- a -

• add14DistanceConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addAngle() : CDPL.ConfGen.TorsionRule
• addAtom() : CDPL.Chem.ElectronSystem , CDPL.Chem.Fragment , CDPL.Chem.Molecule
• addAtomConfigurationConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addAtomMappingConstraint() : CDPL.Chem.AutomorphismGroupSearch , CDPL.Chem.SubstructureSearch
• addAtomPlanarityConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addAtoms() : CDPL.Chem.ElectronSystem
• addBond() : CDPL.Chem.Fragment , CDPL.Chem.Molecule
• addBondAngleConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addBondConfigurationConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addBondLengthConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addBondMappingConstraint() : CDPL.Chem.AutomorphismGroupSearch , CDPL.Chem.SubstructureSearch
• addBondPlanarityConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addCategory() : CDPL.ConfGen.TorsionCategory
• addComponent() : CDPL.Chem.BasicReaction , CDPL.Chem.Reaction
• addConformation() : CDPL.Chem.MultiConfMoleculeInputProcessor
• addConformer() : CDPL.ConfGen.FragmentLibraryEntry
• addDefaultDistanceConstraints() : CDPL.ConfGen.DGConstraintGenerator
• addDistanceConstraint() : CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• addElement() : 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.DRegularGridSet , CDPL.Grid.FRegularGridSet , CDPL.Math.Vector2DArray , CDPL.Math.Vector2FArray , CDPL.Math.Vector2LArray , CDPL.Math.Vector2ULArray , CDPL.Math.Vector3DArray , CDPL.Math.Vector3FArray , CDPL.Math.Vector3LArray , CDPL.Math.Vector3ULArray , CDPL.Shape.GaussianShape , CDPL.Shape.GaussianShapeSet , CDPL.Util.BitSetArray , CDPL.Util.DArray , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPairArray , CDPL.Util.UIArray
• addElements() : 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.DRegularGridSet , CDPL.Grid.FRegularGridSet , CDPL.Math.Vector2DArray , CDPL.Math.Vector2FArray , CDPL.Math.Vector2LArray , CDPL.Math.Vector2ULArray , CDPL.Math.Vector3DArray , CDPL.Math.Vector3FArray , CDPL.Math.Vector3LArray , CDPL.Math.Vector3ULArray , CDPL.Shape.GaussianShapeSet , CDPL.Util.BitSetArray , CDPL.Util.DArray , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPairArray , CDPL.Util.UIArray
• addEllipse() : CDPL.Vis.Path2D
• addEnergyWindowRange() : CDPL.ConfGen.ConformerGeneratorSettings
• addEntity() : CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Chem.TopologicalAtomAlignment , CDPL.Chem.TopologicalEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment , CDPL.Pharm.TopologicalFeatureAlignment
• addEntries() : CDPL.ConfGen.FragmentLibrary
• addEntry() : CDPL.Biomol.ResidueDictionary , CDPL.Chem.AtomDictionary , CDPL.Chem.StringDataBlock , CDPL.ConfGen.FragmentLibrary , 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
• addExcludePattern() : CDPL.Chem.FragmentGenerator , CDPL.Chem.PatternBasedTautomerizationRule , CDPL.Pharm.PatternBasedFeatureGenerator
• addExcludePatterns() : CDPL.Chem.PatternBasedTautomerizationRule
• addExclusionVolumes() : CDPL.Pharm.InteractionPharmacophoreGenerator
• addFeature() : CDPL.Pharm.FeatureSet , CDPL.Pharm.Pharmacophore
• addFeatures() : CDPL.Pharm.PharmacophoreAlignment
• addFileExtension() : CDPL.Base.DataFormat
• addFragmentationRule() : CDPL.Chem.FragmentGenerator
• addFragmentLibrary() : CDPL.ConfGen.ConformerGenerator , CDPL.ConfGen.FragmentAssembler , CDPL.ConfGen.StructureGenerator
• addIncludePattern() : CDPL.Pharm.PatternBasedFeatureGenerator
• addInputCoordinates() : CDPL.ConfGen.TorsionDriver
• addMargin() : CDPL.Vis.Rectangle2D
• addMaxNumOutputConformersRange() : CDPL.ConfGen.ConformerGeneratorSettings
• addMinRMSDRange() : CDPL.ConfGen.ConformerGeneratorSettings
• addParameters() : CDPL.Base.ControlParameterContainer
• addPattern() : CDPL.Chem.PatternAtomTyper , CDPL.Chem.SubstructureHistogramCalculator
• addPoint() : CDPL.Vis.Rectangle2D
• addProperties() : CDPL.Base.PropertyContainer
• addQuery() : CDPL.Shape.ScreeningProcessor
• addReader() : CDPL.Chem.CompoundMoleculeReader , CDPL.Chem.CompoundReactionReader , CDPL.Grid.CompoundDRegularGridReader , CDPL.Grid.CompoundDRegularGridSetReader , CDPL.Pharm.CompoundPharmacophoreReader
• addRectangle() : CDPL.Vis.Path2D , CDPL.Vis.Rectangle2D
• addReferenceShape() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.GaussianShapeAlignment
• addReferenceShapes() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.GaussianShapeAlignment
• addRule() : CDPL.ConfGen.TorsionCategory
• addTautomerizationRule() : CDPL.Chem.TautomerGenerator
• addTorsionLibrary() : CDPL.ConfGen.ConformerGenerator , CDPL.ConfGen.StructureGenerator , CDPL.ConfGen.TorsionDriver
• addTransformationPattern() : CDPL.Chem.PatternBasedTautomerizationRule
• addVolumeConstraint() : CDPL.Util.DG3DCoordinatesGenerator
• addXYData() : CDPL.Math.DMLRModel , CDPL.Math.FMLRModel
• align() : CDPL.Math.DKabschAlgorithm , CDPL.Math.FKabschAlgorithm , CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.GaussianShapeAlignment , CDPL.Shape.GaussianShapeFunctionAlignment
• alignHitMolecule() : CDPL.Pharm.FileScreeningHitCollector
• allCarbonMode() : CDPL.Shape.ScreeningSettings
• allowDuplicateEntries() : CDPL.Pharm.ScreeningDBCreator
• analyze() : CDPL.Chem.BemisMurckoAnalyzer , CDPL.Pharm.InteractionAnalyzer
• append() : CDPL.Chem.BasicMolecule , CDPL.Chem.Molecule , CDPL.Pharm.BasicPharmacophore , CDPL.Pharm.Pharmacophore , CDPL.Util.BitSet
• applyConfiguration() : CDPL.Pharm.DefaultPharmacophoreGenerator
• arc() : CDPL.Vis.Path2D
• arcTo() : CDPL.Vis.Path2D , CDPL.Vis.Path2DConverter
• assemble() : CDPL.ConfGen.FragmentAssembler
• assign() : CDPL.Base.ControlParameterList , CDPL.Base.DataFormat , CDPL.Base.LookupKey , CDPL.Biomol.PDBData , CDPL.Biomol.ResidueDictionary , CDPL.Biomol.ResidueDictionary.Entry , CDPL.Chem.ANDAtomMatchExpressionList , CDPL.Chem.ANDBondMatchExpressionList , CDPL.Chem.ANDMolecularGraphMatchExpressionList , CDPL.Chem.ANDReactionMatchExpressionList , CDPL.Chem.Atom , CDPL.Chem.Atom3DCoordinatesFunctor , CDPL.Chem.AtomArray3DCoordinatesFunctor , CDPL.Chem.AtomBondMapping , CDPL.Chem.AtomConformer3DCoordinatesFunctor , CDPL.Chem.AtomDictionary , CDPL.Chem.AtomDictionary.Entry , CDPL.Chem.AtomMapping , CDPL.Chem.AtomMatchExpressionList , CDPL.Chem.AtomTypeMatchExpression , CDPL.Chem.BasicAtom , CDPL.Chem.BasicBond , CDPL.Chem.BasicMolecule , CDPL.Chem.BasicReaction , CDPL.Chem.BemisMurckoAnalyzer , CDPL.Chem.Bond , CDPL.Chem.BondDirectionMatchExpression , CDPL.Chem.BondMapping , CDPL.Chem.BondMatchExpressionList , CDPL.Chem.BondReactionCenterStatusMatchExpression , CDPL.Chem.BondSubstituentDirectionMatchExpression , CDPL.Chem.BRICSFragmentGenerator , CDPL.Chem.ChEMBLStandardizer , CDPL.Chem.CIPConfigurationLabeler , CDPL.Chem.ElectronSystem , CDPL.Chem.ElectronSystemList , CDPL.Chem.Entity3DMapping , CDPL.Chem.Fragment , CDPL.Chem.FragmentGenerator , CDPL.Chem.FragmentGenerator.ExcludePattern , CDPL.Chem.FragmentGenerator.FragmentationRule , CDPL.Chem.FragmentGenerator.FragmentLink , CDPL.Chem.FragmentList , CDPL.Chem.MatchConstraint , CDPL.Chem.MatchConstraintList , CDPL.Chem.MolecularGraphComponentGroupingMatchExpression , CDPL.Chem.MolecularGraphMatchExpressionList , CDPL.Chem.Molecule , CDPL.Chem.NOTAtomMatchExpression , CDPL.Chem.NOTBondMatchExpression , CDPL.Chem.NOTMolecularGraphMatchExpression , CDPL.Chem.NOTReactionMatchExpression , CDPL.Chem.ORAtomMatchExpressionList , CDPL.Chem.ORBondMatchExpressionList , CDPL.Chem.ORMolecularGraphMatchExpressionList , CDPL.Chem.ORReactionMatchExpressionList , CDPL.Chem.PatternAtomTyper , CDPL.Chem.PatternAtomTyper.Pattern , CDPL.Chem.PatternBasedTautomerizationRule , CDPL.Chem.PatternBasedTautomerizationRule.BondOrderChange , CDPL.Chem.ProtonationStateStandardizer , CDPL.Chem.Reaction , CDPL.Chem.ReactionAtomMappingMatchExpression , CDPL.Chem.ReactionComponentGroupingMatchExpression , CDPL.Chem.ReactionMatchExpressionList , CDPL.Chem.RECAPFragmentGenerator , CDPL.Chem.ResonanceStructureGenerator , CDPL.Chem.ResonanceStructureGenerator.StructureData , CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Chem.StereoDescriptor , CDPL.Chem.StereoisomerGenerator , CDPL.Chem.StringDataBlock , CDPL.Chem.StringDataBlockEntry , CDPL.Chem.SubstructureHistogramCalculator , CDPL.Chem.SubstructureHistogramCalculator.Pattern , CDPL.Chem.SurfaceAtomExtractor , CDPL.Chem.TautomerGenerator , CDPL.Chem.TautomerScore , CDPL.Chem.TopologicalAtomAlignment , CDPL.Chem.TopologicalEntity3DAlignment , CDPL.ConfGen.CanonicalFragment , CDPL.ConfGen.ConformerData , CDPL.ConfGen.ConformerGeneratorSettings , CDPL.ConfGen.DGConstraintGenerator , CDPL.ConfGen.DGConstraintGeneratorSettings , CDPL.ConfGen.DGStructureGenerator , CDPL.ConfGen.DGStructureGeneratorSettings , CDPL.ConfGen.FragmentAssemblerSettings , CDPL.ConfGen.FragmentConformerGeneratorSettings , CDPL.ConfGen.FragmentConformerGeneratorSettings.FragmentSettings , CDPL.ConfGen.FragmentLibrary , CDPL.ConfGen.FragmentLibraryEntry , CDPL.ConfGen.StructureGeneratorSettings , CDPL.ConfGen.TorsionCategory , CDPL.ConfGen.TorsionDriverSettings , CDPL.ConfGen.TorsionLibrary , CDPL.ConfGen.TorsionRule.AngleEntry , CDPL.ConfGen.TorsionRule , CDPL.ConfGen.TorsionRuleMatch , CDPL.Descr.AtomAutoCorrelation3DVectorCalculator , CDPL.Descr.AtomRDFCodeCalculator , CDPL.Descr.AutoCorrelation2DVectorCalculator , CDPL.Descr.CircularFingerprintGenerator , CDPL.Descr.FeatureAutoCorrelation3DVectorCalculator , CDPL.Descr.FeatureRDFCodeCalculator , CDPL.Descr.MoleculeAutoCorr2DDescriptorCalculator , CDPL.Descr.MoleculeAutoCorr3DDescriptorCalculator , CDPL.Descr.MoleculeRDFDescriptorCalculator , CDPL.Descr.PathFingerprintGenerator , CDPL.Descr.PharmacophoreAutoCorr3DDescriptorCalculator , CDPL.Descr.PharmacophoreRDFDescriptorCalculator , CDPL.ForceField.ElasticPotential , CDPL.ForceField.ElasticPotentialList , CDPL.ForceField.MMFF94AngleBendingInteraction , CDPL.ForceField.MMFF94AngleBendingInteractionList , CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer , CDPL.ForceField.MMFF94AngleBendingParameterTable , CDPL.ForceField.MMFF94AngleBendingParameterTable.Entry , CDPL.ForceField.MMFF94AromaticAtomTypeDefinitionTable , CDPL.ForceField.MMFF94AromaticAtomTypeDefinitionTable.Entry , CDPL.ForceField.MMFF94AtomTypePropertyTable , CDPL.ForceField.MMFF94AtomTypePropertyTable.Entry , CDPL.ForceField.MMFF94AtomTyper , CDPL.ForceField.MMFF94BondChargeIncrementTable , CDPL.ForceField.MMFF94BondChargeIncrementTable.Entry , CDPL.ForceField.MMFF94BondStretchingInteraction , CDPL.ForceField.MMFF94BondStretchingInteractionList , CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer , CDPL.ForceField.MMFF94BondStretchingParameterTable , CDPL.ForceField.MMFF94BondStretchingParameterTable.Entry , CDPL.ForceField.MMFF94BondStretchingRuleParameterTable , CDPL.ForceField.MMFF94BondStretchingRuleParameterTable.Entry , CDPL.ForceField.MMFF94BondTyper , CDPL.ForceField.MMFF94ChargeCalculator , CDPL.ForceField.MMFF94DefaultStretchBendParameterTable , CDPL.ForceField.MMFF94DefaultStretchBendParameterTable.Entry , CDPL.ForceField.MMFF94ElectrostaticInteraction , CDPL.ForceField.MMFF94ElectrostaticInteractionList , CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer , CDPL.ForceField.MMFF94EnergyCalculator , CDPL.ForceField.MMFF94FormalAtomChargeDefinitionTable , CDPL.ForceField.MMFF94FormalAtomChargeDefinitionTable.Entry , CDPL.ForceField.MMFF94GradientCalculator , CDPL.ForceField.MMFF94HeavyToHydrogenAtomTypeMap , CDPL.ForceField.MMFF94InteractionData , CDPL.ForceField.MMFF94InteractionParameterizer , CDPL.ForceField.MMFF94OutOfPlaneBendingInteraction , CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionList , CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL.ForceField.MMFF94OutOfPlaneBendingParameterTable , CDPL.ForceField.MMFF94OutOfPlaneBendingParameterTable.Entry , CDPL.ForceField.MMFF94PartialBondChargeIncrementTable , CDPL.ForceField.MMFF94PartialBondChargeIncrementTable.Entry , CDPL.ForceField.MMFF94PrimaryToParameterAtomTypeMap , CDPL.ForceField.MMFF94PrimaryToParameterAtomTypeMap.Entry , CDPL.ForceField.MMFF94StretchBendInteraction , CDPL.ForceField.MMFF94StretchBendInteractionList , CDPL.ForceField.MMFF94StretchBendInteractionParameterizer , CDPL.ForceField.MMFF94StretchBendParameterTable , CDPL.ForceField.MMFF94StretchBendParameterTable.Entry , CDPL.ForceField.MMFF94SymbolicAtomTypePatternTable , CDPL.ForceField.MMFF94SymbolicAtomTypePatternTable.Entry , CDPL.ForceField.MMFF94SymbolicToNumericAtomTypeMap , CDPL.ForceField.MMFF94TorsionInteraction , CDPL.ForceField.MMFF94TorsionInteractionList , CDPL.ForceField.MMFF94TorsionInteractionParameterizer , CDPL.ForceField.MMFF94TorsionParameterTable , CDPL.ForceField.MMFF94TorsionParameterTable.Entry , CDPL.ForceField.MMFF94VanDerWaalsInteraction , CDPL.ForceField.MMFF94VanDerWaalsInteractionList , CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer , CDPL.ForceField.MMFF94VanDerWaalsParameterTable , CDPL.ForceField.MMFF94VanDerWaalsParameterTable.Entry , CDPL.ForceField.UFFAtomTypePropertyTable , CDPL.ForceField.UFFAtomTypePropertyTable.Entry , CDPL.GRAIL.AtomDensityGridCalculator , CDPL.GRAIL.BuriednessGridCalculator , CDPL.GRAIL.BuriednessScore , CDPL.GRAIL.FeatureInteractionScoreGridCalculator , CDPL.GRAIL.GeneralizedBellAtomDensity , CDPL.GRAIL.GRAILDataSetGenerator , CDPL.GRAIL.GRAILDescriptorCalculator , CDPL.GRAIL.GRAILXDescriptorCalculator , CDPL.Grid.DRegularGrid , CDPL.Grid.DRegularGridSet , CDPL.Grid.FRegularGrid , CDPL.Grid.FRegularGridSet , CDPL.Math.DGrid , CDPL.Math.DGridExpression , CDPL.Math.DHomogenousCoordsAdapter , CDPL.Math.DIdentityMatrix , CDPL.Math.DKabschAlgorithm , CDPL.Math.DMatrix , CDPL.Math.DMatrixColumn , CDPL.Math.DMatrixExpression , CDPL.Math.DMatrixRange , CDPL.Math.DMatrixRow , CDPL.Math.DMatrixSlice , CDPL.Math.DMatrixTranspose , CDPL.Math.DMLRModel , 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.FKabschAlgorithm , CDPL.Math.FMatrix , CDPL.Math.FMatrixColumn , CDPL.Math.FMatrixExpression , CDPL.Math.FMatrixRange , CDPL.Math.FMatrixRow , CDPL.Math.FMatrixSlice , CDPL.Math.FMatrixTranspose , CDPL.Math.FMLRModel , 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.Vector2DArray , CDPL.Math.Vector2DArrayAlignmentCalculator , CDPL.Math.Vector2F , CDPL.Math.Vector2FArray , CDPL.Math.Vector2FArrayAlignmentCalculator , CDPL.Math.Vector2L , CDPL.Math.Vector2LArray , CDPL.Math.Vector2UL , CDPL.Math.Vector2ULArray , CDPL.Math.Vector3D , CDPL.Math.Vector3DArray , CDPL.Math.Vector3DArrayAlignmentCalculator , CDPL.Math.Vector3F , CDPL.Math.Vector3FArray , CDPL.Math.Vector3FArrayAlignmentCalculator , 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.MolProp.AtomHydrophobicityCalculator , CDPL.MolProp.ElementHistogram , CDPL.MolProp.HBondAcceptorAtomTyper , CDPL.MolProp.HBondDonorAtomTyper , CDPL.MolProp.LogSCalculator , CDPL.MolProp.MassComposition , CDPL.MolProp.TPSACalculator , CDPL.MolProp.XLogPCalculator , CDPL.Pharm.AromaticFeatureGenerator , CDPL.Pharm.BasicFeature , CDPL.Pharm.BasicPharmacophore , CDPL.Pharm.CationPiInteractionConstraint , CDPL.Pharm.CationPiInteractionScore , CDPL.Pharm.DefaultInteractionAnalyzer , CDPL.Pharm.Feature , CDPL.Pharm.FeatureDistanceConstraint , CDPL.Pharm.FeatureDistanceScore , CDPL.Pharm.FeatureGeometryMatchFunctor , CDPL.Pharm.FeatureInteractionScoreCombiner , CDPL.Pharm.FeatureMapping , CDPL.Pharm.FeaturePairDistanceMatchFunctor , CDPL.Pharm.FeaturePositionMatchFunctor , CDPL.Pharm.FeatureSet , CDPL.Pharm.FeatureTypeHistogram , CDPL.Pharm.FeatureTypeMatchFunctor , CDPL.Pharm.FileScreeningHitCollector , CDPL.Pharm.HBondAcceptorFeatureGenerator , CDPL.Pharm.HBondDonorFeatureGenerator , CDPL.Pharm.HBondingInteractionConstraint , CDPL.Pharm.HBondingInteractionScore , CDPL.Pharm.HydrophobicAtomFeatureGenerator , CDPL.Pharm.HydrophobicFeatureGenerator , CDPL.Pharm.InteractionAnalyzer , CDPL.Pharm.InteractionConstraintConnector , CDPL.Pharm.InteractionPharmacophoreGenerator , CDPL.Pharm.NegIonizableFeatureGenerator , CDPL.Pharm.OrthogonalPiPiInteractionConstraint , CDPL.Pharm.OrthogonalPiPiInteractionScore , CDPL.Pharm.ParallelPiPiInteractionConstraint , CDPL.Pharm.ParallelPiPiInteractionScore , CDPL.Pharm.PatternBasedFeatureGenerator , CDPL.Pharm.Pharmacophore , CDPL.Pharm.PharmacophoreAlignment , CDPL.Pharm.PharmacophoreFitScore , CDPL.Pharm.PharmacophoreGenerator , CDPL.Pharm.PosIonizableFeatureGenerator , CDPL.Pharm.ScreeningProcessor.SearchHit , CDPL.Pharm.SpatialFeatureAlignment , CDPL.Pharm.SpatialFeatureMapping , CDPL.Pharm.TopologicalFeatureAlignment , CDPL.Pharm.XBondAcceptorFeatureGenerator , CDPL.Pharm.XBondDonorFeatureGenerator , CDPL.Pharm.XBondingInteractionConstraint , CDPL.Pharm.XBondingInteractionScore , CDPL.Shape.AlignedColorTverskyScore , CDPL.Shape.AlignedShapeTverskyScore , CDPL.Shape.AlignedTotalOverlapTverskyScore , CDPL.Shape.AlignedTverskyComboScore , CDPL.Shape.AlignmentResult , CDPL.Shape.ColorTanimotoScore , CDPL.Shape.ColorTverskyScore , CDPL.Shape.ExactGaussianShapeOverlapFunction , CDPL.Shape.FastGaussianShapeOverlapFunction , CDPL.Shape.GaussianShape , CDPL.Shape.GaussianShape.Element , CDPL.Shape.GaussianShapeFunction , CDPL.Shape.GaussianShapeFunctionAlignment.Result , CDPL.Shape.GaussianShapeGenerator , CDPL.Shape.GaussianShapeSet , CDPL.Shape.PrincipalAxesAlignmentStartGenerator , CDPL.Shape.ReferenceColorTverskyScore , CDPL.Shape.ReferenceShapeTverskyScore , CDPL.Shape.ReferenceTotalOverlapTverskyScore , CDPL.Shape.ReferenceTverskyComboScore , CDPL.Shape.ScreeningSettings , CDPL.Shape.ShapeTanimotoScore , CDPL.Shape.ShapeTverskyScore , CDPL.Shape.TanimotoComboScore , CDPL.Shape.TotalOverlapTanimotoScore , CDPL.Shape.TotalOverlapTverskyScore , CDPL.Shape.TverskyComboScore , CDPL.Shape.Vector7D , CDPL.Util.BitSet , CDPL.Util.BitSetArray , CDPL.Util.BronKerboschAlgorithm , CDPL.Util.DArray , CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG2DCoordinatesGenerator.DistanceConstraint , CDPL.Util.DG3DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator.DistanceConstraint , CDPL.Util.DG3DCoordinatesGenerator.VolumeConstraint , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPair , CDPL.Util.STPairArray , CDPL.Util.UIArray , CDPL.Vis.Brush , CDPL.Vis.ClipPathPrimitive2D , CDPL.Vis.Color , CDPL.Vis.ColorTable , CDPL.Vis.EllipsePrimitive2D , CDPL.Vis.Font , CDPL.Vis.Line2D , CDPL.Vis.LinePrimitive2D , CDPL.Vis.LineSegmentListPrimitive2D , CDPL.Vis.Path2D , CDPL.Vis.PathPrimitive2D , CDPL.Vis.Pen , CDPL.Vis.PointListPrimitive2D , CDPL.Vis.PolygonPrimitive2D , CDPL.Vis.PolylinePrimitive2D , CDPL.Vis.Rectangle2D , CDPL.Vis.SizeSpecification , CDPL.Vis.TextLabelPrimitive2D
• atomConfigEnumerated() : CDPL.Chem.StereoisomerGenerator