- r -

• read() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Chem.MoleculeReaderBase , CDPL.Chem.ReactionReaderBase , CDPL.Grid.DRegularGridReaderBase , CDPL.Grid.DRegularGridSetReaderBase , CDPL.Pharm.PharmacophoreReaderBase , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2IStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipIStream
• readline() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2IStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipIStream
• readlines() : CDPL.Base.FileIOStream , CDPL.Base.StringIOStream , CDPL.Util.BZip2IOStream , CDPL.Util.BZip2IStream , CDPL.Util.GZipIOStream , CDPL.Util.GZipIStream
• regardAtomConfiguration() : CDPL.ConfGen.DGConstraintGeneratorSettings
• regardBondConfiguration() : CDPL.ConfGen.DGConstraintGeneratorSettings
• regardIsotopes() : CDPL.Chem.TautomerGenerator
• regardStereochemistry() : CDPL.Chem.TautomerGenerator
• registerCopyPostprocessingFunction() : CDPL.Chem.Molecule , CDPL.Chem.Reaction
• registerInputHandler() : CDPL.Chem.MolecularGraphIOManager , CDPL.Chem.MoleculeIOManager , CDPL.Chem.ReactionIOManager , CDPL.Grid.DRegularGridIOManager , CDPL.Grid.DRegularGridSetIOManager , CDPL.Pharm.FeatureContainerIOManager , CDPL.Pharm.PharmacophoreIOManager
• registerIOCallback() : CDPL.Base.DataIOBase
• registerOutputHandler() : CDPL.Chem.MolecularGraphIOManager , CDPL.Chem.MoleculeIOManager , CDPL.Chem.ReactionIOManager , CDPL.Grid.DRegularGridIOManager , CDPL.Grid.DRegularGridSetIOManager , CDPL.Pharm.FeatureContainerIOManager , CDPL.Pharm.PharmacophoreIOManager
• registerParameterChangedCallback() : CDPL.Base.ControlParameterContainer
• registerParameterRemovedCallback() : CDPL.Base.ControlParameterContainer
• registerParentChangedCallback() : CDPL.Base.ControlParameterContainer
• remove() : CDPL.Chem.Molecule , CDPL.Pharm.Pharmacophore
• removeAngle() : CDPL.ConfGen.TorsionRule
• removeAtom() : CDPL.Chem.ElectronSystem , CDPL.Chem.Fragment , CDPL.Chem.Molecule
• removeBond() : CDPL.Chem.Fragment , CDPL.Chem.Molecule
• removeCategory() : CDPL.ConfGen.TorsionCategory
• removeComponent() : CDPL.Chem.Reaction
• removeComponents() : CDPL.Chem.Reaction
• removeConstraintFunction() : CDPL.Pharm.InteractionAnalyzer
• removeDistanceConstraint() : CDPL.Util.DG2DCoordinatesGenerator , CDPL.Util.DG3DCoordinatesGenerator
• removeElement() : 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
• removeElements() : 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
• removeEntries() : CDPL.Chem.AtomMapping , CDPL.Chem.BondMapping , CDPL.Chem.Entity3DMapping , CDPL.Pharm.FeatureMapping
• removeEntry() : CDPL.Biomol.ResidueDictionary , CDPL.Chem.AtomDictionary , CDPL.Chem.AtomMapping , CDPL.Chem.BondMapping , CDPL.Chem.Entity3DMapping , 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 , CDPL.MolProp.ElementHistogram , CDPL.MolProp.MassComposition , CDPL.Pharm.FeatureMapping , CDPL.Pharm.FeatureTypeHistogram , CDPL.Vis.ColorTable
• removeExcludePattern() : CDPL.Chem.FragmentGenerator
• removeFeature() : CDPL.Pharm.FeatureSet , CDPL.Pharm.Pharmacophore
• removeFeatureGenerator() : CDPL.Pharm.PharmacophoreGenerator
• removeFileExtension() : CDPL.Base.DataFormat
• removeFragmentationRule() : CDPL.Chem.FragmentGenerator
• removeGridName() : CDPL.GRAIL.GRAILDataSetGenerator
• removeParameter() : CDPL.Base.ControlParameterContainer
• removePattern() : CDPL.Chem.PatternAtomTyper , CDPL.Chem.SubstructureHistogramCalculator
• removeProperty() : CDPL.Base.PropertyContainer
• removeReader() : CDPL.Chem.CompoundMoleculeReader , CDPL.Chem.CompoundReactionReader , CDPL.Grid.CompoundDRegularGridReader , CDPL.Grid.CompoundDRegularGridSetReader , CDPL.Pharm.CompoundPharmacophoreReader
• removeRecord() : CDPL.Biomol.PDBData
• removeResonanceDuplicates() : CDPL.Chem.TautomerGenerator
• removeRule() : CDPL.ConfGen.TorsionCategory
• removeScoringFunction() : CDPL.GRAIL.GRAILDataSetGenerator
• removeTautomerizationRule() : CDPL.Chem.TautomerGenerator
• removeVolumeConstraint() : CDPL.Util.DG3DCoordinatesGenerator
• render() : CDPL.Vis.GraphicsPrimitive2D , CDPL.Vis.View2D
• requiresAtomBondMapping() : CDPL.Chem.AtomMatchExpression , CDPL.Chem.BondMatchExpression , CDPL.Chem.MolecularGraphMatchExpression , CDPL.Chem.ReactionMatchExpression
• reserve() : 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
• reserveMemoryForAtoms() : CDPL.Chem.Fragment , CDPL.Chem.Molecule
• reserveMemoryForBonds() : CDPL.Chem.Fragment , CDPL.Chem.Molecule
• reset() : CDPL.Chem.ConnectedSubstructureSet , CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment , CDPL.Util.BitSet , CDPL.Vis.Rectangle2D
• resize() : 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.DGrid , CDPL.Math.DIdentityMatrix , CDPL.Math.DMatrix , CDPL.Math.DRegularSpatialGrid , CDPL.Math.DScalarGrid , CDPL.Math.DScalarMatrix , CDPL.Math.DScalarVector , CDPL.Math.DUnitVector , CDPL.Math.DVector , CDPL.Math.DZeroGrid , CDPL.Math.DZeroMatrix , CDPL.Math.DZeroVector , CDPL.Math.FGrid , CDPL.Math.FIdentityMatrix , CDPL.Math.FMatrix , CDPL.Math.FRegularSpatialGrid , CDPL.Math.FScalarGrid , CDPL.Math.FScalarMatrix , CDPL.Math.FScalarVector , CDPL.Math.FUnitVector , CDPL.Math.FVector , CDPL.Math.FZeroGrid , CDPL.Math.FZeroMatrix , CDPL.Math.FZeroVector , CDPL.Math.LIdentityMatrix , CDPL.Math.LMatrix , CDPL.Math.LScalarMatrix , CDPL.Math.LScalarVector , CDPL.Math.LUnitVector , CDPL.Math.LVector , CDPL.Math.LZeroMatrix , CDPL.Math.LZeroVector , 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.ULIdentityMatrix , CDPL.Math.ULMatrix , CDPL.Math.ULScalarMatrix , CDPL.Math.ULScalarVector , CDPL.Math.ULUnitVector , CDPL.Math.ULVector , CDPL.Math.ULZeroMatrix , CDPL.Math.ULZeroVector , 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.BitSet , CDPL.Util.BitSetArray , CDPL.Util.DArray , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPairArray , CDPL.Util.UIArray
• resizeDataSet() : CDPL.Math.DMLRModel , CDPL.Math.FMLRModel
• resonanceDuplicatesRemoved() : CDPL.Chem.TautomerGenerator
• restoreState() : CDPL.Vis.CairoBackend.CairoRenderer2D , CDPL.Vis.QtBackend.QtRenderer2D , CDPL.Vis.Renderer2D
• ringBondsIncluded() : CDPL.Chem.StereoisomerGenerator