- p -

• parameterize() : CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer , CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer , CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer , CDPL.ForceField.MMFF94InteractionParameterizer , CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer , CDPL.ForceField.MMFF94StretchBendInteractionParameterizer , CDPL.ForceField.MMFF94TorsionInteractionParameterizer , CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer
• perceive() : CDPL.Chem.AromaticRingSet , CDPL.Chem.AromaticSubstructure , CDPL.Chem.CompleteRingSet , CDPL.Chem.ComponentSet , CDPL.Chem.CyclicSubstructure , CDPL.Chem.PiElectronSystemList , CDPL.Chem.SmallestSetOfSmallestRings , CDPL.Pharm.SpatialFeatureMapping
• perceiveTypes() : CDPL.ForceField.MMFF94AtomTyper , CDPL.ForceField.MMFF94BondTyper , CDPL.MolProp.HBondAcceptorAtomTyper , CDPL.MolProp.HBondDonorAtomTyper
• performAlignment() : CDPL.Shape.FastGaussianShapeAlignment , CDPL.Shape.GaussianShapeAlignment , CDPL.Shape.GaussianShapeFunctionAlignment
• performExhaustiveSearch() : CDPL.Chem.SpatialAtomAlignment , CDPL.Chem.SpatialEntity3DAlignment , CDPL.Pharm.SpatialFeatureAlignment
• performReaction() : CDPL.Chem.Reactor
• popLastElement() : CDPL.Chem.AtomMatchExpressionList , CDPL.Chem.BondMatchExpressionList , CDPL.Chem.FragmentList , CDPL.Chem.MolecularGraphMatchExpressionList , CDPL.Chem.ReactionMatchExpressionList , 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.Util.BitSetArray , CDPL.Util.DArray , CDPL.Util.LArray , CDPL.Util.SArray , CDPL.Util.STArray , CDPL.Util.STPairArray , CDPL.Util.UIArray
• preserveInputBondingGeometries() : CDPL.ConfGen.FragmentConformerGeneratorSettings
• process() : CDPL.ConfGen.FragmentLibraryGenerator , CDPL.Pharm.ScreeningDBCreator , CDPL.Shape.ScreeningProcessor
• processAllMatches() : CDPL.Chem.PatternAtomTyper.Pattern , CDPL.Chem.SubstructureHistogramCalculator.Pattern
• processUniqueMatchesOnly() : CDPL.Chem.PatternAtomTyper.Pattern , CDPL.Chem.SubstructureHistogramCalculator.Pattern
• proximityOptimization() : CDPL.Shape.FastGaussianShapeOverlapFunction