenderer2D , CDPL.Vis.EllipsePrimitive2D , CDPL.Vis.PathPrimitive2D , CDPL.Vis.PolygonPrimitive2D , CDPL.Vis.QtBackend.QtRenderer2D , CDPL.Vis.Renderer2D
• setC1() : CDPL.Math.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULVectorQuaternionAdapter
• setC2() : CDPL.Math.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULVectorQuaternionAdapter
• setC3() : CDPL.Math.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULVectorQuaternionAdapter
• setC4() : CDPL.Math.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULVectorQuaternionAdapter
• setCallbackFunction() : CDPL.Chem.TautomerGenerator
• setCapStyle() : CDPL.Vis.Pen
• setChainHydrophobicityThreshold() : CDPL.Pharm.HydrophobicFeatureGenerator
• setChargeCountWindow() : CDPL.Chem.ResonanceStructureGenerator
• setClipPath() : CDPL.Vis.CairoBackend.CairoRenderer2D , CDPL.Vis.QtBackend.QtRenderer2D , CDPL.Vis.Renderer2D
• setColor() : CDPL.Shape.GaussianShape.Element , CDPL.Vis.Brush , CDPL.Vis.Pen
• setColorFeatureType() : CDPL.Shape.ScreeningSettings
• setColorFilterFunction() : CDPL.Shape.GaussianShapeAlignment , CDPL.Shape.GaussianShapeFunctionAlignment , CDPL.Shape.GaussianShapeOverlapFunction
• setColorMatchFunction() : 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.DRegularSpatialGrid , CDPL.Math.FRegularSpatialGrid
• setCoreEnvironmentRadius() : CDPL.Pharm.InteractionPharmacophoreGenerator
• setCustomSetupFunction() : CDPL.Chem.TautomerGenerator
• setCycleStepCountFactor() : CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• setDampingFactor() : CDPL.MolProp.PEOESigmaChargeCalculator
• setData() : CDPL.Chem.StringDataBlockEntry
• setDataMode() : CDPL.Math.DRegularSpatialGrid , CDPL.Math.FRegularSpatialGrid
• 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.Chem.AtomMatchExpressionList , CDPL.Chem.BondMatchExpressionList , CDPL.Chem.ElectronSystemList , CDPL.Chem.FragmentList , CDPL.Chem.MatchConstraintList , CDPL.Chem.MolecularGraphMatchExpressionList , CDPL.Chem.ReactionMatchExpressionList , CDPL.Chem.StringDataBlock , CDPL.ForceField.ElasticPotentialList , CDPL.ForceField.MMFF94AngleBendingInteractionList , CDPL.ForceField.MMFF94BondStretchingInteractionList , CDPL.ForceField.MMFF94ElectrostaticInteractionList , CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionList , CDPL.ForceField.MMFF94StretchBendInteractionList , CDPL.ForceField.MMFF94TorsionInteractionList , CDPL.ForceField.MMFF94VanDerWaalsInteractionList , CDPL.Grid.DRegularGrid , CDPL.Grid.DRegularGridSet , CDPL.Grid.DSpatialGrid , CDPL.Grid.FRegularGrid , CDPL.Grid.FRegularGridSet , CDPL.Grid.FSpatialGrid , CDPL.Math.DGrid , CDPL.Math.DGridExpression , CDPL.Math.DHomogenousCoordsAdapter , CDPL.Math.DMatrix , CDPL.Math.DMatrixColumn , CDPL.Math.DMatrixExpression , CDPL.Math.DMatrixRange , CDPL.Math.DMatrixRow , CDPL.Math.DMatrixSlice , CDPL.Math.DMatrixTranspose , CDPL.Math.DQuaternionVectorAdapter , CDPL.Math.DRegularSpatialGrid , CDPL.Math.DVector , CDPL.Math.DVectorExpression , CDPL.Math.DVectorRange , CDPL.Math.DVectorSlice , CDPL.Math.FGrid , CDPL.Math.FGridExpression , CDPL.Math.FHomogenousCoordsAdapter , CDPL.Math.FMatrix , CDPL.Math.FMatrixColumn , CDPL.Math.FMatrixExpression , CDPL.Math.FMatrixRange , CDPL.Math.FMatrixRow , CDPL.Math.FMatrixSlice , CDPL.Math.FMatrixTranspose , CDPL.Math.FQuaternionVectorAdapter , CDPL.Math.FRegularSpatialGrid , CDPL.Math.FVector , CDPL.Math.FVectorExpression , CDPL.Math.FVectorRange , CDPL.Math.FVectorSlice , CDPL.Math.LHomogenousCoordsAdapter , CDPL.Math.LMatrix , CDPL.Math.LMatrixColumn , CDPL.Math.LMatrixExpression , CDPL.Math.LMatrixRange , CDPL.Math.LMatrixRow , CDPL.Math.LMatrixSlice , CDPL.Math.LMatrixTranspose , CDPL.Math.LQuaternionVectorAdapter , CDPL.Math.LVector , CDPL.Math.LVectorExpression , CDPL.Math.LVectorRange , CDPL.Math.LVectorSlice , CDPL.Math.Matrix2D , CDPL.Math.Matrix2F , CDPL.Math.Matrix2L , CDPL.Math.Matrix2UL , CDPL.Math.Matrix3D , CDPL.Math.Matrix3F , CDPL.Math.Matrix3L , CDPL.Math.Matrix3UL , CDPL.Math.Matrix4D , CDPL.Math.Matrix4F , CDPL.Math.Matrix4L , CDPL.Math.Matrix4UL , CDPL.Math.SparseDMatrix , CDPL.Math.SparseDVector , CDPL.Math.SparseFMatrix , CDPL.Math.SparseFVector , CDPL.Math.SparseLMatrix , CDPL.Math.SparseLVector , CDPL.Math.SparseULMatrix , CDPL.Math.SparseULVector , CDPL.Math.ULHomogenousCoordsAdapter , CDPL.Math.ULMatrix , CDPL.Math.ULMatrixColumn , CDPL.Math.ULMatrixExpression , CDPL.Math.ULMatrixRange , CDPL.Math.ULMatrixRow , CDPL.Math.ULMatrixSlice , CDPL.Math.ULMatrixTranspose , CDPL.Math.ULQuaternionVectorAdapter , CDPL.Math.ULVector , CDPL.Math.ULVectorExpression , CDPL.Math.ULVectorRange , CDPL.Math.ULVectorSlice , CDPL.Math.Vector2D , CDPL.Math.Vector2DArray , CDPL.Math.Vector2F , CDPL.Math.Vector2FArray , CDPL.Math.Vector2L , CDPL.Math.Vector2LArray , CDPL.Math.Vector2UL , CDPL.Math.Vector2ULArray , CDPL.Math.Vector3D , CDPL.Math.Vector3DArray , CDPL.Math.Vector3F , CDPL.Math.Vector3FArray , CDPL.Math.Vector3L , CDPL.Math.Vector3LArray , CDPL.Math.Vector3UL , CDPL.Math.Vector3ULArray , CDPL.Math.Vector4D , CDPL.Math.Vector4F , CDPL.Math.Vector4L , CDPL.Math.Vector4UL , CDPL.Math.Vector7D , CDPL.Shape.GaussianShapeSet , CDPL.Shape.Vector7D , CDPL.Util.BitSetArray , CDPL.Util.DArray , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPairArray , CDPL.Util.UIArray
• setEnabledInteractionTypes() : CDPL.ForceField.MMFF94EnergyCalculator , CDPL.ForceField.MMFF94GradientCalculator
• 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.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Descr.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Pharm.SpatialFeatureAlignment
• setEntityMatchFunction() : CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Chem.TopologicalAtomAlignment , CDPL.Chem.TopologicalEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment , CDPL.Pharm.TopologicalFeatureAlignment
• setEntityPairMatchFunction() : CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Chem.TopologicalAtomAlignment , CDPL.Chem.TopologicalEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment , CDPL.Pharm.TopologicalFeatureAlignment
• setEntityPairWeightFunction() : CDPL.Descr.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator
• setEntityWeightFunction() : CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment
• setEntry() : CDPL.Chem.AtomMapping , CDPL.Chem.BondMapping , CDPL.Chem.Entity3DMapping , CDPL.MolProp.ElementHistogram , CDPL.MolProp.MassComposition , CDPL.Pharm.FeatureMapping , CDPL.Pharm.FeatureTypeHistogram , CDPL.Vis.ColorTable
• 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
• setFirst() : CDPL.Util.STPair
• setFixedAtomMask() : CDPL.ForceField.MMFF94GradientCalculator
• setFixedPitch() : CDPL.Vis.Font
• setFont() : CDPL.Vis.CairoBackend.CairoFontMetrics , CDPL.Vis.CairoBackend.CairoRenderer2D , CDPL.Vis.FontMetrics , CDPL.Vis.QtBackend.QtFontMetrics , CDPL.Vis.QtBackend.QtRenderer2D , CDPL.Vis.Renderer2D , CDPL.Vis.TextLabelPrimitive2D
• setFontMetrics() : 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
• setItalic() : CDPL.Vis.Font
• setJoinStyle() : CDPL.Vis.Pen
• setLearningRateDecrement() : CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• 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
• 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.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment
• 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.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• setNumericAtomTypeFunction() : CDPL.ForceField.MMFF94ChargeCalculator
• setNumIterations() : CDPL.Descr.CircularFingerprintGenerator , CDPL.MolProp.PEOESigmaChargeCalculator
• setNumRandomStarts() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.PrincipalAxesAlignmentStartGenerator , CDPL.Shape.ScreeningSettings
• setNumSteps() : CDPL.Descr.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeAutoCorr3DDescriptorCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PharmacophoreAutoCorr3DDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator
• setNumTestPoints() : CDPL.Chem.SurfaceAtomExtractor
• setNumTestRays() : CDPL.GRAIL.BuriednessGridCalculator , CDPL.GRAIL.BuriednessScore
• setOptimizationStopGradient() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.GaussianShapeAlignment , CDPL.Shape.GaussianShapeFunctionAlignment , CDPL.Shape.ScreeningSettings
• setOrderChange() : CDPL.Chem.PatternBasedTautomerizationRule.BondOrderChange
• 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.CairoBackend.CairoRenderer2D , CDPL.Vis.EllipsePrimitive2D , CDPL.Vis.LinePrimitive2D , CDPL.Vis.LineSegmentListPrimitive2D , CDPL.Vis.PathPrimitive2D , CDPL.Vis.PointListPrimitive2D , CDPL.Vis.PolygonPrimitive2D , CDPL.Vis.PolylinePrimitive2D , CDPL.Vis.QtBackend.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.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeAutoCorr3DDescriptorCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PharmacophoreAutoCorr3DDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator
• setRadiusScalingFactor() : CDPL.Shape.FastGaussianShapeOverlapFunction
• setRandomSeed() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.PrincipalAxesAlignmentStartGenerator , CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• setReaction() : CDPL.Vis.ReactionView2D
• setReactionPattern() : CDPL.Chem.Reactor
• setRecord() : CDPL.Biomol.PDBData
• setRecordIndex() : CDPL.Chem.MoleculeReaderBase , CDPL.Chem.ReactionReaderBase , CDPL.Grid.DRegularGridReaderBase , CDPL.Grid.DRegularGridSetReaderBase , CDPL.Pharm.PharmacophoreReaderBase
• setRed() : CDPL.Vis.Color
• setReference() : CDPL.Shape.GaussianShapeAlignmentStartGenerator , CDPL.Shape.GaussianShapeFunctionAlignment
• 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.ConformerGeneratorSettings , CDPL.ConfGen.FragmentConformerGeneratorSettings
• setRefinementTolerance() : 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.AtomRDFCodeCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator
• 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
• setSecond() : CDPL.Util.STPair
• setShape() : CDPL.Shape.GaussianShapeFunction
• setShapeFunction() : CDPL.Shape.GaussianShapeOverlapFunction
• setSize() : CDPL.Vis.Font
• setSmallRingSystemSamplingFactor() : CDPL.ConfGen.FragmentConformerGeneratorSettings
• setSMILES() : CDPL.ConfGen.FragmentLibraryEntry
• setSmoothingFactor() : CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator
• setSoftSpace() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2OStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipOStream
• setStartGenerator() : CDPL.Shape.GaussianShapeAlignment , CDPL.Shape.GaussianShapeFunctionAlignment
• setStartLearningRate() : CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• setStartRadius() : CDPL.Descr.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeAutoCorr3DDescriptorCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PharmacophoreAutoCorr3DDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator
• 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.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment
• 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.CairoBackend.CairoRenderer2D , CDPL.Vis.QtBackend.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.StereoisomerGenerator , CDPL.Chem.TautomerizationRule , CDPL.ConfGen.DGConstraintGenerator , CDPL.ConfGen.DGStructureGenerator , CDPL.ConfGen.RMSDConformerSelector , CDPL.ConfGen.TorsionDriver , CDPL.ForceField.MMFF94EnergyCalculator , CDPL.ForceField.MMFF94GradientCalculator , CDPL.Math.DVectorBFGSMinimizer , CDPL.Math.FVectorBFGSMinimizer , CDPL.Math.Vector2DArrayBFGSMinimizer , CDPL.Math.Vector2FArrayBFGSMinimizer , CDPL.Math.Vector3DArrayBFGSMinimizer , CDPL.Math.Vector3FArrayBFGSMinimizer
• setupAligned() : CDPL.Shape.GaussianShapeAlignmentStartGenerator , CDPL.Shape.GaussianShapeFunctionAlignment
• setupReference() : CDPL.Shape.GaussianShapeAlignmentStartGenerator , CDPL.Shape.GaussianShapeFunctionAlignment
• setvalue() : CDPL.Base.StringIOStream
• 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.DRegularSpatialGrid , CDPL.Math.FRegularSpatialGrid
• setXYData() : CDPL.Math.DMLRModel , CDPL.Math.FMLRModel
• setYStepSize() : CDPL.Math.DRegularSpatialGrid , CDPL.Math.FRegularSpatialGrid
• setZStepSize() : CDPL.Math.DRegularSpatialGrid , CDPL.Math.FRegularSpatialGrid
• singleConformerSearch() : CDPL.Shape.ScreeningSettings
• skip() : CDPL.Chem.MoleculeReaderBase , CDPL.Chem.ReactionReaderBase , CDPL.Grid.DRegularGridReaderBase , CDPL.Grid.DRegularGridSetReaderBase , CDPL.Pharm.PharmacophoreReaderBase
• sp1GeometryViolationsMinimized() : CDPL.Chem.ResonanceStructureGenerator
• specifiedCentersIncluded() : CDPL.Chem.StereoisomerGenerator
• standardize() : CDPL.Chem.ChEMBLStandardizer , CDPL.Chem.ProtonationStateStandardizer
• stereochemistryRegarded() : CDPL.Chem.TautomerGenerator
• stopAtFirstMatchingRule() : CDPL.ConfGen.TorsionRuleMatcher
• storeEnvironmentAtomDensityGrid() : CDPL.GRAIL.GRAILDataSetGenerator
• strictForceFieldParameterization() : CDPL.ConfGen.ConformerGeneratorSettings , CDPL.ConfGen.FragmentConformerGeneratorSettings , CDPL.ConfGen.StructureGeneratorSettings , CDPL.ConfGen.TorsionDriverSettings
• stripHydrogens() : CDPL.Chem.BemisMurckoAnalyzer
• swap() : CDPL.Base.PropertyContainer , CDPL.Chem.ElectronSystem , CDPL.Chem.Fragment , CDPL.ConfGen.ConformerData , CDPL.ConfGen.TorsionCategory , CDPL.ConfGen.TorsionRule , CDPL.ForceField.MMFF94InteractionData , CDPL.Grid.DRegularGrid , CDPL.Grid.FRegularGrid , CDPL.Math.DGrid , CDPL.Math.DGridExpression , CDPL.Math.DHomogenousCoordsAdapter , CDPL.Math.DIdentityMatrix , CDPL.Math.DMatrix , CDPL.Math.DMatrixColumn , CDPL.Math.DMatrixExpression , CDPL.Math.DMatrixRange , CDPL.Math.DMatrixRow , CDPL.Math.DMatrixSlice , CDPL.Math.DMatrixTranspose , CDPL.Math.DQuaternion , CDPL.Math.DQuaternionExpression , CDPL.Math.DQuaternionVectorAdapter , CDPL.Math.DRealQuaternion , CDPL.Math.DRegularSpatialGrid , CDPL.Math.DRotationMatrix , CDPL.Math.DScalarGrid , CDPL.Math.DScalarMatrix , CDPL.Math.DScalarVector , CDPL.Math.DScalingMatrix , CDPL.Math.DTranslationMatrix , CDPL.Math.DUnitVector , CDPL.Math.DVector , CDPL.Math.DVectorExpression , CDPL.Math.DVectorQuaternionAdapter , CDPL.Math.DVectorRange , CDPL.Math.DVectorSlice , CDPL.Math.DZeroGrid , CDPL.Math.DZeroMatrix , CDPL.Math.DZeroVector , CDPL.Math.FGrid , CDPL.Math.FGridExpression , CDPL.Math.FHomogenousCoordsAdapter , CDPL.Math.FIdentityMatrix , CDPL.Math.FMatrix , CDPL.Math.FMatrixColumn , CDPL.Math.FMatrixExpression , CDPL.Math.FMatrixRange , CDPL.Math.FMatrixRow , CDPL.Math.FMatrixSlice , CDPL.Math.FMatrixTranspose , CDPL.Math.FQuaternion , CDPL.Math.FQuaternionExpression , CDPL.Math.FQuaternionVectorAdapter , CDPL.Math.FRealQuaternion , CDPL.Math.FRegularSpatialGrid , CDPL.Math.FRotationMatrix , CDPL.Math.FScalarGrid , CDPL.Math.FScalarMatrix , CDPL.Math.FScalarVector , CDPL.Math.FScalingMatrix , CDPL.Math.FTranslationMatrix , CDPL.Math.FUnitVector , CDPL.Math.FVector , CDPL.Math.FVectorExpression , CDPL.Math.FVectorQuaternionAdapter , CDPL.Math.FVectorRange , CDPL.Math.FVectorSlice , CDPL.Math.FZeroGrid , CDPL.Math.FZeroMatrix , CDPL.Math.FZeroVector , CDPL.Math.LHomogenousCoordsAdapter , CDPL.Math.LIdentityMatrix , CDPL.Math.LMatrix , CDPL.Math.LMatrixColumn , CDPL.Math.LMatrixExpression , CDPL.Math.LMatrixRange , CDPL.Math.LMatrixRow , CDPL.Math.LMatrixSlice , CDPL.Math.LMatrixTranspose , CDPL.Math.LQuaternion , CDPL.Math.LQuaternionExpression , CDPL.Math.LQuaternionVectorAdapter , CDPL.Math.LRealQuaternion , CDPL.Math.LRotationMatrix , CDPL.Math.LScalarMatrix , CDPL.Math.LScalarVector , CDPL.Math.LScalingMatrix , CDPL.Math.LTranslationMatrix , CDPL.Math.LUnitVector , CDPL.Math.LVector , CDPL.Math.LVectorExpression , CDPL.Math.LVectorQuaternionAdapter , CDPL.Math.LVectorRange , CDPL.Math.LVectorSlice , CDPL.Math.LZeroMatrix , CDPL.Math.LZeroVector , CDPL.Math.Matrix2D , CDPL.Math.Matrix2F , CDPL.Math.Matrix2L , CDPL.Math.Matrix2UL , CDPL.Math.Matrix3D , CDPL.Math.Matrix3F , CDPL.Math.Matrix3L , CDPL.Math.Matrix3UL , CDPL.Math.Matrix4D , CDPL.Math.Matrix4F , CDPL.Math.Matrix4L , CDPL.Math.Matrix4UL , CDPL.Math.Range , CDPL.Math.Slice , CDPL.Math.SparseDMatrix , CDPL.Math.SparseDVector , CDPL.Math.SparseFMatrix , CDPL.Math.SparseFVector , CDPL.Math.SparseLMatrix , CDPL.Math.SparseLVector , CDPL.Math.SparseULMatrix , CDPL.Math.SparseULVector , CDPL.Math.ULHomogenousCoordsAdapter , CDPL.Math.ULIdentityMatrix , CDPL.Math.ULMatrix , CDPL.Math.ULMatrixColumn , CDPL.Math.ULMatrixExpression , CDPL.Math.ULMatrixRange , CDPL.Math.ULMatrixRow , CDPL.Math.ULMatrixSlice , CDPL.Math.ULMatrixTranspose , CDPL.Math.ULQuaternion , CDPL.Math.ULQuaternionExpression , CDPL.Math.ULQuaternionVectorAdapter , CDPL.Math.ULRealQuaternion , CDPL.Math.ULRotationMatrix , CDPL.Math.ULScalarMatrix , CDPL.Math.ULScalarVector , CDPL.Math.ULScalingMatrix , CDPL.Math.ULTranslationMatrix , CDPL.Math.ULUnitVector , CDPL.Math.ULVector , CDPL.Math.ULVectorExpression , CDPL.Math.ULVectorQuaternionAdapter , CDPL.Math.ULVectorRange , CDPL.Math.ULVectorSlice , CDPL.Math.ULZeroMatrix , CDPL.Math.ULZeroVector , CDPL.Math.Vector2D , CDPL.Math.Vector2F , CDPL.Math.Vector2L , CDPL.Math.Vector2UL , CDPL.Math.Vector3D , CDPL.Math.Vector3F , CDPL.Math.Vector3L , CDPL.Math.Vector3UL , CDPL.Math.Vector4D , CDPL.Math.Vector4F , CDPL.Math.Vector4L , CDPL.Math.Vector4UL , CDPL.Math.Vector7D , CDPL.Shape.Vector7D , CDPL.Util.BitSet
• swapComponentRoles() : CDPL.Chem.Reaction
• swapPoints() : CDPL.Vis.Line2D
• symmetricCentersIncluded() : CDPL.Chem.StereoisomerGenerator