| ►CBoost.Python.enum | |
| CCDPL.Base.IOStream.OpenMode | |
| CCDPL.Biomol.PDBData.RecordType | Identifies the type of PDB data record |
| CCDPL.Chem.ChEMBLStandardizer.ChangeFlags | Bitwise-OR-combined flags reporting which standardization steps modified the input molecule |
| CCDPL.Chem.MatchConstraint.Relation | Defines constants for the specification of relational constraints on the values of query/target attribute pairs |
| CCDPL.Chem.MatchConstraintList.Type | Defines constants that describe the logical type of the match constraint list |
| CCDPL.Chem.ProtonationStateStandardizer.Flavor | Selects the objective driving the protonation-state adjustment |
| CCDPL.Chem.TautomerGenerator.Mode | Constants specifying the output tautomer filtering strategy |
| CCDPL.Descr.MoleculeAutoCorr2DDescriptorCalculator.Mode | Specifies how the descriptor is partitioned by atom types |
| CCDPL.Descr.NPoint2DPharmacophoreFingerprintGenerator.FeatureDistanceType | Specifies how the topological distance between two features is derived from the topological distances between their underlying atoms |
| CCDPL.ForceField.MMFF94VanDerWaalsInteraction.HDonorAcceptorType | MMFF94 hydrogen-bond donor/acceptor classification of an atom |
| CCDPL.GRAIL.BindingAffinityCalculator.AffinityMeasure | Specifies the affinity measure the prediction targets |
| CCDPL.GRAIL.GRAILDescriptorCalculator.ElementIndex | Indices of the individual elements of the GRAIL descriptor vector |
| CCDPL.GRAIL.GRAILXDescriptorCalculator.ElementIndex | Indices of the individual elements of the extended GRAIL-X descriptor vector |
| CCDPL.Math.DVectorBFGSMinimizer.Status | Status bitmask reported by minimize() and getStatus() |
| CCDPL.Math.FVectorBFGSMinimizer.Status | Status bitmask reported by minimize() and getStatus() |
| CCDPL.Math.Vector2DArrayBFGSMinimizer.Status | |
| CCDPL.Math.Vector2FArrayBFGSMinimizer.Status | |
| CCDPL.Math.Vector3DArrayBFGSMinimizer.Status | |
| CCDPL.Math.Vector3FArrayBFGSMinimizer.Status | |
| CCDPL.Pharm.DefaultPharmacophoreGenerator.Configuration | Flags controlling feature generation |
| CCDPL.Pharm.PatternBasedFeatureGenerator.PatternAtomLabelFlag | Role-flags assigned (via the atom-mapping-ID property) to atoms of feature substructure patterns added through addIncludePattern() |
| CCDPL.Pharm.ScreeningDBCreator.Mode | Specifies how an existing database file is treated by open() |
| CCDPL.Pharm.ScreeningProcessor.HitReportMode | Specifies which conformer-level hits are reported per molecule |
| CCDPL.Shape.ScreeningSettings.AlignmentMode | Bitmask flags specifying the strategies used to seed alignment starting transformations |
| CCDPL.Shape.ScreeningSettings.ColorFeatureType | Specifies which kind of color (pharmacophore) features are used during shape alignment |
| CCDPL.Shape.ScreeningSettings.ScreeningMode | Specifies which alignment hits are reported by the screening processor |
| CCDPL.Vis.Brush.Style | Defines constants for supported fill pattern styles |
| CCDPL.Vis.Path2D.FillRule | Specifies which method to use for filling closed shapes described by the Path2D object |
| CCDPL.Vis.Pen.CapStyle | Defines constants for supported line cap styles |
| CCDPL.Vis.Pen.JoinStyle | Defines constants for supported line join styles |
| CCDPL.Vis.Pen.LineStyle | Defines constants for supported line styles |
| ►CBoost.Python.instance | |
| CCDPL.Base.Any | Safe, type checked container for arbitrary data of variable type |
| ►CCDPL.Base.ControlParameterContainer | Base class providing methods for the storage and lookup of control-parameter values |
| CCDPL.Base.ControlParameterList | Data structure for the storage and lookup of control-parameter values |
| ►CCDPL.Base.DataIOBase | Provides infrastructure for the registration of I/O callback functions |
| ►CCDPL.Chem.MolecularGraphWriterBase | Interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink |
| CCDPL.Biomol.FileMMCIFBZ2MolecularGraphWriter | |
| CCDPL.Biomol.FileMMCIFGZMolecularGraphWriter | |
| CCDPL.Biomol.FileMMCIFMolecularGraphWriter | |
| CCDPL.Biomol.FileMMTFBZ2MolecularGraphWriter | |
| CCDPL.Biomol.FileMMTFGZMolecularGraphWriter | |
| CCDPL.Biomol.FileMMTFMolecularGraphWriter | |
| CCDPL.Biomol.FilePDBBZ2MolecularGraphWriter | |
| CCDPL.Biomol.FilePDBGZMolecularGraphWriter | |
| CCDPL.Biomol.FilePDBMolecularGraphWriter | |
| CCDPL.Biomol.MMCIFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFMolecularGraphWriter | Writer for molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMTFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFMolecularGraphWriter | Writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.PDBBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBMolecularGraphWriter | Writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Chem.CDFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFMolecularGraphWriter | Writer for molecular graph data in the native I/O format of the CDPL |
| CCDPL.Chem.CMLBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLMolecularGraphWriter | Writer for molecular graph data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.FileCDFBZ2MolecularGraphWriter | |
| CCDPL.Chem.FileCDFGZMolecularGraphWriter | |
| CCDPL.Chem.FileCDFMolecularGraphWriter | |
| CCDPL.Chem.FileCMLBZ2MolecularGraphWriter | |
| CCDPL.Chem.FileCMLGZMolecularGraphWriter | |
| CCDPL.Chem.FileCMLMolecularGraphWriter | |
| CCDPL.Chem.FileINCHIMolecularGraphWriter | |
| CCDPL.Chem.FileJMEMolecularGraphWriter | |
| CCDPL.Chem.FileMOL2BZ2MolecularGraphWriter | |
| CCDPL.Chem.FileMOL2GZMolecularGraphWriter | |
| CCDPL.Chem.FileMOL2MolecularGraphWriter | |
| CCDPL.Chem.FileMOLMolecularGraphWriter | |
| CCDPL.Chem.FileSDFBZ2MolecularGraphWriter | |
| CCDPL.Chem.FileSDFGZMolecularGraphWriter | |
| CCDPL.Chem.FileSDFMolecularGraphWriter | |
| CCDPL.Chem.FileSMARTSMolecularGraphWriter | |
| CCDPL.Chem.FileSMILESBZ2MolecularGraphWriter | |
| CCDPL.Chem.FileSMILESGZMolecularGraphWriter | |
| CCDPL.Chem.FileSMILESMolecularGraphWriter | |
| CCDPL.Chem.FileXYZBZ2MolecularGraphWriter | |
| CCDPL.Chem.FileXYZGZMolecularGraphWriter | |
| CCDPL.Chem.FileXYZMolecularGraphWriter | |
| CCDPL.Chem.INCHIMolecularGraphWriter | Writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CCDPL.Chem.JMEMolecularGraphWriter | Writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.MOL2BZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format |
| CCDPL.Chem.MOL2GZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format |
| CCDPL.Chem.MOL2MolecularGraphWriter | Writer for molecular graph data in the Sybyl MOL2 format |
| CCDPL.Chem.MOLMolecularGraphWriter | Writer for molecular graph data in the MDL Mol-File [CTFILE] format |
| CCDPL.Chem.MolecularGraphWriter | Writer for molecule data in any supported format |
| CCDPL.Chem.SDFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFMolecularGraphWriter | Writer for molecular graph data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SMARTSMolecularGraphWriter | Writer for molecular graph data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESMolecularGraphWriter | Writer for molecular graph data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.XYZBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed XYZ format |
| CCDPL.Chem.XYZGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed XYZ format |
| CCDPL.Chem.XYZMolecularGraphWriter | Writer for molecular graph data in XYZ format to an output stream |
| CCDPL.Pharm.PSDMolecularGraphWriter | Writer for molecular graph data in the CDPL PSD-format |
| CCDPL.Vis.FilePDFMolecularGraphWriter | |
| CCDPL.Vis.FilePNGMolecularGraphWriter | |
| CCDPL.Vis.FilePSMolecularGraphWriter | |
| CCDPL.Vis.FileSVGMolecularGraphWriter | |
| CCDPL.Vis.PDFMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Portable Document Format (PDF) [WPDF] |
| CCDPL.Vis.PNGMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Portable Network Graphics (PNG) [WPNG] format |
| CCDPL.Vis.PSMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the PostScript (PS) [WPS] format |
| CCDPL.Vis.SVGMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Scalable Vector Graphics (SVG) [WSVG] format |
| ►CCDPL.Chem.MoleculeReaderBase | Interface for reading data objects of type Chem.Molecule from an arbitrary data source |
| CCDPL.Biomol.FileMMCIFBZ2MoleculeReader | |
| CCDPL.Biomol.FileMMCIFGZMoleculeReader | |
| CCDPL.Biomol.FileMMCIFMoleculeReader | |
| CCDPL.Biomol.FileMMTFBZ2MoleculeReader | |
| CCDPL.Biomol.FileMMTFGZMoleculeReader | |
| CCDPL.Biomol.FileMMTFMoleculeReader | |
| CCDPL.Biomol.FilePDBBZ2MoleculeReader | |
| CCDPL.Biomol.FilePDBGZMoleculeReader | |
| CCDPL.Biomol.FilePDBMoleculeReader | |
| CCDPL.Biomol.MMCIFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFGZMoleculeReader | Reader for molecule data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFMoleculeReader | Reader for molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMTFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFGZMoleculeReader | Reader for molecule data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFMoleculeReader | Reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.PDBBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBGZMoleculeReader | Reader for molecule data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBMoleculeReader | Reader for molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Chem.CDFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFGZMoleculeReader | Reader for molecule data in the gzip-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFMoleculeReader | Reader for molecule data in the native I/O format of the CDPL |
| CCDPL.Chem.CMLBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLGZMoleculeReader | Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLMoleculeReader | Reader for molecule data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.CompoundMoleculeReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCDPL.Chem.FileCDFBZ2MoleculeReader | |
| CCDPL.Chem.FileCDFGZMoleculeReader | |
| CCDPL.Chem.FileCDFMoleculeReader | |
| CCDPL.Chem.FileCMLBZ2MoleculeReader | |
| CCDPL.Chem.FileCMLGZMoleculeReader | |
| CCDPL.Chem.FileCMLMoleculeReader | |
| CCDPL.Chem.FileINCHIMoleculeReader | |
| CCDPL.Chem.FileJMEMoleculeReader | |
| CCDPL.Chem.FileMOL2BZ2MoleculeReader | |
| CCDPL.Chem.FileMOL2GZMoleculeReader | |
| CCDPL.Chem.FileMOL2MoleculeReader | |
| CCDPL.Chem.FileMOLMoleculeReader | |
| CCDPL.Chem.FileSDFBZ2MoleculeReader | |
| CCDPL.Chem.FileSDFGZMoleculeReader | |
| CCDPL.Chem.FileSDFMoleculeReader | |
| CCDPL.Chem.FileSMARTSMoleculeReader | |
| CCDPL.Chem.FileSMILESBZ2MoleculeReader | |
| CCDPL.Chem.FileSMILESGZMoleculeReader | |
| CCDPL.Chem.FileSMILESMoleculeReader | |
| CCDPL.Chem.FileXYZBZ2MoleculeReader | |
| CCDPL.Chem.FileXYZGZMoleculeReader | |
| CCDPL.Chem.FileXYZMoleculeReader | |
| CCDPL.Chem.INCHIMoleculeReader | Reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CCDPL.Chem.JMEMoleculeReader | Reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.MOL2BZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Sybyl MOL2 format |
| CCDPL.Chem.MOL2GZMoleculeReader | Reader for molecule data in the gzip-compressed Sybyl MOL2 format |
| CCDPL.Chem.MOL2MoleculeReader | Reader for molecule data in the Sybyl MOL2 format |
| CCDPL.Chem.MOLMoleculeReader | Reader for molecule data in the MDL Mol-File [CTFILE] format |
| CCDPL.Chem.MoleculeReader | Reader for molecule data in any supported format |
| CCDPL.Chem.SDFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFGZMoleculeReader | Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFMoleculeReader | Reader for molecule data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SMARTSMoleculeReader | Reader for molecule data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZMoleculeReader | Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESMoleculeReader | Reader for molecule data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.XYZBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed XYZ format |
| CCDPL.Chem.XYZGZMoleculeReader | Reader for molecule data in the gzip-compressed XYZ format |
| CCDPL.Chem.XYZMoleculeReader | Reader for molecule data in XYZ format from an input stream |
| CCDPL.ConfGen.CFLMoleculeReader | Reader for molecule fragment data stored in the CDPL Conformer Generator Fragment Library (CFL) format |
| CCDPL.ConfGen.FileCFLMoleculeReader | |
| CCDPL.Pharm.PSDMoleculeReader | Reader for molecule data in the CDPL PSD-format |
| ►CCDPL.Chem.ReactionReaderBase | Interface for reading data objects of type Chem.Reaction from an arbitrary data source |
| CCDPL.Chem.CDFBZ2ReactionReader | Reader for reaction data in the bzip2-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFGZReactionReader | Reader for reaction data in the gzip-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFReactionReader | Reader for reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.CompoundReactionReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCDPL.Chem.FileCDFBZ2ReactionReader | |
| CCDPL.Chem.FileCDFGZReactionReader | |
| CCDPL.Chem.FileCDFReactionReader | |
| CCDPL.Chem.FileJMEReactionReader | |
| CCDPL.Chem.FileRDFBZ2ReactionReader | |
| CCDPL.Chem.FileRDFGZReactionReader | |
| CCDPL.Chem.FileRDFReactionReader | |
| CCDPL.Chem.FileSMARTSReactionReader | |
| CCDPL.Chem.FileSMILESBZ2ReactionReader | |
| CCDPL.Chem.FileSMILESGZReactionReader | |
| CCDPL.Chem.FileSMILESReactionReader | |
| CCDPL.Chem.JMEReactionReader | Reader for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.RDFBZ2ReactionReader | Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFGZReactionReader | Reader for reaction data in the gzip-compressed MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFReactionReader | Reader for reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RXNReactionReader | Reader for reaction data in the MDL Rxn-File [CTFILE] format |
| CCDPL.Chem.ReactionReader | Reader for reaction data in any supported format |
| CCDPL.Chem.SMARTSReactionReader | Reader for reaction data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2ReactionReader | Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZReactionReader | Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESReactionReader | Reader for reaction data in the Daylight SMILES [SMILES] format |
| ►CCDPL.Chem.ReactionWriterBase | Interface for writing data objects of type Chem.Reaction to an arbitrary data sink |
| CCDPL.Chem.CDFBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFGZReactionWriter | Writer for reaction data in the gzip-compressed native I/O format of the CDPL |
| CCDPL.Chem.CDFReactionWriter | Writer for reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.FileCDFBZ2ReactionWriter | |
| CCDPL.Chem.FileCDFGZReactionWriter | |
| CCDPL.Chem.FileCDFReactionWriter | |
| CCDPL.Chem.FileJMEReactionWriter | |
| CCDPL.Chem.FileRDFBZ2ReactionWriter | |
| CCDPL.Chem.FileRDFGZReactionWriter | |
| CCDPL.Chem.FileRDFReactionWriter | |
| CCDPL.Chem.FileRXNReactionWriter | |
| CCDPL.Chem.FileSMARTSReactionWriter | |
| CCDPL.Chem.FileSMILESBZ2ReactionWriter | |
| CCDPL.Chem.FileSMILESGZReactionWriter | |
| CCDPL.Chem.FileSMILESReactionWriter | |
| CCDPL.Chem.JMEReactionWriter | Writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.RDFBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFGZReactionWriter | Writer for reaction data in the gzip-compressed MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFReactionWriter | Writer for reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RXNReactionWriter | Writer for reaction data in the MDL Rxn-File [CTFILE] format |
| CCDPL.Chem.ReactionWriter | Writer for reaction data in any supported format |
| CCDPL.Chem.SMARTSReactionWriter | Writer for reaction data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZReactionWriter | Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESReactionWriter | Writer for reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Vis.FilePDFReactionWriter | |
| CCDPL.Vis.FilePNGReactionWriter | |
| CCDPL.Vis.FilePSReactionWriter | |
| CCDPL.Vis.FileSVGReactionWriter | |
| CCDPL.Vis.PDFReactionWriter | Creates 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF] |
| CCDPL.Vis.PNGReactionWriter | Creates 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG] format |
| CCDPL.Vis.PSReactionWriter | Creates 2D depictions of chemical reactions in the PostScript (PS) [WPS] format |
| CCDPL.Vis.SVGReactionWriter | Creates 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG] format |
| ►CCDPL.Grid.DRegularGridReaderBase | Interface for reading data objects of type Grid.DRegularGrid from an arbitrary data source |
| CCDPL.Grid.CDFBZ2DRegularGridReader | Reader for bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridReader | Reader for regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridReader | Reader for gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CUBEDRegularGridReader | Reader for regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCDPL.Grid.CompoundDRegularGridReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCDPL.Grid.DRegularGridReader | Reader for regular spatial grid data of type Grid.DRegularGrid in any supported format |
| CCDPL.Grid.FileCDFBZ2DRegularGridReader | |
| CCDPL.Grid.FileCDFDRegularGridReader | |
| CCDPL.Grid.FileCDFGZDRegularGridReader | |
| CCDPL.Grid.FileCUBEDRegularGridReader | |
| ►CCDPL.Grid.DRegularGridSetReaderBase | Interface for reading data objects of type Grid.DRegularGridSet from an arbitrary data source |
| CCDPL.Grid.CDFBZ2DRegularGridSetReader | Reader for bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridSetReader | Reader for regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridSetReader | Reader for gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CompoundDRegularGridSetReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCDPL.Grid.DRegularGridSetReader | Reader for regular spatial grid set data of type Grid.DRegularGridSet in any supported format |
| CCDPL.Grid.FileCDFBZ2DRegularGridSetReader | |
| CCDPL.Grid.FileCDFDRegularGridSetReader | |
| CCDPL.Grid.FileCDFGZDRegularGridSetReader | |
| ►CCDPL.Grid.DRegularGridSetWriterBase | Interface for writing data objects of type Grid.DRegularGridSet to an arbitrary data sink |
| CCDPL.Grid.CDFBZ2DRegularGridSetWriter | Writer for bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridSetWriter | Writer for regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridSetWriter | Writer for gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.DRegularGridSetWriter | Writer for regular spatial grid set data of type Grid.DRegularGridSet in any supported format |
| CCDPL.Grid.FileCDFBZ2DRegularGridSetWriter | |
| CCDPL.Grid.FileCDFDRegularGridSetWriter | |
| CCDPL.Grid.FileCDFGZDRegularGridSetWriter | |
| ►CCDPL.Grid.DRegularGridWriterBase | Interface for writing data objects of type Grid.DRegularGrid to an arbitrary data sink |
| CCDPL.Grid.CDFBZ2DRegularGridWriter | Writer for bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridWriter | Writer for regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridWriter | Writer for gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CUBEDRegularGridWriter | Writer for regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCDPL.Grid.DRegularGridWriter | Writer for grid data of type Grid.DRegularGrid in any supported format |
| CCDPL.Grid.FileCDFBZ2DRegularGridWriter | |
| CCDPL.Grid.FileCDFDRegularGridWriter | |
| CCDPL.Grid.FileCDFGZDRegularGridWriter | |
| CCDPL.Grid.FileCUBEDRegularGridWriter | |
| ►CCDPL.Pharm.FeatureContainerWriterBase | Interface for writing data objects of type Pharm.FeatureContainer to an arbitrary data sink |
| CCDPL.Pharm.CDFBZ2FeatureContainerWriter | Writer for bzip2-compressed feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFFeatureContainerWriter | Writer for feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFGZFeatureContainerWriter | Writer for gzip-compressed feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.FeatureContainerWriter | Writer for pharmacophore data in any supported format |
| CCDPL.Pharm.FileCDFBZ2FeatureContainerWriter | |
| CCDPL.Pharm.FileCDFFeatureContainerWriter | |
| CCDPL.Pharm.FileCDFGZFeatureContainerWriter | |
| CCDPL.Pharm.FilePMLFeatureContainerWriter | |
| CCDPL.Pharm.PMLFeatureContainerWriter | Writer for feature container data in the native I/O format of LigandScout |
| CCDPL.Vis.FilePLYFeatureContainerWriter | |
| CCDPL.Vis.FileR3DFeatureContainerWriter | |
| CCDPL.Vis.FileSTLFeatureContainerWriter | |
| CCDPL.Vis.FileVRMLFeatureContainerWriter | |
| CCDPL.Vis.PLYFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the Polygon File Format [PLYFMT] |
| CCDPL.Vis.R3DFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the Raster3D [R3DFMT] format |
| CCDPL.Vis.STLFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the STL [STLFMT] format |
| CCDPL.Vis.VRMLFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the VRML [VRML97] format |
| ►CCDPL.Pharm.PharmacophoreReaderBase | Interface for reading data objects of type Pharm.Pharmacophore from an arbitrary data source |
| CCDPL.Pharm.CDFBZ2PharmacophoreReader | Reader for bzip2-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFGZPharmacophoreReader | Reader for gzip-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFPharmacophoreReader | Reader for pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.CompoundPharmacophoreReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCDPL.Pharm.FileCDFBZ2PharmacophoreReader | |
| CCDPL.Pharm.FileCDFGZPharmacophoreReader | |
| CCDPL.Pharm.FileCDFPharmacophoreReader | |
| CCDPL.Pharm.FilePMLPharmacophoreReader | |
| CCDPL.Pharm.PMLPharmacophoreReader | Reader for pharmacophore data in the native I/O format of LigandScout |
| CCDPL.Pharm.PSDPharmacophoreReader | Reader for pharmacophore data in the CDPL PSD-format |
| CCDPL.Pharm.PharmacophoreReader | Reader for pharmacophore data in any supported format |
| ►CCDPL.Vis.Object3DReaderBase | |
| CCDPL.Vis.CompoundObject3DReader | |
| CCDPL.Vis.Object3DReader | Reader for Vis.Object3D data in any supported format |
| ►CCDPL.Vis.Object3DWriterBase | |
| CCDPL.Vis.FilePLYObject3DWriter | |
| CCDPL.Vis.FileR3DObject3DWriter | |
| CCDPL.Vis.FileSTLObject3DWriter | |
| CCDPL.Vis.FileVRMLObject3DWriter | |
| CCDPL.Vis.Object3DWriter | Writer for Vis.Object3D data in any supported format |
| CCDPL.Vis.PLYObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the Polygon File Format [PLYFMT] |
| CCDPL.Vis.R3DObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the Raster3D [R3DFMT] format |
| CCDPL.Vis.STLObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the STL [STLFMT] format |
| CCDPL.Vis.VRMLObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the VRML [VRML97] format |
| ►CCDPL.Vis.FeatureContainerObject3DFactoryBase | |
| CCDPL.Vis.FeatureContainerObject3DFactory | Class implementing the creation of Vis.Object3D instances providing a 3D representation of Pharm.FeatureContainer data objects for visualization purposes |
| ►CCDPL.Vis.View2D | The abstract base of classes implementing the 2D visualization of data objects |
| CCDPL.Vis.ReactionView2D | Implements the 2D visualization of chemical reactions |
| CCDPL.Vis.StructureGridView2D | Implements the 2D visualization of multiple chemical structures arranged in a grid |
| CCDPL.Vis.StructureView2D | Implements the 2D visualization of chemical structures |
| CCDPL.Base.DataFormat | Provides meta-information about a particular data storage format |
| CCDPL.Base.DataFormat.FileExtensionSequence | |
| ►CCDPL.Base.IStream | |
| ►CCDPL.Base.IOStream | |
| CCDPL.Base.FileIOStream | |
| CCDPL.Base.StringIOStream | |
| CCDPL.Util.BZip2IOStream | Bidirectional stream that transparently (de)compresses bzip2 data |
| CCDPL.Util.GZipIOStream | Bidirectional stream that transparently (de)compresses gzip data |
| CCDPL.Util.BZip2IStream | Input stream that transparently decompresses bzip2-compressed data |
| CCDPL.Util.GZipIStream | Input stream that transparently decompresses gzip-compressed data |
| CCDPL.Base.LookupKey | Unique lookup key for control-parameter and property values |
| ►CCDPL.Base.OStream | |
| CCDPL.Base.IOStream | |
| CCDPL.Util.BZip2OStream | Output stream that transparently writes bzip2-compressed data |
| CCDPL.Util.GZipOStream | Output stream that transparently writes gzip-compressed data |
| ►CCDPL.Base.PropertyContainer | Base class providing methods for the storage and lookup of object properties |
| ►CCDPL.Chem.Bond | Abstract base class representing a chemical bond between two Chem.Atom instances |
| CCDPL.Chem.BasicBond | Default implementation of the Chem.Bond interface |
| ►CCDPL.Chem.Entity3D | Base class for objects that have a position in 3D space (e.g |
| ►CCDPL.Chem.Atom | Abstract base class representing a chemical atom and its bonded neighborhood |
| CCDPL.Chem.BasicAtom | Concrete Chem.Atom implementation used as the atom type of Chem.BasicMolecule |
| ►CCDPL.Pharm.Feature | Abstract base class representing a single pharmacophore feature within a parent Pharm.Pharmacophore |
| CCDPL.Pharm.BasicFeature | Pharm.Feature implementation owned by a Pharm.BasicPharmacophore parent |
| ►CCDPL.Chem.MolecularGraph | Abstract base class for representations of a chemical structure as a graph of bonded atoms |
| ►CCDPL.Chem.Fragment | Concrete Chem.MolecularGraph implementation that stores references to a selectable subset of atoms and bonds (typically of a parent Chem.Molecule) |
| ►CCDPL.Biomol.HierarchyViewNode | Abstract base class for nodes of the Biomol.HierarchyView tree (models, chains, residues) |
| CCDPL.Biomol.HierarchyViewChain | Data structure for the representation of biological macromolecule chains |
| CCDPL.Biomol.HierarchyViewFragment | Data structure for the representation of a single contiguous fragment of a biological macromolecule chain |
| CCDPL.Biomol.HierarchyViewModel | Data structure for the representation of individual biological macromolecule models |
| CCDPL.Chem.AromaticSubstructure | Implements the perception of aromatic atoms and bonds in a molecular graph |
| CCDPL.Chem.CyclicSubstructure | Implements the perception of ring atoms and bonds in a molecular graph |
| ►CCDPL.Chem.Molecule | Abstract base class representing a mutable molecular graph that owns its atoms and bonds |
| CCDPL.Chem.BasicMolecule | Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances |
| CCDPL.ConfGen.CanonicalFragment | Data structure representing a canonicalized molecular fragment |
| ►CCDPL.Chem.Reaction | Abstract base class for chemical reactions composed of role-tagged Chem.Molecule components |
| CCDPL.Chem.BasicReaction | Default concrete implementation of the Chem.Reaction abstract interface |
| ►CCDPL.Grid.AttributedGrid | Abstract base class for grid types that also carry generic key/value properties |
| ►CCDPL.Grid.DSpatialGrid | Convenience alias for the double-precision spatial-grid abstract base |
| CCDPL.Grid.DRegularGrid | A regular spatial grid storing double-precision floating-point values |
| ►CCDPL.Grid.FSpatialGrid | Convenience alias for the single-precision spatial-grid abstract base |
| CCDPL.Grid.FRegularGrid | A regular spatial grid storing single-precision floating-point values |
| ►CCDPL.Pharm.FeatureContainer | Abstract base class for containers holding a sequence of Pharm.Feature objects with associated properties (e.g |
| CCDPL.Pharm.FeatureSet | Concrete Pharm.FeatureContainer implementation that stores references to existing Pharm.Feature instances |
| ►CCDPL.Pharm.Pharmacophore | Abstract base class for mutable containers of Pharm.Feature instances representing a pharmacophore model |
| CCDPL.Pharm.BasicPharmacophore | Concrete Pharm.Pharmacophore implementation that owns its features as Pharm.BasicFeature instances managed through an internal object pool |
| CCDPL.Shape.GaussianShape | Data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions |
| CCDPL.Vis.Object3D | Hierarchical 3D scene object that owns a list of nested sub-objects and inherits its property bag from Base.PropertyContainer |
| CCDPL.Base.VoidDataIOBaseFunctor | |
| CCDPL.Base.VoidFunctor | |
| CCDPL.Base.VoidLookupKeyAnyFunctor | |
| CCDPL.Base.VoidLookupKeyFunctor | |
| CCDPL.Biomol.AtomProperty | Provides keys for built-in Chem.Atom properties |
| CCDPL.Biomol.AtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CCDPL.Biomol.AtomPropertyFlag | Provides flags for the specification of basic Chem.Atom properties |
| CCDPL.Biomol.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.Biomol.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.Biomol.DataFormat | Provides preinitialized Base.DataFormat objects for all supported biopolymer data formats |
| CCDPL.Biomol.HierarchyView | Data structure providing a hierarchical view on biological macromolecules |
| CCDPL.Biomol.MMCIFData | Data structure for the storage of imported MMCIF data (see [MMCIF]) |
| CCDPL.Biomol.MMCIFData.Category | A single mmCIF data category, holding an ordered list of data items (columns) |
| CCDPL.Biomol.MMCIFData.Item | A single data item (column) of an mmCIF category, holding an ordered list of string values |
| CCDPL.Biomol.MMCIFDataProcessingFunction | Generic wrapper class used to store a user-defined function for the processing of Biomol.MMCIFData instances |
| CCDPL.Biomol.MolecularGraphPointerStringFunctor | |
| CCDPL.Biomol.MolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CCDPL.Biomol.MolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CCDPL.Biomol.PDBData | Data structure for the storage of data records found in PDB formatted data [PDB] |
| CCDPL.Biomol.PDBFormatVersion | Provides constants for the specification of the Brookhaven Protein Data Bank (PDB) [PDB] format version |
| CCDPL.Biomol.ResidueDictionary | Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules |
| CCDPL.Biomol.ResidueDictionary.Entry | A single residue dictionary entry |
| CCDPL.Biomol.ResidueType | Provides constants for the specification of the type of a chemical component (residue) |
| CCDPL.Chem.Atom2DCoordinatesCalculator | Generates 2D coordinates for the atoms of a molecular graph using a layout algorithm that combines ring-system templates, chain extension, and substituent placement |
| CCDPL.Chem.Atom3DCoordinatesFunction | Generic wrapper class used to store a user-defined Chem.Atom 3D-coordinates function |
| CCDPL.Chem.Atom3DCoordinatesFunctor | Helper-functor for retrieving the 3D coordinates of an atom (via the Chem.AtomProperty.COORDINATES_3D property) |
| CCDPL.Chem.Atom.AtomSequence | |
| CCDPL.Chem.Atom.BondSequence | |
| CCDPL.Chem.AtomArray3DCoordinatesFunctor | Helper-functor for retrieving the 3D coordinates of an atom from a separately-stored coordinates array, indexed by the atom's position in the underlying molecular graph |
| CCDPL.Chem.AtomBondMapping | Data structure for the common storage of related atom to atom and bond to bond mappings |
| CCDPL.Chem.AtomConfiguration | Provides constants that are used to specify the configuration of stereogenic atoms |
| CCDPL.Chem.AtomConformer3DCoordinatesFunctor | Helper-functor for retrieving the 3D coordinates of an atom for a specific conformer (via the Chem.AtomProperty.CONFORMER_COORDINATES_3D conformer-array property) |
| CCDPL.Chem.AtomDictionary | A global dictionary for the lookup of data associated with the atom types defined in namespace Chem.AtomType |
| CCDPL.Chem.AtomDictionary.Entry | A single dictionary entry describing the properties of an (atom type, isotope) pair |
| CCDPL.Chem.AtomMapping | Data type for the storage and lookup of arbitrary atom to atom mappings |
| CCDPL.Chem.AtomMatchConstraint | Provides numerical identifiers for built-in Chem.Atom matching constraints |
| ►CCDPL.Chem.AtomMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CCDPL.Chem.AtomConfigurationMatchExpression | Chem.MatchExpression that constrains target atoms by their stereo configuration relative to a query atom |
| CCDPL.Chem.AtomEnvironmentMatchExpression | Chem.MatchExpression that constrains target atoms by the structural environment encoded as a SMARTS substructure pattern |
| ►CCDPL.Chem.AtomMatchExpressionList | Container for the storage and evaluation of logical match expression lists |
| CCDPL.Chem.ANDAtomMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CCDPL.Chem.ORAtomMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CCDPL.Chem.AtomTypeMatchExpression | MatchExpression that checks the atom type of a target atom against a query atom type |
| CCDPL.Chem.NOTAtomMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CCDPL.Chem.AtomMatchExpressionPtrAtomFunctor | |
| CCDPL.Chem.AtomPredicate | Generic wrapper class used to store a user-defined atom predicate |
| CCDPL.Chem.AtomProperty | Provides keys for built-in Chem.Atom properties |
| CCDPL.Chem.AtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CCDPL.Chem.AtomPropertyFlag | Provides flags for the specification of basic Chem.Atom properties |
| CCDPL.Chem.AtomType | Provides constants for the specification of the chemical element or generic type of an atom |
| CCDPL.Chem.AutomorphismGroupSearch | Enumerates the atom/bond automorphisms of a molecular graph |
| CCDPL.Chem.BRICSAtomLabel | Provides constants for the labeling of atoms of bonds matched by a BRICS fragmentation rule |
| CCDPL.Chem.BRICSRuleID | Provides constants for the identification of BRICS fragmentation rules |
| CCDPL.Chem.BemisMurckoAnalyzer | Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains |
| CCDPL.Chem.Bond.AtomSequence | |
| CCDPL.Chem.BondConfiguration | Provides constants that are used to specify the cis/trans configuration of bonds |
| ►CCDPL.Chem.BondContainer | Common interface for data structures that support a random access to stored Chem.Bond instances |
| CCDPL.Chem.Atom | Abstract base class representing a chemical atom and its bonded neighborhood |
| CCDPL.Chem.MolecularGraph | Abstract base class for representations of a chemical structure as a graph of bonded atoms |
| CCDPL.Chem.BondDirection | Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings |
| CCDPL.Chem.BondMapping | Data type for the storage and lookup of arbitrary bond to bond mappings |
| CCDPL.Chem.BondMatchConstraint | Provides numerical identifiers for built-in Chem.Bond matching constraints and flags for the specification of bond orders |
| ►CCDPL.Chem.BondMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CCDPL.Chem.BondConfigurationMatchExpression | Chem.MatchExpression that constrains target bonds by their stereo configuration relative to a query bond |
| CCDPL.Chem.BondDirectionMatchExpression | Chem.MatchExpression that constrains target bonds by their SMILES/SMARTS bond direction |
| ►CCDPL.Chem.BondMatchExpressionList | Container for the storage and evaluation of logical match expression lists |
| CCDPL.Chem.ANDBondMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CCDPL.Chem.ORBondMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CCDPL.Chem.BondReactionCenterStatusMatchExpression | Chem.MatchExpression that constrains target bonds by their reaction-center status (see Chem.ReactionCenterStatus) |
| CCDPL.Chem.BondSubstituentDirectionMatchExpression | Chem.MatchExpression that constrains target double bond geometry via the per-substituent bond-direction annotations carried by the query (in the style of Daylight SMARTS [SMARTS] cis/trans patterns) |
| CCDPL.Chem.NOTBondMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CCDPL.Chem.BondMatchExpressionPtrBondFunctor | |
| CCDPL.Chem.BondOrderCalculator | Perceives bond orders of a molecular graph from its 3D structure and atom connectivity |
| CCDPL.Chem.BondPredicate | Generic wrapper class used to store a user-defined bond predicate |
| CCDPL.Chem.BondProperty | Provides keys for built-in Chem.Bond properties |
| CCDPL.Chem.BondPropertyDefault | Provides default values for built-in Chem.Bond properties |
| CCDPL.Chem.BondPropertyFlag | Provides flags for the specification of basic Chem.Bond properties |
| CCDPL.Chem.BondStereoFlag | Provides constants for the specification of stereo bonds in 2D depictions of chemical structures |
| CCDPL.Chem.BondStereoFlagCalculator | Calculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph |
| CCDPL.Chem.BoolAtom2Functor | |
| CCDPL.Chem.BoolAtom4Functor | |
| CCDPL.Chem.BoolAtomMappingFunctor | |
| CCDPL.Chem.BoolBond2Functor | |
| CCDPL.Chem.BoolConstMolecularGraphFunctor | |
| CCDPL.Chem.BoolEntity3D2Functor | |
| CCDPL.Chem.BoolEntity3D4Functor | |
| CCDPL.Chem.BoolEntity3DMappingFunctor | |
| CCDPL.Chem.BoolMolecularGraphAtomBondMappingFunctor | |
| CCDPL.Chem.BoolMolecularGraphFunctor | |
| CCDPL.Chem.BoolSTPairArrayFunctor | |
| CCDPL.Chem.CIPConfigurationLabeler | Assigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph |
| CCDPL.Chem.CIPDescriptor | Provides constants for the specification of stereogenic atom/bond configurations determined by the Cahn-Ingold-Prelog (CIP) sequence rules |
| CCDPL.Chem.CIPPriorityCalculator | Computes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph |
| CCDPL.Chem.CanonicalNumberingCalculator | Calculation of canonical atom numberings for molecular graphs using McKay's algorithm |
| CCDPL.Chem.ChEMBLStandardizer | Implementation of the ChEMBL structure preprocessing pipeline |
| CCDPL.Chem.CommonConnectedSubstructureSearch | Enumerates all maximal common connected substructures shared between a query and a target molecular graph |
| CCDPL.Chem.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.Chem.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.Chem.DataFormat | Provides preinitialized Base.DataFormat objects for all supported chemical data formats |
| CCDPL.Chem.DoubleAtom2Functor | |
| CCDPL.Chem.DoubleAtom2UInt2Functor | |
| CCDPL.Chem.DoubleAtom2UIntFunctor | |
| CCDPL.Chem.DoubleAtomFunctor | |
| CCDPL.Chem.DoubleDVectorFunctor | |
| CCDPL.Chem.DoubleEntity3D2Functor | |
| CCDPL.Chem.DoubleEntity3DFunctor | |
| CCDPL.Chem.DoubleVector3D2AtomFunctor | |
| ►CCDPL.Chem.ElectronSystemList | Data type for the storage of Chem.ElectronSystem objects |
| CCDPL.Chem.PiElectronSystemList | Implements the perception of all π-electron systems present in a molecule |
| ►CCDPL.Chem.Entity3DContainer | Common interface for data structures that support a random access to stored Chem.Entity3D instances |
| ►CCDPL.Chem.AtomContainer | Common interface for data structures that support a random access to stored Chem.Atom instances |
| CCDPL.Chem.Atom | Abstract base class representing a chemical atom and its bonded neighborhood |
| CCDPL.Chem.Bond | Abstract base class representing a chemical bond between two Chem.Atom instances |
| CCDPL.Chem.ElectronSystem | Describes an electron system of a molecule in terms of involved atoms and their electron contributions |
| CCDPL.Chem.MolecularGraph | Abstract base class for representations of a chemical structure as a graph of bonded atoms |
| CCDPL.Pharm.FeatureContainer | Abstract base class for containers holding a sequence of Pharm.Feature objects with associated properties (e.g |
| CCDPL.Chem.Entity3DMapping | Data type for the storage and lookup of arbitrary entity to entity mappings |
| CCDPL.Chem.Entity3DProperty | Provides keys for built-in Chem.Entity3D properties |
| CCDPL.Chem.Fragment.AtomSequence | |
| CCDPL.Chem.Fragment.BondSequence | |
| ►CCDPL.Chem.FragmentGenerator | Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules |
| CCDPL.Chem.BRICSFragmentGenerator | Chem.FragmentGenerator preconfigured with the 16 BRICS bond-cleavage rules and the associated exclude patterns for combinatorial fragmentation of organic molecules |
| CCDPL.Chem.RECAPFragmentGenerator | Chem.FragmentGenerator implementation applying the RECAP [RECAP] cleavage rules (see Chem.RECAPRuleID) to produce a set of fragment building blocks from a molecular graph |
| CCDPL.Chem.FragmentGenerator.ExcludePattern | A pattern descriptor specifying bonds that shall not be cleaved |
| CCDPL.Chem.FragmentGenerator.FragmentLink | Records the connectivity between two fragments produced by a single bond cleavage |
| CCDPL.Chem.FragmentGenerator.FragmentationRule | A single fragmentation rule, consisting of a bond substructure match pattern and a numeric rule ID |
| ►CCDPL.Chem.FragmentList | Data type for the storage of Chem.Fragment objects |
| CCDPL.Biomol.ResidueList | Data structure for the storage of residues extracted from biological macromolecules |
| CCDPL.Chem.AromaticRingSet | Implements the perception of aromatic rings in a molecular graph |
| CCDPL.Chem.AromaticSSSRSubset | Implements the extraction of the aromatic rings in the SSSR of a molecular graph |
| CCDPL.Chem.CompleteRingSet | Implements the exhaustive perception of rings in a molecular graph |
| CCDPL.Chem.ComponentSet | Implements the perception of molecular graph components |
| CCDPL.Chem.ConnectedSubstructureSet | Enumerates the connected substructures of a molecular graph of a specified bond count |
| CCDPL.Chem.ExtendedSSSR | Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph |
| CCDPL.Chem.SmallestSetOfSmallestRings | Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs |
| CCDPL.ForceField.MMFF94AromaticSSSRSubset | Implements the extraction of all rings in the SSSR of a molecular graph that are considered aromatic according to the MMFF94 aromaticity model |
| CCDPL.MolProp.FunctionalGroupList | Implementation of Ertl's algorithm [FGPE] for the identification of functional groups in organic molecules |
| CCDPL.Chem.HashCodeCalculator | Computes a 64-bit hash code that identifies a molecular graph up to a configurable set of atom and bond properties |
| CCDPL.Chem.HashCodeCalculator.DefAtomHashSeedFunctor | The default functor for the generation of atom hash seeds |
| CCDPL.Chem.HashCodeCalculator.DefBondHashSeedFunctor | The default functor for the generation of bond hash seeds |
| CCDPL.Chem.HybridizationState | Provides constants for the specification of atom hybridization states |
| CCDPL.Chem.Hydrogen3DCoordinatesCalculator | Generates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors |
| CCDPL.Chem.INCHIReturnCode | Provides constants that are used to describe the status of an InChI [INCHI] output or input operation |
| CCDPL.Chem.KekuleStructureCalculator | Assigns an alternating single/double bond pattern (Kekulé structure) to the previously undefined bonds of a molecular graph (typically used to convert aromatic-bond annotations into explicit single/double bonds) |
| CCDPL.Chem.MDLDataFormatVersion | Provides constants that are used to specify the connection table (CTAB) and Rxn-File version for the I/O of molecular graphs and reactions in an MDL CTFile based data format |
| CCDPL.Chem.MDLParity | Provides constants that are used to specify the MDL stereo parity of atoms |
| CCDPL.Chem.MOL2ChargeType | Provides constants for the specification of the atom charge type in Sybyl MOL2 files |
| CCDPL.Chem.MOL2MoleculeType | Provides constants for the specification of the molecule type in Sybyl MOL2 files |
| CCDPL.Chem.MatchConstraint | Describes a single attribute-comparison constraint between a query and a target object used by molecular graph matching algorithms |
| CCDPL.Chem.MatchConstraintList | List of Chem.MatchConstraint instances combined with a logical Type (AND_LIST, NOT_AND_LIST, OR_LIST, or NOT_OR_LIST) that controls how the contained constraints are aggregated during query/target evaluation |
| CCDPL.Chem.MaxCommonAtomSubstructureSearch | Computes the maximum common atom substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on an association (modular product) graph |
| CCDPL.Chem.MaxCommonBondSubstructureSearch | Computes the maximum common bond substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on a bond-based association graph |
| CCDPL.Chem.MolGraphMatchExpressionPtrMolGraphFunctor | |
| CCDPL.Chem.MolecularGraph.AtomSequence | |
| CCDPL.Chem.MolecularGraph.BondSequence | |
| CCDPL.Chem.MolecularGraphIOManager | Singleton class that serves as a global registry for Chem.MolecularGraphInputHandler and Chem.MolecularGraphOutputHandler implementation instances |
| CCDPL.Chem.MolecularGraphIOManager.InputHandlerSequence | |
| CCDPL.Chem.MolecularGraphIOManager.OutputHandlerSequence | |
| CCDPL.Chem.MolecularGraphInputHandler | |
| CCDPL.Chem.MolecularGraphMatchConstraint | Provides numerical identifiers for built-in Chem.MolecularGraph matching constraints |
| ►CCDPL.Chem.MolecularGraphMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CCDPL.Chem.MolecularGraphComponentGroupingMatchExpression | Chem.MatchExpression that constrains the substructure mapping by the query's component-level groupings (typically derived from the parenthesization of a Daylight SMARTS [SMARTS] pattern) |
| ►CCDPL.Chem.MolecularGraphMatchExpressionList | |
| CCDPL.Chem.ANDMolecularGraphMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CCDPL.Chem.ORMolecularGraphMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CCDPL.Chem.NOTMolecularGraphMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| ►CCDPL.Chem.MolecularGraphOutputHandler | Factory interface providing methods for the creation of Chem.MolecularGraphWriterBase instances for data output in a particular storage format |
| CCDPL.Biomol.MMCIFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMTFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.MMTFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CCDPL.Biomol.PDBBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Chem.CDFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the native I/O format of the CDPL |
| CCDPL.Chem.CMLBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.INCHIMolecularGraphOutputHandler | Handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CCDPL.Chem.JMEMolecularGraphOutputHandler | Handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.MOL2BZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format |
| CCDPL.Chem.MOL2GZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format |
| CCDPL.Chem.MOL2MolecularGraphOutputHandler | Handler for the output of molecular graph data in the Sybyl MOL2 format |
| CCDPL.Chem.MOLMolecularGraphOutputHandler | Handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format |
| CCDPL.Chem.SDFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SMARTSMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.XYZBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the XYZ format |
| CCDPL.Chem.XYZGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the XYZ format |
| CCDPL.Chem.XYZMolecularGraphOutputHandler | Handler for the output of molecular graph data in the XYZ format |
| CCDPL.Pharm.PSDMolecularGraphOutputHandler | Handler for the output of molecular graph data in the CDPL PSD-format |
| CCDPL.Vis.PDFMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Portable Document Format (PDF) [WPDF] |
| CCDPL.Vis.PNGMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Portable Network Graphics (PNG) [WPNG] format |
| CCDPL.Vis.PSMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the PostScript (PS) [WPS] format |
| CCDPL.Vis.SVGMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Scalable Vector Graphics (SVG) [WSVG] format |
| CCDPL.Chem.MolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CCDPL.Chem.MolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CCDPL.Chem.Molecule.AtomSequence | |
| CCDPL.Chem.Molecule.BondSequence | |
| CCDPL.Chem.MoleculeIOManager | Singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances |
| CCDPL.Chem.MoleculeIOManager.InputHandlerSequence | |
| CCDPL.Chem.MoleculeIOManager.OutputHandlerSequence | |
| ►CCDPL.Chem.MoleculeInputHandler | Factory interface providing methods for the creation of Chem.MoleculeReaderBase instances for reading data provided in a particular storage format |
| CCDPL.Biomol.MMCIFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMCIFMoleculeInputHandler | Handler for the input of molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CCDPL.Biomol.MMTFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CCDPL.Biomol.MMTFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CCDPL.Biomol.MMTFMoleculeInputHandler | Handler for the input of molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CCDPL.Biomol.PDBBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Biomol.PDBMoleculeInputHandler | Handler for the input of molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CCDPL.Chem.CDFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFMoleculeInputHandler | Handler for the input of molecule data in the native I/O format of the CDPL |
| CCDPL.Chem.CMLBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.CMLMoleculeInputHandler | Handler for the input of molecule data in the Chemical Markup Language [CML] format |
| CCDPL.Chem.INCHIMoleculeInputHandler | Handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CCDPL.Chem.JMEMoleculeInputHandler | Handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.MOL2BZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format |
| CCDPL.Chem.MOL2GZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format |
| CCDPL.Chem.MOL2MoleculeInputHandler | Handler for the input of molecule data in the Sybyl MOL2 format |
| CCDPL.Chem.MOLMoleculeInputHandler | Handler for the input of molecule data in the MDL Mol-File [CTFILE] format |
| CCDPL.Chem.SDFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SDFMoleculeInputHandler | Handler for the input of molecule data in the MDL SD-File [CTFILE] format |
| CCDPL.Chem.SMARTSMoleculeInputHandler | Handler for the input of molecule data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESMoleculeInputHandler | Handler for the input of molecule data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.XYZBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the XYZ format |
| CCDPL.Chem.XYZGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the XYZ format |
| CCDPL.Chem.XYZMoleculeInputHandler | Handler for the input of molecule data in the XYZ format |
| CCDPL.ConfGen.CFLMoleculeInputHandler | Handler for the input of molecule fragments stored in the CDPL Conformer Generator Fragment Library (CFL) format |
| CCDPL.Pharm.PSDMoleculeInputHandler | Handler for the input of molecule data in the CDPL PSD-format |
| CCDPL.Chem.MoleculeOutputHandler | |
| CCDPL.Chem.MorganNumberingCalculator | Computes a canonical atom numbering of a molecular graph using a modified Morgan algorithm |
| ►CCDPL.Chem.MultiConfMoleculeInputProcessor | Abstract base interface for processors that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules |
| CCDPL.Chem.DefaultMultiConfMoleculeInputProcessor | Default Chem.MultiConfMoleculeInputProcessor implementation that detects multi-conformer input by comparing atom and bond properties (and optionally molecule names) between successive input molecules |
| CCDPL.Chem.MultiSubstructureSearch | Evaluates a boolean expression over multiple substructure queries against a target molecular graph |
| CCDPL.Chem.PatternAtomTyper | Assigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns |
| CCDPL.Chem.PatternAtomTyper.Pattern | Stores a single substructure query molecular graph, its atom label value, its priority and match-handling flags |
| CCDPL.Chem.PatternBasedTautomerizationRule.BondOrderChange | Encodes a single bond order change between two pattern atoms applied when the parent transformation pattern matches |
| CCDPL.Chem.ProtonationStateStandardizer | Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives |
| CCDPL.Chem.RECAPAtomLabel | Provides constants for the labeling of atoms of bonds matched by a RECAP fragmentation rule |
| CCDPL.Chem.RECAPRuleID | Provides constants for the identification of RECAP fragmentation rules |
| CCDPL.Chem.RadicalType | Provides constants that are used to specify the degeneracy of the electronic state of radical atoms |
| CCDPL.Chem.Reaction.ComponentSequence | |
| CCDPL.Chem.ReactionCenterStatus | Provides flags that are used to describe state changes of atoms and bonds in a reaction center |
| CCDPL.Chem.ReactionIOManager | Singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances |
| CCDPL.Chem.ReactionIOManager.InputHandlerSequence | |
| CCDPL.Chem.ReactionIOManager.OutputHandlerSequence | |
| ►CCDPL.Chem.ReactionInputHandler | Factory interface providing methods for the creation of Chem.ReactionReaderBase instances for reading data provided in a particular storage format |
| CCDPL.Chem.CDFBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFReactionInputHandler | Handler for the input of reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.JMEReactionInputHandler | Handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.RDFBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFReactionInputHandler | Handler for the input of reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RXNReactionInputHandler | Handler for the input of reaction data in the MDL Rxn-File [CTFILE] format |
| CCDPL.Chem.SMARTSReactionInputHandler | Handler for the input of reaction data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESReactionInputHandler | Handler for the input of reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.ReactionMatchConstraint | Provides numerical identifiers for built-in Chem.Reaction matching constraints |
| ►CCDPL.Chem.ReactionMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CCDPL.Chem.NOTReactionMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CCDPL.Chem.ReactionAtomMappingMatchExpression | Chem.MatchExpression that constrains reaction substructure matches by a required reactant-to-product atom mapping |
| CCDPL.Chem.ReactionComponentGroupingMatchExpression | Chem.MatchExpression that constrains reaction substructure matches by the query's component-level groupings (typically derived from the parenthesization of a Daylight SMARTS [SMARTS] pattern) |
| ►CCDPL.Chem.ReactionMatchExpressionList | |
| CCDPL.Chem.ANDReactionMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CCDPL.Chem.ORReactionMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| ►CCDPL.Chem.ReactionOutputHandler | Factory interface providing methods for the creation of Chem.ReactionWriterBase instances for data output in a particular storage format |
| CCDPL.Chem.CDFBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.CDFReactionOutputHandler | Handler for the output of reaction data in the native I/O format of the CDPL |
| CCDPL.Chem.JMEReactionOutputHandler | Handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CCDPL.Chem.RDFBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RDFReactionOutputHandler | Handler for the output of reaction data in the MDL RD-File [CTFILE] format |
| CCDPL.Chem.RXNReactionOutputHandler | Handler for the output of reaction data in the MDL Rxn-File [CTFILE] format |
| CCDPL.Chem.SMARTSReactionOutputHandler | Handler for the output of reaction data in the Daylight SMARTS [SMARTS] format |
| CCDPL.Chem.SMILESBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Chem.SMILESReactionOutputHandler | Handler for the output of reaction data in the Daylight SMILES [SMILES] format |
| CCDPL.Vis.PDFReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF] |
| CCDPL.Vis.PNGReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG] format |
| CCDPL.Vis.PSReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the PostScript (PS) [WPS] format |
| CCDPL.Vis.SVGReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG] format |
| CCDPL.Chem.ReactionProperty | Provides keys for built-in Chem.Reaction properties |
| CCDPL.Chem.ReactionPropertyDefault | Provides default values for built-in Chem.Reaction properties |
| CCDPL.Chem.ReactionRole | Provides constants that are used to specify the role of molecules (components) in a chemical reaction |
| CCDPL.Chem.ReactionSubstructureSearch | Reaction-level analogue of Chem.SubstructureSearch that locates atom/bond mappings of a query reaction pattern in a target reaction |
| CCDPL.Chem.Reactor | Applies a Chem.Reaction template to the reactant components of a target Chem.Reaction to generate the corresponding product molecules |
| CCDPL.Chem.ResonanceStructureGenerator | Enumerates the resonance structures of a molecular graph by redistributing π-electrons across the resonance-active bonds |
| CCDPL.Chem.ResonanceStructureGenerator.StructureData | Holds the per-atom formal charges and per-bond orders that define a single resonance structure |
| CCDPL.Chem.SizeTypeAtomFunctor | |
| CCDPL.Chem.SizeTypeAtomMolecularGraphFunctor | |
| CCDPL.Chem.SpatialAtomAlignment | |
| CCDPL.Chem.SpatialEntity3DAlignment | |
| CCDPL.Chem.StereoDescriptor | Data structure for the storage and retrieval of stereochemical information about atoms and bonds |
| CCDPL.Chem.StereoDescriptor.ReferenceAtomArray | |
| CCDPL.Chem.StereoisomerGenerator | Enumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters |
| CCDPL.Chem.StereoisomerGenerator.StereoDescriptorArray | Array of StereoDescriptor values (one per atom or one per bond of the input molecular graph) |
| CCDPL.Chem.StringDataBlock | Array of Chem.StringDataBlockEntry objects |
| CCDPL.Chem.StringDataBlockEntry | Represents a data item consisting of a header and a data payload |
| CCDPL.Chem.SubstructureEditor | Pattern-driven editor that rewrites matched substructures of a Chem.Molecule using a result template, with optional exclude patterns guarding sites that must not be touched |
| CCDPL.Chem.SubstructureHistogramCalculator | Counts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container |
| CCDPL.Chem.SubstructureHistogramCalculator.Pattern | Stores a single substructure query molecular graph, its histogram ID, its priority and match-handling flags |
| CCDPL.Chem.SubstructureSearch | Subgraph-isomorphism search of a query molecular graph against a target molecular graph, implemented after the VF2 algorithm |
| CCDPL.Chem.SurfaceAtomExtractor | Extracts the solvent-accessible surface atoms of a set of atoms |
| CCDPL.Chem.SybylAtomType | Provides constants for the specification of the Tripos Sybyl atom type |
| CCDPL.Chem.SybylBondType | Provides constants for the specification of the Tripos Sybyl bond type |
| CCDPL.Chem.SymmetryClassCalculator | Perceives topological-symmetry classes of the atoms in a molecular graph |
| ►CCDPL.Chem.TautomerGenerator | Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem.TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback |
| CCDPL.Chem.DefaultTautomerGenerator | Chem.TautomerGenerator preconfigured with the standard CDPKit tautomerization rules |
| CCDPL.Chem.TautomerScore | Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph |
| ►CCDPL.Chem.TautomerizationRule | Abstract base class for all tautomerization rule implementations used by the Chem.TautomerGenerator |
| CCDPL.Chem.ConjugatedRingBondPatternSwitching | Chem.TautomerizationRule implementation that enumerates tautomers obtained by switching the single/double bond pattern of conjugated rings (e.g |
| ►CCDPL.Chem.PatternBasedTautomerizationRule | Match pattern-based implementation of the Chem.TautomerizationRule interface |
| CCDPL.Chem.AmideImidicAcidTautomerization | Implementation of the amide ↔ imidic-acid tautomerization rule |
| CCDPL.Chem.GenericHydrogen13ShiftTautomerization | Chem.TautomerizationRule implementation that enumerates tautomers obtained by a generic 1,3-hydrogen shift (a proton migrates between atoms separated by two bonds, with the corresponding single/double bond pattern flipping) |
| CCDPL.Chem.GenericHydrogen15ShiftTautomerization | Chem.TautomerizationRule implementation that enumerates tautomers obtained by a generic 1,5-hydrogen shift (a proton migrates between atoms separated by four bonds along a conjugated path, with the corresponding single/double bond pattern flipping) |
| CCDPL.Chem.ImineEnamineTautomerization | Chem.TautomerizationRule implementation that enumerates the imine/enamine tautomers of an \( R_2C=N{-}CHR_2 \rightleftharpoons R_2CH{-}N=CR_2 \) system |
| CCDPL.Chem.KeteneYnolTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates ketene/ynol tautomers (Chem.TautomerizationType.KETENE_YNOL) |
| CCDPL.Chem.KetoEnolTautomerization | Chem.TautomerizationRule implementation that enumerates the keto/enol tautomers of an \( R_2C{-}C(=O)R' \rightleftharpoons RC=C(OH)R' \) system |
| CCDPL.Chem.LactamLactimTautomerization | Chem.TautomerizationRule implementation that enumerates the lactam/lactim tautomers of a cyclic amide \( {-}NH{-}C(=O){-} \rightleftharpoons {-}N=C(OH){-} \) system |
| CCDPL.Chem.NitroAciTautomerization | Implementation of the nitro ↔ aci-nitro tautomerization rule |
| CCDPL.Chem.NitrosoOximeTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates nitroso/oxime tautomers (Chem.TautomerizationType.NITROSO_OXIME) |
| CCDPL.Chem.PhosphinicAcidTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates phosphinic-acid tautomers (Chem.TautomerizationType.PHOSPHINIC_ACID) |
| CCDPL.Chem.SulfenicAcidTautomerization | Chem.TautomerizationRule implementation that enumerates the sulfenic-acid tautomers of an \( R{-}S{-}OH \rightleftharpoons R{-}S(=O)H \) system |
| CCDPL.Chem.TautomerizationType | Provides constants serving as identifiers for built-in Chem.TautomerizationRule implementations |
| CCDPL.Chem.TopologicalAtomAlignment | |
| CCDPL.Chem.TopologicalEntity3DAlignment | |
| CCDPL.Chem.UInt64AtomFunctor | |
| CCDPL.Chem.UInt64AtomMolecularGraphFunctor | |
| CCDPL.Chem.UInt64BondFunctor | |
| CCDPL.Chem.Vector2DAtomFunctor | |
| CCDPL.Chem.Vector3DEntity3DFunctor | |
| CCDPL.Chem.VoidMolecularGraphFunctor | |
| CCDPL.Chem.VoidMoleculeMolecularGraphFunctor | |
| CCDPL.ConfGen.CallbackFunction | Generic wrapper for storing user-defined callback functions returning a bool status flag (see [FUNWRP]) |
| CCDPL.ConfGen.CanonicalFragment.AtomMapping | Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph |
| CCDPL.ConfGen.ConformerGenerator | High-level driver for the generation of low-energy conformer ensembles of molecular graphs |
| CCDPL.ConfGen.ConformerGeneratorSettings | Bundle of configuration parameters for conformer ensemble generation via class ConfGen.ConformerGenerator |
| CCDPL.ConfGen.ConformerSamplingMode | Provides constants used to specify the employed conformer sampling method |
| CCDPL.ConfGen.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.ConfGen.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.ConfGen.DGConstraintGenerator | Constructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation |
| CCDPL.ConfGen.DGConstraintGenerator.StereoCenterData | Pair holding an atom or bond index plus the associated stereo descriptor |
| ►CCDPL.ConfGen.DGConstraintGeneratorSettings | Bundle of configuration parameters for distance-geometry constraint generation via class ConfGen.DGConstraintGenerator |
| CCDPL.ConfGen.DGStructureGeneratorSettings | Bundle of configuration parameters for raw coordinates generation via class ConfGen.DGStructureGenerator |
| CCDPL.ConfGen.DGStructureGenerator | Distance-geometry-based generation of raw 3D structures for molecular graphs |
| CCDPL.ConfGen.DataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CCDPL.ConfGen.ForceFieldType | Provides constants used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations |
| CCDPL.ConfGen.FragmentAssembler | Driver for the fragment-based generation of 3D starting conformers |
| CCDPL.ConfGen.FragmentAssemblerSettings | Bundle of configuration parameters for fragment conformer assembly via class ConfGen.FragmentAssembler |
| CCDPL.ConfGen.FragmentConformerGenerator | Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle) |
| CCDPL.ConfGen.FragmentConformerGeneratorSettings | Bundle of configuration parameters for fragment conformer ensemble generation via class ConfGen.FragmentConformerGenerator |
| CCDPL.ConfGen.FragmentConformerGeneratorSettings.FragmentSettings | Per-fragment-class settings (separate parameters for chain, small ring system and macrocycle fragments) |
| CCDPL.ConfGen.FragmentLibrary | Data structure representing a library of pre-generated molecular fragment conformer ensembles |
| CCDPL.ConfGen.FragmentLibraryEntry | Data structure representing a single entry of a conformer generation fragment library |
| CCDPL.ConfGen.FragmentLibraryGenerator | Driver for populating a ConfGen.FragmentLibrary with conformers of canonicalized molecular fragments |
| CCDPL.ConfGen.FragmentType | Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models |
| CCDPL.ConfGen.LogMessageCallbackFunction | Generic wrapper for storing user-defined log message callback functions (see [FUNWRP]) |
| CCDPL.ConfGen.NitrogenEnumerationMode | Provides constants for specifying the mode of invertible nitrogen enumeration |
| CCDPL.ConfGen.RMSDConformerSelector | Greedy RMSD-based conformer-diversity filter |
| CCDPL.ConfGen.ReturnCode | Provides constants that are used to describe the result of operations related to conformer generation |
| CCDPL.ConfGen.StructureGenerationMode | Provides constants used to specify the 3D structure generation method that shall be employed |
| CCDPL.ConfGen.StructureGenerator | High-level driver for the generation of a single low-energy 3D structure from a molecular graph |
| CCDPL.ConfGen.StructureGeneratorSettings | Bundle of configuration parameters for single 3D structure generation via class ConfGen.StructureGenerator |
| ►CCDPL.ConfGen.TorsionCategory | Represents a node of a hierarchical torsion library |
| CCDPL.ConfGen.TorsionLibrary | Data structure representing a hierarchical library of torsion rules organized into categories |
| CCDPL.ConfGen.TorsionCategory.CategorySequence | |
| CCDPL.ConfGen.TorsionCategory.RuleSequence | |
| CCDPL.ConfGen.TorsionDriver | Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen.TorsionLibrary instances |
| CCDPL.ConfGen.TorsionDriverSettings | Bundle of configuration parameters for systematic conformer enumeration via class ConfGen.TorsionDriver |
| CCDPL.ConfGen.TorsionRule | Data structure for the representation of single torsion library rules |
| CCDPL.ConfGen.TorsionRule.AngleEntry | One preferred torsion angle for a rule, characterized by its value, the two tolerance bands and a score |
| CCDPL.ConfGen.TorsionRuleMatch | A single match of a ConfGen.TorsionRule against a rotatable bond: the rule, the bond and the four atoms that span the torsion |
| CCDPL.ConfGen.TorsionRuleMatch.AtomArray | |
| CCDPL.ConfGen.TorsionRuleMatcher | Finds torsion rules from a ConfGen.TorsionLibrary instance that match a given rotatable bond |
| CCDPL.Descr.AtomAutoCorrelation3DVectorCalculator | AutoCorrelation3DVectorCalculator implementation for the calculation of atom-centered 3D auto-correlation vectors of chemical structures |
| CCDPL.Descr.AtomRDFCodeCalculator | RDFCodeCalculator implementation for the calculation of atom-centered radial distribution function (RDF) codes of chemical structures |
| CCDPL.Descr.AutoCorrelation2DVectorCalculator | Calculation of the topological (2D) auto-correlation vector of a molecular graph |
| CCDPL.Descr.BCUTDescriptorCalculator | Calculation of the BCUT (Burden-CAS-University-of-Texas) descriptor of a molecular graph |
| CCDPL.Descr.BitSetBulkSimilarityCalculator | |
| CCDPL.Descr.BurdenMatrixGenerator | Calculation of the Burden matrix of a molecular graph |
| CCDPL.Descr.CircularFingerprintGenerator | Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP) |
| CCDPL.Descr.CircularFingerprintGenerator.DefAtomIdentifierFunctor | The functor for the generation of ECFP atom identifiers |
| CCDPL.Descr.CircularFingerprintGenerator.DefBondIdentifierFunctor | The default functor for the generation of bond identifiers |
| CCDPL.Descr.CosineSimilarity | Functor class for calculating Cosine Similarities [WCOS] of bitsets and vectors |
| CCDPL.Descr.DVectorBulkSimilarityCalculator | |
| CCDPL.Descr.DiceSimilarity | Functor class for calculating the Dice Similarity [GSIM] of bitsets |
| CCDPL.Descr.DoubleBitSet2Functor | |
| CCDPL.Descr.DoubleDVector2Functor | |
| CCDPL.Descr.DoubleFVector2Functor | |
| CCDPL.Descr.DoubleLVector2Functor | |
| CCDPL.Descr.DoubleULVector2Functor | |
| CCDPL.Descr.EuclideanDistance | Functor class for calculating the Euclidean Distance [CITB] between bitsets and vectors |
| CCDPL.Descr.EuclideanSimilarity | Functor class for calculating the Euclidean Similarity [GSIM] of bitsets |
| CCDPL.Descr.FVectorBulkSimilarityCalculator | |
| CCDPL.Descr.FeatureAutoCorrelation3DVectorCalculator | AutoCorrelation3DVectorCalculator specialization for feature-centered 3D auto-correlation vectors of pharmacophores |
| CCDPL.Descr.FeatureRDFCodeCalculator | RDFCodeCalculator implementation for the calculation of feature-centered radial distribution function (RDF) codes of pharmacophores |
| CCDPL.Descr.HammingDistance | Functor class for calculating the Hamming Distance [WHAM, CITB] between bitsets |
| CCDPL.Descr.KuvekPocketDescriptorCalculator | Implements the algorithm devised by Kuvek et al |
| CCDPL.Descr.LVectorBulkSimilarityCalculator | |
| CCDPL.Descr.MACCSFingerprintGenerator | Generation of 166 bit MACCS key fingerprints |
| CCDPL.Descr.ManhattanDistance | Functor class for calculating the Manhattan Distance [MADI] between bitsets and vectors |
| CCDPL.Descr.ManhattanSimilarity | Functor class for calculating the Manhattan Similarity [GSIM] of bitsets |
| CCDPL.Descr.MolecularComplexityCalculator | Calculation of the molecular complexity of a molecular graph after Hendrickson, Huang and Toczko |
| CCDPL.Descr.MoleculeAutoCorr2DDescriptorCalculator | Calculation of a topological (2D) auto-correlation descriptor of a molecular graph partitioned by specific atom types |
| CCDPL.Descr.MoleculeAutoCorr3DDescriptorCalculator | Calculation of a 3D auto-correlation descriptor of a molecular graph partitioned by specific atom types |
| CCDPL.Descr.MoleculeRDFDescriptorCalculator | Calculation of an RDF descriptor of a molecular graph partitioned by specific atom types |
| ►CCDPL.Descr.NPointPharmacophoreFingerprintGenerator | Abstract base for N-point pharmacophore fingerprint generators |
| CCDPL.Descr.NPoint2DPharmacophoreFingerprintGenerator | N-point pharmacophore fingerprint generator that uses topological feature distances |
| CCDPL.Descr.NPoint3DPharmacophoreFingerprintGenerator | N-point pharmacophore fingerprint generator that uses spatial 3D feature distances |
| CCDPL.Descr.PathFingerprintGenerator | Generation of Daylight-style path fingerprints of molecular graphs |
| CCDPL.Descr.PathFingerprintGenerator.DefAtomDescriptorFunctor | The default functor for the generation of atom descriptors |
| CCDPL.Descr.PathFingerprintGenerator.DefBondDescriptorFunctor | The default functor for the generation of bond descriptors |
| CCDPL.Descr.PharmacophoreAutoCorr3DDescriptorCalculator | Calculation of a 3D auto-correlation descriptor of a pharmacophore partitioned by specific feature types |
| CCDPL.Descr.PharmacophoreRDFDescriptorCalculator | Calculation of an RDF descriptor of a pharmacophore partitioned by specific feature types |
| CCDPL.Descr.PubChemFingerprintGenerator | Generation of 881 bit PubChem fingerprints |
| CCDPL.Descr.TanimotoSimilarity | Functor class for calculating Tanimoto Similarities [CITB] of bitsets and vectors |
| CCDPL.Descr.TverskySimilarity | Functor class for calculating the Tversky Similarity [GSIM] of bitsets |
| CCDPL.Descr.ULVectorBulkSimilarityCalculator | |
| CCDPL.ForceField.AtomProperty | Provides keys for built-in Chem.Atom properties |
| CCDPL.ForceField.BondProperty | Provides keys for built-in Chem.Bond properties |
| CCDPL.ForceField.ElasticPotential | Stores parameters for an elastic potential (harmonic distance restraint) between a pair of atoms |
| CCDPL.ForceField.ElasticPotentialList | Data structure for the storage of elastic potential parameter set records |
| CCDPL.ForceField.InteractionFilterFunction3 | Generic wrapper for storing user-defined three-atom interaction filtering functions (see [FUNWRP]) |
| CCDPL.ForceField.InteractionFilterFunction4 | Generic wrapper for storing user-defined four-atom interaction filtering functions (see [FUNWRP]) |
| CCDPL.ForceField.InteractionType | Provides flags for the specification of a set of force field interaction types |
| CCDPL.ForceField.MMFF94AngleBendingInteraction | Stores parameters for a single MMFF94 angle-bending interaction defined over an atom triplet |
| CCDPL.ForceField.MMFF94AngleBendingInteractionList | Data structure for the storage of MMFF94 angle-bending interaction parameter records |
| CCDPL.ForceField.MMFF94AngleBendingInteractionParameterizer | Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph |
| CCDPL.ForceField.MMFF94AngleBendingParameterTable | Data structure for the storage and lookup of MMFF94 angle-bending interaction parameters |
| CCDPL.ForceField.MMFF94AngleBendingParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94AromaticAtomTypeDefinitionTable | Data structure for the storage and lookup of MMFF94 aromatic atom type definitions |
| CCDPL.ForceField.MMFF94AromaticAtomTypeDefinitionTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94AtomChargeFunction | Generic wrapper class used to store a user-defined MMFF94 partial atom charge retrieval function |
| CCDPL.ForceField.MMFF94AtomTypePropertyTable | Data structure for the storage and lookup of structural and chemical property data associated with numeric MMFF94 atom types |
| CCDPL.ForceField.MMFF94AtomTypePropertyTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94AtomTyper | Assigns MMFF94 symbolic and numeric atom types to the atoms of a molecular graph |
| CCDPL.ForceField.MMFF94BondChargeIncrementTable | Data structure for the storage and lookup of MMFF94 bond charge increments |
| CCDPL.ForceField.MMFF94BondChargeIncrementTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94BondStretchingInteraction | Stores parameters for a single MMFF94 bond-stretching interaction between two bonded atoms |
| CCDPL.ForceField.MMFF94BondStretchingInteractionList | Data structure for the storage of MMFF94 bond-stretching interaction parameter records |
| CCDPL.ForceField.MMFF94BondStretchingInteractionParameterizer | Detects and parameterizes the MMFF94 bond-stretching interactions of a molecular graph |
| CCDPL.ForceField.MMFF94BondStretchingParameterTable | Data structure for the storage and lookup of MMFF94 bond-stretching interaction parameters |
| CCDPL.ForceField.MMFF94BondStretchingParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94BondStretchingRuleParameterTable | Data structure for the storage and lookup of MMFF94 bond-stretching interaction fallback parameters |
| CCDPL.ForceField.MMFF94BondStretchingRuleParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94BondTypeIndexFunction | Generic wrapper class used to store a user-defined MMFF94 bond type index retrieval function |
| CCDPL.ForceField.MMFF94BondTyper | Assigns MMFF94 bond type indices to the bonds of a molecular graph |
| CCDPL.ForceField.MMFF94ChargeCalculator | Calculator for the MMFF94 partial atomic charges of a molecular graph |
| CCDPL.ForceField.MMFF94DefaultStretchBendParameterTable | Data structure for the storage and lookup of MMFF94 stretch-bend interaction fallback parameters |
| CCDPL.ForceField.MMFF94DefaultStretchBendParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94ElectrostaticInteraction | Stores parameters for a single MMFF94 electrostatic interaction between two non-bonded atoms |
| CCDPL.ForceField.MMFF94ElectrostaticInteractionList | Data structure for the storage of MMFF94 electrostatic interaction parameter records |
| CCDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer | Detects and parameterizes the MMFF94 electrostatic interactions of a molecular graph |
| CCDPL.ForceField.MMFF94EnergyCalculator | Calculates the total MMFF94 force field energy for a set of atom 3D coordinates |
| CCDPL.ForceField.MMFF94FormalAtomChargeDefinitionTable | Data structure for the storage and lookup of formal charge definitions used by the MMFF94 charge model |
| CCDPL.ForceField.MMFF94FormalAtomChargeDefinitionTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94GradientCalculator | Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates |
| CCDPL.ForceField.MMFF94HeavyToHydrogenAtomTypeMap | Data structure for the storage and lookup of heavy-to-hydrogen symbolic MMFF94 atom type mappings |
| CCDPL.ForceField.MMFF94HeavyToHydrogenAtomTypeMap.Entry | The type of the map entries |
| CCDPL.ForceField.MMFF94InteractionData | Container holding the full set of MMFF94 interaction parameter records for a molecular graph |
| CCDPL.ForceField.MMFF94InteractionParameterizer | Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization |
| CCDPL.ForceField.MMFF94NumericAtomTypeFunction | Generic wrapper class used to store a user-defined numeric MMFF94 atom type retrieval function |
| CCDPL.ForceField.MMFF94OutOfPlaneBendingInteraction | Stores parameters for a single MMFF94 out-of-plane bending interaction at a trigonal center |
| CCDPL.ForceField.MMFF94OutOfPlaneBendingInteractionList | Data structure for the storage of MMFF94 out-of-plane bending interaction parameter records |
| CCDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer | Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph |
| CCDPL.ForceField.MMFF94OutOfPlaneBendingParameterTable | Data structure for the storage and lookup of MMFF94 out-of-plane bending interaction force constants |
| CCDPL.ForceField.MMFF94OutOfPlaneBendingParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94ParameterSet | Provides constants for the specification of a MMFF94 parameter set variant |
| CCDPL.ForceField.MMFF94PartialBondChargeIncrementTable | Data structure for the storage and lookup of MMFF94 per-atom partial bond charge increment and formal charge adjustment factors |
| CCDPL.ForceField.MMFF94PartialBondChargeIncrementTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94PrimaryToParameterAtomTypeMap | Data structure for the storage and lookup of primary numeric MMFF94 atom type to fallback parameter atom type list mappings |
| CCDPL.ForceField.MMFF94PrimaryToParameterAtomTypeMap.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94RingSetFunction | Generic wrapper class used to store a user-defined MMFF94 ring set retrieval function |
| CCDPL.ForceField.MMFF94StretchBendInteraction | Stores paramters for a single MMFF94 stretch-bend coupling interaction |
| CCDPL.ForceField.MMFF94StretchBendInteractionList | Data structure for the storage of MMFF94 stretch-bend coupling interaction parameter records |
| CCDPL.ForceField.MMFF94StretchBendInteractionParameterizer | Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph |
| CCDPL.ForceField.MMFF94StretchBendParameterTable | Data structure for the storage and lookup of MMFF94 stretch-bend interaction parameters |
| CCDPL.ForceField.MMFF94StretchBendParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94SymbolicAtomTypeFunction | Generic wrapper class used to store a user-defined symbolic MMFF94 atom type retrieval function |
| CCDPL.ForceField.MMFF94SymbolicAtomTypePatternTable | Data structure storing SMARTS substructure patterns used to assign symbolic MMFF94 atom types during atom typing |
| CCDPL.ForceField.MMFF94SymbolicAtomTypePatternTable.Entry | A single atom type pattern record |
| CCDPL.ForceField.MMFF94SymbolicToNumericAtomTypeMap | Lookup table mapping each symbolic MMFF94 atom type to its corresponding numeric MMFF94 atom type |
| CCDPL.ForceField.MMFF94SymbolicToNumericAtomTypeMap.Entry | The map entry type (a (symbolic type, numeric type) key/value pair) |
| CCDPL.ForceField.MMFF94TorsionInteraction | Stores parameters for a single MMFF94 torsion interaction over an atom quadruplet i-j-k-l |
| CCDPL.ForceField.MMFF94TorsionInteractionList | Data structure for the storage of MMFF94 torsion interaction parameter records |
| CCDPL.ForceField.MMFF94TorsionInteractionParameterizer | Detects and parameterizes the MMFF94 torsion interactions of a molecular graph |
| CCDPL.ForceField.MMFF94TorsionParameterTable | Data structure for the storage and lookup of MMFF94 torsion interaction parameters |
| CCDPL.ForceField.MMFF94TorsionParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MMFF94VanDerWaalsAtomParameters | |
| CCDPL.ForceField.MMFF94VanDerWaalsInteraction | Stores parameters for a single MMFF94 Van der Waals interaction between two non-bonded atoms |
| CCDPL.ForceField.MMFF94VanDerWaalsInteractionList | Data structure for the storage of MMFF94 Van der Waals interaction parameter records |
| CCDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer | Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph |
| CCDPL.ForceField.MMFF94VanDerWaalsParameterTable | Data structure for the storage and lookup of MMFF94 interaction parameters |
| CCDPL.ForceField.MMFF94VanDerWaalsParameterTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.ForceField.MolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CCDPL.ForceField.TopologicalAtomDistanceFunction | Generic wrapper class used to store a user-defined topological atom-pair distance function |
| CCDPL.ForceField.UFFAtomType | Provides constants for the specification of numeric Universal Force Field (UFF) atom types |
| CCDPL.ForceField.UFFAtomTypePropertyTable | Data structure for the storage and lookup of various properties associated with numeric UFF atom types |
| CCDPL.ForceField.UFFAtomTypePropertyTable.Entry | Data structure for the storage of values associated with a single table entry |
| CCDPL.GRAIL.AtomDensityGridCalculator | Calculator that fills a spatial grid with combined per-atom density contributions |
| CCDPL.GRAIL.AttributedGridProperty | Provides keys for built-in Grid.AttributedGrid properties |
| CCDPL.GRAIL.AttributedGridPropertyDefault | Provides default values for built-in Grid.AttributedGrid properties |
| CCDPL.GRAIL.BindingAffinityCalculator | Predicts the binding affinity of a ligand pose from its GRAIL descriptor vector |
| CCDPL.GRAIL.BuriednessGridCalculator | Calculator that fills a spatial grid with per-cell buriedness scores derived from GRAIL.BuriednessScore |
| CCDPL.GRAIL.BuriednessScore | Functor for the calculation of the buriedness of a 3D query position with respect to the surrounding atoms |
| CCDPL.GRAIL.DoubleVector3DFeatureFunctor | |
| CCDPL.GRAIL.FeatureInteractionScoreGridCalculator | Calculator that fills a spatial grid with per-cell feature-interaction scores against a set of target pharmacophore features |
| CCDPL.GRAIL.FeatureInteractionScoreGridCalculator.MaxScoreFunctor | Score-combination functor returning the maximum (infinity norm) of the per-feature scores |
| CCDPL.GRAIL.FeatureInteractionScoreGridCalculator.ScoreSumFunctor | Score-combination functor returning the sum of the per-feature scores |
| CCDPL.GRAIL.FeatureType | Provides constants for the specification of GRAIL-specific extended pharmacophore feature types that refine H-bond donor and acceptor categories by the chemical environment (atom element + SYBYL-like type) of the participating heavy atom |
| CCDPL.GRAIL.GRAILDataSetGenerator | Generator that pre-computes the per-cell interaction-score grids and the atom-density grid used by GRAIL scoring of ligand poses against a target environment |
| CCDPL.GRAIL.GRAILDescriptorCalculator | Calculation of GRAIL descriptors for protein-ligand complexes |
| CCDPL.GRAIL.GRAILXDescriptorCalculator | Calculation of the extended GRAIL-X descriptor for protein-ligand complexes |
| CCDPL.GRAIL.GeneralizedBellAtomDensity | Functor for the evaluation of the generalized-bell atom density contribution of an atom at a query position |
| CCDPL.GRAIL.VoidPharmacophoreFunctor | |
| CCDPL.Grid.AttributedGridProperty | Provides keys for built-in Grid.AttributedGrid properties |
| CCDPL.Grid.AttributedGridPropertyDefault | Provides default values for built-in Grid.AttributedGrid properties |
| CCDPL.Grid.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.Grid.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.Grid.DRegularGridIOManager | Singleton class that serves as a global registry for Grid.DRegularGridInputHandler and Grid.DRegularGridOutputHandler implementation instances |
| CCDPL.Grid.DRegularGridIOManager.InputHandlerSequence | |
| CCDPL.Grid.DRegularGridIOManager.OutputHandlerSequence | |
| ►CCDPL.Grid.DRegularGridInputHandler | Factory interface providing methods for the creation of Grid.DRegularGridReaderBase instances for reading data provided in a particular storage format |
| CCDPL.Grid.CDFBZ2DRegularGridInputHandler | Handler for the input of bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridInputHandler | Handler for the input of regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridInputHandler | Handler for the input of gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CUBEDRegularGridInputHandler | Handler for the input of regular spatial grid data in the Gaussian CUBE [CUBE] format |
| ►CCDPL.Grid.DRegularGridOutputHandler | Factory interface providing methods for the creation of Grid.DRegularGridWriterBase instances for data output in a particular storage format |
| CCDPL.Grid.CDFBZ2DRegularGridOutputHandler | Handler for the output of bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridOutputHandler | Handler for the output of regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridOutputHandler | Handler for the output of gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDPL.Grid.CUBEDRegularGridOutputHandler | Handler for the output of regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCDPL.Grid.DRegularGridSet | Convenience alias for the double-precision regular spatial grid sets |
| CCDPL.Grid.DRegularGridSetIOManager | Singleton class that serves as a global registry for Grid.DRegularGridSetInputHandler and Grid.DRegularGridSetOutputHandler implementation instances |
| CCDPL.Grid.DRegularGridSetIOManager.InputHandlerSequence | |
| CCDPL.Grid.DRegularGridSetIOManager.OutputHandlerSequence | |
| ►CCDPL.Grid.DRegularGridSetInputHandler | Factory interface providing methods for the creation of Grid.DRegularGridSetReaderBase instances for reading data provided in a particular storage format |
| CCDPL.Grid.CDFBZ2DRegularGridSetInputHandler | Handler for the input of bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridSetInputHandler | Handler for the input of regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridSetInputHandler | Handler for the input of gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| ►CCDPL.Grid.DRegularGridSetOutputHandler | Factory interface providing methods for the creation of Grid.DRegularGridSetWriterBase instances for data output in a particular storage format |
| CCDPL.Grid.CDFBZ2DRegularGridSetOutputHandler | Handler for the output of bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFDRegularGridSetOutputHandler | Handler for the output of regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.CDFGZDRegularGridSetOutputHandler | Handler for the output of gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDPL.Grid.DataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CCDPL.Grid.FRegularGridSet | Convenience alias for the single-precision regular spatial grid sets |
| ►CCDPL.Math.ConstDGridExpression | |
| CCDPL.Math.DGridExpression | |
| CCDPL.Math.ConstDHomogenousCoordsAdapter | |
| CCDPL.Math.ConstDMatrixColumn | |
| ►CCDPL.Math.ConstDMatrixExpression | |
| CCDPL.Math.DMatrixExpression | |
| CCDPL.Math.ConstDMatrixRange | |
| CCDPL.Math.ConstDMatrixRow | |
| CCDPL.Math.ConstDMatrixSlice | |
| CCDPL.Math.ConstDMatrixTranspose | |
| ►CCDPL.Math.ConstDQuaternionExpression | |
| CCDPL.Math.DQuaternionExpression | |
| CCDPL.Math.ConstDQuaternionVectorAdapter | |
| ►CCDPL.Math.ConstDVectorExpression | |
| CCDPL.Math.DVectorExpression | |
| CCDPL.Math.ConstDVectorQuaternionAdapter | |
| CCDPL.Math.ConstDVectorRange | |
| CCDPL.Math.ConstDVectorSlice | |
| ►CCDPL.Math.ConstFGridExpression | |
| CCDPL.Math.FGridExpression | |
| CCDPL.Math.ConstFHomogenousCoordsAdapter | |
| CCDPL.Math.ConstFMatrixColumn | |
| ►CCDPL.Math.ConstFMatrixExpression | |
| CCDPL.Math.FMatrixExpression | |
| CCDPL.Math.ConstFMatrixRange | |
| CCDPL.Math.ConstFMatrixRow | |
| CCDPL.Math.ConstFMatrixSlice | |
| CCDPL.Math.ConstFMatrixTranspose | |
| ►CCDPL.Math.ConstFQuaternionExpression | |
| CCDPL.Math.FQuaternionExpression | |
| CCDPL.Math.ConstFQuaternionVectorAdapter | |
| ►CCDPL.Math.ConstFVectorExpression | |
| CCDPL.Math.FVectorExpression | |
| CCDPL.Math.ConstFVectorQuaternionAdapter | |
| CCDPL.Math.ConstFVectorRange | |
| CCDPL.Math.ConstFVectorSlice | |
| CCDPL.Math.ConstLHomogenousCoordsAdapter | |
| CCDPL.Math.ConstLMatrixColumn | |
| ►CCDPL.Math.ConstLMatrixExpression | |
| CCDPL.Math.LMatrixExpression | |
| CCDPL.Math.ConstLMatrixRange | |
| CCDPL.Math.ConstLMatrixRow | |
| CCDPL.Math.ConstLMatrixSlice | |
| CCDPL.Math.ConstLMatrixTranspose | |
| ►CCDPL.Math.ConstLQuaternionExpression | |
| CCDPL.Math.LQuaternionExpression | |
| CCDPL.Math.ConstLQuaternionVectorAdapter | |
| ►CCDPL.Math.ConstLVectorExpression | |
| CCDPL.Math.LVectorExpression | |
| CCDPL.Math.ConstLVectorQuaternionAdapter | |
| CCDPL.Math.ConstLVectorRange | |
| CCDPL.Math.ConstLVectorSlice | |
| CCDPL.Math.ConstLowerTriangularDMatrixAdapter | |
| CCDPL.Math.ConstLowerTriangularFMatrixAdapter | |
| CCDPL.Math.ConstLowerTriangularLMatrixAdapter | |
| CCDPL.Math.ConstLowerTriangularULMatrixAdapter | |
| CCDPL.Math.ConstULHomogenousCoordsAdapter | |
| CCDPL.Math.ConstULMatrixColumn | |
| ►CCDPL.Math.ConstULMatrixExpression | |
| CCDPL.Math.ULMatrixExpression | |
| CCDPL.Math.ConstULMatrixRange | |
| CCDPL.Math.ConstULMatrixRow | |
| CCDPL.Math.ConstULMatrixSlice | |
| CCDPL.Math.ConstULMatrixTranspose | |
| ►CCDPL.Math.ConstULQuaternionExpression | |
| CCDPL.Math.ULQuaternionExpression | |
| CCDPL.Math.ConstULQuaternionVectorAdapter | |
| ►CCDPL.Math.ConstULVectorExpression | |
| CCDPL.Math.ULVectorExpression | |
| CCDPL.Math.ConstULVectorQuaternionAdapter | |
| CCDPL.Math.ConstULVectorRange | |
| CCDPL.Math.ConstULVectorSlice | |
| CCDPL.Math.ConstUnitLowerTriangularDMatrixAdapter | |
| CCDPL.Math.ConstUnitLowerTriangularFMatrixAdapter | |
| CCDPL.Math.ConstUnitLowerTriangularLMatrixAdapter | |
| CCDPL.Math.ConstUnitLowerTriangularULMatrixAdapter | |
| CCDPL.Math.ConstUnitUpperTriangularDMatrixAdapter | |
| CCDPL.Math.ConstUnitUpperTriangularFMatrixAdapter | |
| CCDPL.Math.ConstUnitUpperTriangularLMatrixAdapter | |
| CCDPL.Math.ConstUnitUpperTriangularULMatrixAdapter | |
| CCDPL.Math.ConstUpperTriangularDMatrixAdapter | |
| CCDPL.Math.ConstUpperTriangularFMatrixAdapter | |
| CCDPL.Math.ConstUpperTriangularLMatrixAdapter | |
| CCDPL.Math.ConstUpperTriangularULMatrixAdapter | |
| CCDPL.Math.DGrid | Unbounded dense grid storing floating-point values of type double |
| CCDPL.Math.DHomogenousCoordsAdapter | |
| CCDPL.Math.DIdentityMatrix | Memory-efficient immutable identity matrix with element values of type double |
| CCDPL.Math.DKabschAlgorithm | |
| CCDPL.Math.DMLRModel | Performs Multiple Linear Regression [WLIREG] on a set of data points \( (y_i, \vec{X}_i) \) |
| CCDPL.Math.DMatrix | Unbounded dense matrix holding floating-point values of type double |
| CCDPL.Math.DMatrixColumn | |
| CCDPL.Math.DMatrixRange | |
| CCDPL.Math.DMatrixRow | |
| CCDPL.Math.DMatrixSlice | |
| CCDPL.Math.DMatrixTranspose | |
| CCDPL.Math.DQuaternion | General 4-component quaternion with component values of type double |
| CCDPL.Math.DQuaternionVectorAdapter | |
| CCDPL.Math.DRealQuaternion | A memory-efficient pure-real quaternion with component values of type double |
| ►CCDPL.Math.DRegularSpatialGrid | Unbounded dense regular grid storing floating-point values of type double |
| CCDPL.Grid.DRegularGrid | A regular spatial grid storing double-precision floating-point values |
| CCDPL.Math.DRotationMatrix | Rotation matrix holding floating-point values of type double |
| CCDPL.Math.DScalarGrid | Immutable grid where all elements have the same value of type double |
| CCDPL.Math.DScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type double |
| CCDPL.Math.DScalarVector | Memory-efficient immutable vector where all elements have the same value of type double |
| CCDPL.Math.DScalingMatrix | Scaling matrix holding floating-point values of type double |
| CCDPL.Math.DTranslationMatrix | Translation matrix holding floating-point values of type double |
| CCDPL.Math.DUnitVector | Memory-efficient immutable unit vector with element values of type double |
| CCDPL.Math.DVector | Unbounded dense vector holding floating-point values of type double |
| CCDPL.Math.DVectorBFGSMinimizer | Implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for solving unconstrained nonlinear optimization problems |
| CCDPL.Math.DVectorQuaternionAdapter | |
| CCDPL.Math.DVectorRange | |
| CCDPL.Math.DVectorSlice | |
| CCDPL.Math.DZeroGrid | Immutable grid where all elements have the value zero of type double |
| CCDPL.Math.DZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type double |
| CCDPL.Math.DZeroVector | Memory-efficient immutable vector where all elements have the value zero of type double |
| CCDPL.Math.DoubleDVector2Functor | |
| CCDPL.Math.DoubleDVectorFunctor | |
| CCDPL.Math.DoubleVector2DArray2Functor | |
| CCDPL.Math.DoubleVector2DArrayFunctor | |
| CCDPL.Math.DoubleVector3DArray2Functor | |
| CCDPL.Math.DoubleVector3DArrayFunctor | |
| CCDPL.Math.FGrid | Unbounded dense grid storing floating-point values of type float |
| CCDPL.Math.FHomogenousCoordsAdapter | |
| CCDPL.Math.FIdentityMatrix | Memory-efficient immutable identity matrix with element values of type float |
| CCDPL.Math.FKabschAlgorithm | |
| CCDPL.Math.FMLRModel | Performs Multiple Linear Regression [WLIREG] on a set of data points \( (y_i, \vec{X}_i) \) |
| CCDPL.Math.FMatrix | Unbounded dense matrix holding floating-point values of type float |
| CCDPL.Math.FMatrixColumn | |
| CCDPL.Math.FMatrixRange | |
| CCDPL.Math.FMatrixRow | |
| CCDPL.Math.FMatrixSlice | |
| CCDPL.Math.FMatrixTranspose | |
| CCDPL.Math.FQuaternion | General 4-component quaternion with component values of type float |
| CCDPL.Math.FQuaternionVectorAdapter | |
| CCDPL.Math.FRealQuaternion | A memory-efficient pure-real quaternion with component values of type float |
| ►CCDPL.Math.FRegularSpatialGrid | Unbounded dense regular grid storing floating-point values of type float |
| CCDPL.Grid.FRegularGrid | A regular spatial grid storing single-precision floating-point values |
| CCDPL.Math.FRotationMatrix | Rotation matrix holding floating-point values of type float |
| CCDPL.Math.FScalarGrid | Immutable grid where all elements have the same value of type float |
| CCDPL.Math.FScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type float |
| CCDPL.Math.FScalarVector | Memory-efficient immutable vector where all elements have the same value of type float |
| CCDPL.Math.FScalingMatrix | Scaling matrix holding floating-point values of type float |
| CCDPL.Math.FTranslationMatrix | Translation matrix holding floating-point values of type float |
| CCDPL.Math.FUnitVector | Memory-efficient immutable unit vector with element values of type float |
| CCDPL.Math.FVector | Unbounded dense vector holding floating-point values of type float |
| CCDPL.Math.FVectorBFGSMinimizer | Implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for solving unconstrained nonlinear optimization problems |
| CCDPL.Math.FVectorQuaternionAdapter | |
| CCDPL.Math.FVectorRange | |
| CCDPL.Math.FVectorSlice | |
| CCDPL.Math.FZeroGrid | Immutable grid where all elements have the value zero of type float |
| CCDPL.Math.FZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type float |
| CCDPL.Math.FZeroVector | Memory-efficient immutable vector where all elements have the value zero of type float |
| CCDPL.Math.FloatFVector2Functor | |
| CCDPL.Math.FloatFVectorFunctor | |
| CCDPL.Math.FloatVector2FArray2Functor | |
| CCDPL.Math.FloatVector2FArrayFunctor | |
| CCDPL.Math.FloatVector3FArray2Functor | |
| CCDPL.Math.FloatVector3FArrayFunctor | |
| CCDPL.Math.LHomogenousCoordsAdapter | |
| CCDPL.Math.LIdentityMatrix | Memory-efficient immutable identity matrix with element values of type long |
| CCDPL.Math.LMatrix | Unbounded dense matrix holding signed integers of type long |
| CCDPL.Math.LMatrixColumn | |
| CCDPL.Math.LMatrixRange | |
| CCDPL.Math.LMatrixRow | |
| CCDPL.Math.LMatrixSlice | |
| CCDPL.Math.LMatrixTranspose | |
| CCDPL.Math.LQuaternion | General 4-component quaternion with component values of type long |
| CCDPL.Math.LQuaternionVectorAdapter | |
| CCDPL.Math.LRealQuaternion | A memory-efficient pure-real quaternion with component values of type long |
| CCDPL.Math.LRotationMatrix | Rotation matrix holding integer values of type long |
| CCDPL.Math.LScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type long |
| CCDPL.Math.LScalarVector | Memory-efficient immutable vector where all elements have the same value of type long |
| CCDPL.Math.LScalingMatrix | Scaling matrix holding integer values of type long |
| CCDPL.Math.LTranslationMatrix | Translation matrix holding integer values of type long |
| CCDPL.Math.LUnitVector | Memory-efficient immutable unit vector with element values of type long |
| CCDPL.Math.LVector | Unbounded dense vector holding signed integers of type long |
| CCDPL.Math.LVectorQuaternionAdapter | |
| CCDPL.Math.LVectorRange | |
| CCDPL.Math.LVectorSlice | |
| CCDPL.Math.LZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type long |
| CCDPL.Math.LZeroVector | Memory-efficient immutable vector where all elements have the value zero of type long |
| CCDPL.Math.Lower | Tag selecting the lower-triangular view (entries strictly above the diagonal read as zero) for Math.TriangularAdapter |
| CCDPL.Math.Matrix2D | Bounded 2x2 matrix holding floating-point values of type double |
| CCDPL.Math.Matrix2F | Bounded 2x2 matrix holding floating-point values of type float |
| CCDPL.Math.Matrix2L | Bounded 2x2 matrix holding signed integers of type long |
| CCDPL.Math.Matrix2UL | Bounded 2x2 matrix holding unsigned integers of type unsigned long |
| CCDPL.Math.Matrix3D | Bounded 3x3 matrix holding floating-point values of type double |
| CCDPL.Math.Matrix3F | Bounded 3x3 matrix holding floating-point values of type float |
| CCDPL.Math.Matrix3L | Bounded 3x3 matrix holding signed integers of type long |
| CCDPL.Math.Matrix3UL | Bounded 3x3 matrix holding unsigned integers of type unsigned long |
| CCDPL.Math.Matrix4D | Bounded 4x4 matrix holding floating-point values of type double |
| CCDPL.Math.Matrix4F | Bounded 4x4 matrix holding floating-point values of type float |
| CCDPL.Math.Matrix4L | Bounded 4x4 matrix holding signed integers of type long |
| CCDPL.Math.Matrix4UL | Bounded 4x4 matrix holding unsigned integers of type unsigned long |
| CCDPL.Math.Range | Half-open index range \( [start, stop) \) used for slicing vector and matrix expressions |
| CCDPL.Math.Slice | Index slice ( \( start, stride, size \)) used for strided slicing of vector and matrix expressions |
| CCDPL.Math.SparseDMatrix | Unbounded sparse matrix holding floating-point values of type double |
| CCDPL.Math.SparseDVector | Unbounded sparse vector holding floating-point values of type double |
| CCDPL.Math.SparseFMatrix | Unbounded sparse matrix holding floating-point values of type float |
| CCDPL.Math.SparseFVector | Unbounded sparse vector holding floating-point values of type float |
| CCDPL.Math.SparseLMatrix | Unbounded sparse matrix holding signed integers of type long |
| CCDPL.Math.SparseLVector | Unbounded sparse vector holding signed integers of type long |
| CCDPL.Math.SparseULMatrix | Unbounded sparse matrix holding unsigned integers of type unsigned long |
| CCDPL.Math.SparseULVector | Unbounded sparse vector holding unsigned integers of type unsigned long |
| CCDPL.Math.ULHomogenousCoordsAdapter | |
| CCDPL.Math.ULIdentityMatrix | Memory-efficient immutable identity matrix with element values of type unsigned long |
| CCDPL.Math.ULMatrix | Unbounded dense matrix holding unsigned integers of type unsigned long |
| CCDPL.Math.ULMatrixColumn | |
| CCDPL.Math.ULMatrixRange | |
| CCDPL.Math.ULMatrixRow | |
| CCDPL.Math.ULMatrixSlice | |
| CCDPL.Math.ULMatrixTranspose | |
| CCDPL.Math.ULQuaternion | General 4-component quaternion with component values of type unsigned long |
| CCDPL.Math.ULQuaternionVectorAdapter | |
| CCDPL.Math.ULRealQuaternion | A memory-efficient pure-real quaternion with component values of type unsigned long |
| CCDPL.Math.ULRotationMatrix | Rotation matrix holding unsigned integer values of type unsigned long |
| CCDPL.Math.ULScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type unsigned long |
| CCDPL.Math.ULScalarVector | Memory-efficient immutable vector where all elements have the same value of type unsigned long |
| CCDPL.Math.ULScalingMatrix | Scaling matrix holding unsigned integer values of type unsigned long |
| CCDPL.Math.ULTranslationMatrix | Translation matrix holding unsigned integer values of type unsigned long |
| CCDPL.Math.ULUnitVector | Memory-efficient immutable unit vector with element values of type unsigned long |
| CCDPL.Math.ULVector | Unbounded dense vector holding unsigned integers of type unsigned long |
| CCDPL.Math.ULVectorQuaternionAdapter | |
| CCDPL.Math.ULVectorRange | |
| CCDPL.Math.ULVectorSlice | |
| CCDPL.Math.ULZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type unsigned long |
| CCDPL.Math.ULZeroVector | Memory-efficient immutable vector where all elements have the value zero of type unsigned long |
| CCDPL.Math.UnitLower | Tag selecting the unit-lower-triangular view (zero above the diagonal, one on the diagonal) for Math.TriangularAdapter |
| CCDPL.Math.UnitUpper | Tag selecting the unit-upper-triangular view (zero below the diagonal, one on the diagonal) for Math.TriangularAdapter |
| CCDPL.Math.Upper | Tag selecting the upper-triangular view (entries strictly below the diagonal read as zero) for Math.TriangularAdapter |
| CCDPL.Math.Vector2D | Bounded 2 element vector holding floating-point values of type double |
| ►CCDPL.Math.Vector2DArray | Array storing vectors of type Math.Vector2D |
| ►CCDPL.Vis.PointArray2D | Stores a set of points in 2D space |
| CCDPL.Vis.LineSegmentListPrimitive2D | 2D graphics primitive representing a list of disjoint line segments |
| CCDPL.Vis.PointListPrimitive2D | 2D graphics primitive representing a list of points |
| CCDPL.Vis.PolygonPrimitive2D | 2D graphics primitive representing a polygon |
| CCDPL.Vis.PolylinePrimitive2D | 2D graphics primitive representing a set of connected line segments |
| CCDPL.Math.Vector2DArrayAlignmentCalculator | |
| CCDPL.Math.Vector2DArrayBFGSMinimizer | |
| CCDPL.Math.Vector2F | Bounded 2 element vector holding floating-point values of type float |
| CCDPL.Math.Vector2FArray | Array storing vectors of type Math.Vector2F |
| CCDPL.Math.Vector2FArrayAlignmentCalculator | |
| CCDPL.Math.Vector2FArrayBFGSMinimizer | |
| CCDPL.Math.Vector2L | Bounded 2 element vector holding signed integers of type long |
| CCDPL.Math.Vector2LArray | Array storing vectors of type Math.Vector2L |
| CCDPL.Math.Vector2UL | Bounded 2 element vector holding unsigned integers of type unsigned long |
| CCDPL.Math.Vector2ULArray | Array storing vectors of type Math.Vector2UL |
| CCDPL.Math.Vector3D | Bounded 3 element vector holding floating-point values of type double |
| ►CCDPL.Math.Vector3DArray | Array storing vectors of type Math.Vector3D |
| CCDPL.ConfGen.ConformerData | Container for the 3D coordinates of a generated conformer plus its associated energy value |
| CCDPL.Math.Vector3DArrayAlignmentCalculator | |
| CCDPL.Math.Vector3DArrayBFGSMinimizer | |
| CCDPL.Math.Vector3F | Bounded 3 element vector holding floating-point values of type float |
| CCDPL.Math.Vector3FArray | Array storing vectors of type Math.Vector3F |
| CCDPL.Math.Vector3FArrayAlignmentCalculator | |
| CCDPL.Math.Vector3FArrayBFGSMinimizer | |
| CCDPL.Math.Vector3L | Bounded 3 element vector holding signed integers of type long |
| CCDPL.Math.Vector3LArray | Array storing vectors of type Math.Vector3L |
| CCDPL.Math.Vector3UL | Bounded 3 element vector holding unsigned integers of type unsigned long |
| CCDPL.Math.Vector3ULArray | Array storing vectors of type Math.Vector3UL |
| CCDPL.Math.Vector4D | Bounded 4 element vector holding floating-point values of type double |
| CCDPL.Math.Vector4F | Bounded 4 element vector holding floating-point values of type float |
| CCDPL.Math.Vector4L | Bounded 4 element vector holding signed integers of type long |
| CCDPL.Math.Vector4UL | Bounded 4 element vector holding unsigned integers of type unsigned long |
| CCDPL.Math.Vector7D | Bounded 7 element vector holding floating-point values of type double |
| CCDPL.MolProp.AtomHydrophobicityCalculator | Implementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities |
| CCDPL.MolProp.AtomProperty | Provides keys for built-in Chem.Atom properties |
| CCDPL.MolProp.AtomPropertyDefault | Provides default values for MolProp-specific Chem.Atom properties |
| CCDPL.MolProp.BondProperty | Provides keys for built-in Chem.Bond properties |
| CCDPL.MolProp.CoordinationGeometry | Provides constants used to specify the spatial geometry of atom arrangements around a common central atom |
| CCDPL.MolProp.ElementHistogram | Data type for the storage of element histograms of chemical compounds |
| CCDPL.MolProp.HBondAcceptorAtomType | Provides constants used to specify the structural class of H-bond acceptor atoms |
| CCDPL.MolProp.HBondAcceptorAtomTyper | Implements the perception of H-bond acceptor atom types (see namespace MolProp.HBondAcceptorAtomType) |
| CCDPL.MolProp.HBondDonorAtomType | Provides constants used to specify the structural class of H-bond donor atoms |
| CCDPL.MolProp.HBondDonorAtomTyper | Implements the perception of H-bond donor atom types (see namespace MolProp.HBondDonorAtomType) |
| CCDPL.MolProp.LogSCalculator | Calculation of the aqueous solubility ( \( \log S \)) of molecular graphs using the atom-contribution method of Hou, Xia, Zhang and Xu |
| CCDPL.MolProp.MHMOPiChargeCalculator | Calculator that uses a Modified Hückel Molecular Orbital (MHMO) treatment to compute π-electron densities, π-charges, π-bond orders and the total π-electron energy of a molecular graph |
| CCDPL.MolProp.MassComposition | Data type for the storage of mass percent compositions of chemical compounds |
| CCDPL.MolProp.MolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CCDPL.MolProp.PEOESigmaChargeCalculator | Calculator that uses the Partial Equalization of Orbital Electronegativities (PEOE) method of Gasteiger and Marsili to compute σ atomic charges and electronegativities of a molecular graph |
| CCDPL.MolProp.TPSACalculator | Calculation of the topological polar surface area (TPSA) of molecular graphs based on fragment contributions |
| CCDPL.MolProp.XLogPCalculator | Calculation of the octanol/water partition coefficient ( \( \log P \)) of molecular graphs using the atom-additive method of Wang, Gao and Lai |
| CCDPL.Pharm.BoolDoubleFunctor | |
| CCDPL.Pharm.BoolFeature2Functor | |
| CCDPL.Pharm.BoolFeature2Matrix4DFunctor | |
| CCDPL.Pharm.BoolFeature4Functor | |
| CCDPL.Pharm.BoolFeatureFunctor | |
| CCDPL.Pharm.BoolSearchHitDoubleFunctor | |
| CCDPL.Pharm.BoolSizeType2Functor | |
| CCDPL.Pharm.CationPiInteractionConstraint | Constraint functor that tests whether an aromatic/cationic feature pair satisfies the geometric criteria for a cation-π interaction (center distance plus cation-to-ring-plane-normal angle) |
| CCDPL.Pharm.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.Pharm.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.Pharm.DataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CCDPL.Pharm.DoubleDouble2Functor | |
| CCDPL.Pharm.DoubleDoubleFunctor | |
| CCDPL.Pharm.DoubleFeature2Functor | |
| CCDPL.Pharm.DoubleFeature2Matrix4DFunctor | |
| CCDPL.Pharm.DoubleFeature2UIntFunctor | |
| CCDPL.Pharm.DoubleFeatureFunctor | |
| CCDPL.Pharm.DoubleSearchHitFunctor | |
| CCDPL.Pharm.Feature3DCoordinatesFunction | Generic wrapper class used to store a user-defined Pharm.Feature 3D-coordinates function |
| CCDPL.Pharm.FeatureContainerIOManager | Singleton class that serves as a global registry for Pharm.FeatureContainerInputHandler and Pharm.FeatureContainerOutputHandler implementation instances |
| CCDPL.Pharm.FeatureContainerIOManager.InputHandlerSequence | |
| CCDPL.Pharm.FeatureContainerIOManager.OutputHandlerSequence | |
| ►CCDPL.Pharm.FeatureContainerOutputHandler | Factory interface providing methods for the creation of Pharm.FeatureContainerWriterBase instances for data output in a particular storage format |
| CCDPL.Pharm.CDFBZ2FeatureContainerOutputHandler | Handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFFeatureContainerOutputHandler | Handler for the output of feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFGZFeatureContainerOutputHandler | Handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL |
| CCDPL.Pharm.PMLFeatureContainerOutputHandler | Handler for the output of pharmacophore data in the native I/O format of LigandScout |
| CCDPL.Vis.PLYFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the Polygon File Format [PLYFMT] |
| CCDPL.Vis.R3DFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the Raster3D [R3DFMT] format |
| CCDPL.Vis.STLFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the STL [STLFMT] format |
| CCDPL.Vis.VRMLFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the VRML [VRML97] format |
| CCDPL.Pharm.FeatureContainerProperty | Provides keys for built-in Pharm.FeatureContainer properties |
| CCDPL.Pharm.FeatureContainerPropertyDefault | Provides default values for built-in Pharm.FeatureContainer properties |
| ►CCDPL.Pharm.FeatureDistanceConstraint | Constraint functor that accepts a pair of features whose 3D-position distance lies within a configured [min, max] interval |
| CCDPL.Pharm.HydrophobicInteractionConstraint | Pharm.FeatureDistanceConstraint specialization that accepts a hydrophobic feature pair when its center distance lies within the typical hydrophobic interaction range |
| CCDPL.Pharm.IonicInteractionConstraint | Pharm.FeatureDistanceConstraint specialization that accepts an oppositely-charged ionic feature pair when its center distance lies within the typical salt-bridge range |
| ►CCDPL.Pharm.FeatureGenerator | Abstract base class for generators that perceive one type of pharmacophore feature (e.g |
| ►CCDPL.Pharm.PatternBasedFeatureGenerator | Pharm.FeatureGenerator implementation that perceives pharmacophore features by substructure pattern matching, with separate include and exclude pattern lists |
| CCDPL.Pharm.AromaticFeatureGenerator | Pharm.FeatureGenerator implementation that perceives aromatic ring features by enumerating the aromatic SSSR subset of the input molecular graph |
| CCDPL.Pharm.HBondAcceptorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives H-bond acceptor features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.HBondDonorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives H-bond donor features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.HydrophobicAtomFeatureGenerator | Pharm.FeatureGenerator implementation that emits one hydrophobic feature per atom whose individual hydrophobicity exceeds a configurable threshold |
| CCDPL.Pharm.HydrophobicFeatureGenerator | Pharm.FeatureGenerator implementation that perceives hydrophobic features by grouping atoms into rings, chains and small fragment groups whose total atom hydrophobicity exceeds the per-class threshold |
| CCDPL.Pharm.NegIonizableFeatureGenerator | Pharm.FeatureGenerator implementation that perceives negative ionizable group features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.PosIonizableFeatureGenerator | Pharm.FeatureGenerator implementation that perceives positive ionizable group features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.XBondAcceptorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives halogen-bond acceptor features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.XBondDonorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives halogen-bond donor features by matching a built-in set of SMARTS patterns |
| CCDPL.Pharm.FeatureGeometry | Provides constants for the specification of the generic geometry of a pharmacophore feature |
| CCDPL.Pharm.FeatureGeometryMatchFunctor | Match functor that quantifies the goodness of the spatial orientation match between two pharmacophore features, applying type-specific tolerances for H-bond donor/acceptor, halogen-bond donor/acceptor and aromatic features |
| ►CCDPL.Pharm.FeatureInteractionScore | Abstract base class for scoring functors that quantify the strength of a directional pharmacophore-feature interaction (e.g |
| CCDPL.Pharm.CationPiInteractionScore | Pharm.FeatureInteractionScore implementation that scores an aromatic/cationic feature pair by combining per-component scores for cation-to-ring-center distance and cation-displacement to ring-plane-normal angle |
| ►CCDPL.Pharm.FeatureDistanceScore | Pharm.FeatureInteractionScore implementation that scores a feature pair based on whether their 3D-position distance falls within a configured [min, max] interval |
| CCDPL.Pharm.HydrophobicInteractionScore | Pharm.FeatureDistanceScore specialization that scores a hydrophobic feature pair based on its center distance in the typical hydrophobic interaction range |
| CCDPL.Pharm.IonicInteractionScore | Pharm.FeatureDistanceScore specialization that scores an oppositely-charged ionic feature pair based on its center distance in the typical salt-bridge range |
| CCDPL.Pharm.FeatureInteractionScoreCombiner | Composite Pharm.FeatureInteractionScore that combines two underlying interaction scores via a user-supplied binary combination function (default: maximum) |
| CCDPL.Pharm.HBondingInteractionScore | Pharm.FeatureInteractionScore implementation that scores a donor/acceptor feature pair by combining per-component scores for H-bond length, acceptor-H-donor angle and H-bond direction to acceptor vector angle |
| CCDPL.Pharm.OrthogonalPiPiInteractionScore | Pharm.FeatureInteractionScore implementation that scores an aromatic feature pair for an orthogonal (T-shaped) π-π interaction by combining per-component scores for horizontal/vertical center separations and ring-plane-normal angle |
| CCDPL.Pharm.ParallelPiPiInteractionScore | Pharm.FeatureInteractionScore implementation that scores an aromatic feature pair for a parallel (sandwich/displaced) π-π interaction by combining per-component scores for vertical/horizontal center separations and ring-plane-normal angle |
| CCDPL.Pharm.XBondingInteractionScore | Pharm.FeatureInteractionScore implementation that scores a halogen-bond donor/acceptor feature pair by combining per-component scores for halogen-acceptor distance, acceptor-halogen-bound-atom angle and acceptor direction angle |
| ►CCDPL.Pharm.FeatureMapping | Data type for the storage and lookup of arbitrary feature to feature mappings |
| CCDPL.Pharm.SpatialFeatureMapping | Pharm.FeatureMapping specialization that perceives a reference-to-aligned feature mapping based on type, position and geometry compatibility under a given transformation, caching per-pair position and geometry match scores for later retrieval |
| CCDPL.Pharm.FeaturePairDistanceMatchFunctor | Match functor that tests whether two feature pairs share a compatible inter-feature distance, with the compatibility relation switched between query-mode (asymmetric) and non-query-mode (symmetric) |
| CCDPL.Pharm.FeaturePositionMatchFunctor | Match functor that quantifies the goodness of the 3D-position match between two pharmacophore features by comparing their separation against the configured per-feature tolerance |
| CCDPL.Pharm.FeatureProperty | Provides keys for built-in Pharm.Feature properties |
| CCDPL.Pharm.FeaturePropertyDefault | Provides default values for built-in Pharm.Feature properties |
| CCDPL.Pharm.FeatureType | Provides constants for the specification of the generic type of a pharmacophore feature |
| CCDPL.Pharm.FeatureTypeHistogram | Data type for the storage of feature type histograms of pharmacophores |
| CCDPL.Pharm.FeatureTypeMatchFunctor | Match functor that accepts a feature pair when both features share the same Pharm.FeatureType identifier |
| CCDPL.Pharm.FileScreeningHitCollector | Hit-callback functor for use with Pharm.ScreeningProcessor that writes each accepted hit molecule (optionally aligned and annotated with score/database properties) to a Base.DataWriter sink |
| CCDPL.Pharm.HBondingInteractionConstraint | Constraint functor that tests whether a Pharm.Feature pair satisfies geometric H-bond criteria (H-bond length plus acceptor-H-donor and H-bond direction to acceptor vector angles) |
| ►CCDPL.Pharm.InteractionAnalyzer | Analyzer that detects pairwise interactions between features of two Pharm.FeatureContainer instances based on user-registered per-feature-type-pair interaction constraint functions |
| CCDPL.Pharm.DefaultInteractionAnalyzer | Interaction analyzer pre-configured with the built-in default set of interaction constraints (hydrogen-bonding, ionic, aromatic-aromatic, cation-π, hydrophobic, halogen-bonding) |
| CCDPL.Pharm.InteractionConstraintConnector | Composite feature-interaction constraint that combines two underlying constraint functions via a logical conjunction or disjunction |
| CCDPL.Pharm.InteractionPharmacophoreGenerator | Driver that generates an interaction pharmacophore by perceiving a core pharmacophore on a ligand, an environment pharmacophore on the surrounding pocket residues, analyzing the inter-feature interactions and emitting features representing the detected interactions (optionally with exclusion volumes) |
| CCDPL.Pharm.OrthogonalPiPiInteractionConstraint | Constraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for an orthogonal (T-shaped) π-π interaction (horizontal/vertical center separations plus ring-normal angle) |
| CCDPL.Pharm.ParallelPiPiInteractionConstraint | Constraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for a parallel (sandwich/displaced) π-π interaction (vertical/horizontal center separations plus ring-normal angle) |
| ►CCDPL.Pharm.PharmacophoreFitScore | Scoring functor that quantifies how well a candidate set of features fits a reference pharmacophore, combining feature-match count, per-feature position deviation and geometry-match contributions |
| CCDPL.Pharm.PharmacophoreFitScreeningScore | Pharm.PharmacophoreFitScore specialization that scores a Pharm.ScreeningProcessor.SearchHit by applying the underlying pharmacophore-fit score to its query and hit features |
| ►CCDPL.Pharm.PharmacophoreGenerator | Base class for pharmacophore generators that orchestrate per-feature-type Pharm.FeatureGenerator instances to produce the features of a Pharm.Pharmacophore from a Chem.MolecularGraph |
| CCDPL.Pharm.DefaultPharmacophoreGenerator | Pharmacophore generator pre-configured with the built-in default set of feature generators |
| CCDPL.Pharm.PharmacophoreIOManager | Singleton class that serves as a global registry for Pharm.PharmacophoreInputHandler and Pharm.PharmacophoreOutputHandler implementation instances |
| CCDPL.Pharm.PharmacophoreIOManager.InputHandlerSequence | |
| CCDPL.Pharm.PharmacophoreIOManager.OutputHandlerSequence | |
| ►CCDPL.Pharm.PharmacophoreInputHandler | Factory interface providing methods for the creation of Pharm.PharmacophoreReaderBase instances for reading data provided in a particular storage format |
| CCDPL.Pharm.CDFBZ2PharmacophoreInputHandler | Handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFGZPharmacophoreInputHandler | Handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.CDFPharmacophoreInputHandler | Handler for the input of pharmacophore data in the native I/O format of the CDPL |
| CCDPL.Pharm.PMLPharmacophoreInputHandler | Handler for the input of pharmacophore data in the native I/O format of LigandScout |
| CCDPL.Pharm.PSDPharmacophoreInputHandler | Handler for the input of pharmacophore data in the CDPL PSD-format |
| ►CCDPL.Pharm.ScreeningDBAccessor | Abstract base class for accessors that read the data stored in pharmacophore screening databases |
| CCDPL.Pharm.PSDScreeningDBAccessor | Pharm.ScreeningDBAccessor implementation that reads pharmacophore screening databases stored in the built-in optimized PSD format |
| ►CCDPL.Pharm.ScreeningDBCreator | Abstract base class for creators that build optimized pharmacophore screening databases |
| CCDPL.Pharm.PSDScreeningDBCreator | Pharm.ScreeningDBCreator implementation that builds optimized pharmacophore screening databases in the built-in PSD format |
| CCDPL.Pharm.ScreeningProcessor | High-level driver for pharmacophore-based screening of a Pharm.ScreeningDBAccessor-backed database against a query feature container, reporting alignment hits via a user-supplied callback |
| CCDPL.Pharm.ScreeningProcessor.SearchHit | Data structure representing a single alignment hit produced by the screening processor, bundling the source pharmacophore/molecule, the alignment transformation and the source-database indices |
| ►CCDPL.Pharm.SpatialFeatureAlignment | |
| CCDPL.Pharm.PharmacophoreAlignment | Pharmacophore alignment driver — a Chem.SpatialEntityAlignment specialization for Pharm.Feature objects that aligns two feature sets according to their type, geometry and 3D positions |
| CCDPL.Pharm.TopologicalFeatureAlignment | |
| CCDPL.Pharm.XBondingInteractionConstraint | Constraint functor that tests whether a halogen-bond donor/acceptor feature pair satisfies the geometric criteria for a halogen bond (halogen-acceptor distance plus the two characteristic angles) |
| CCDPL.Shape.AlignedColorTverskyScore | Functor wrapping Shape.calcAlignedColorTverskyScore() |
| CCDPL.Shape.AlignedShapeTverskyScore | Functor wrapping Shape.calcAlignedShapeTverskyScore() |
| CCDPL.Shape.AlignedTotalOverlapTverskyScore | Functor wrapping Shape.calcAlignedTotalOverlapTverskyScore() |
| CCDPL.Shape.AlignedTverskyComboScore | Functor wrapping Shape.calcAlignedTverskyComboScore() |
| CCDPL.Shape.AlignmentResult | Result of a Gaussian-shape alignment between a reference and an aligned shape |
| CCDPL.Shape.AlignmentResultSelectionMode | Provides constants for selecting which alignment results are kept by alignment routines |
| CCDPL.Shape.BoolAlignmentResult2Functor | |
| CCDPL.Shape.BoolSizeType2Functor | |
| CCDPL.Shape.BoolSizeTypeFunctor | |
| CCDPL.Shape.ColorTanimotoScore | Functor wrapping Shape.calcColorTanimotoScore() |
| CCDPL.Shape.ColorTverskyScore | Functor wrapping Shape.calcColorTverskyScore() |
| CCDPL.Shape.DoubleAlignmentResultFunctor | |
| CCDPL.Shape.FastGaussianShapeAlignment | High-level driver for the fast alignment of Gaussian shapes against a set of reference shapes |
| CCDPL.Shape.GaussianShape.Element | Data structure representing a single sphere of the Gaussian shape, characterized by a position, radius, hardness and color |
| CCDPL.Shape.GaussianShapeAlignment | High-level driver for the alignment of Gaussian shapes against a set of reference shapes |
| ►CCDPL.Shape.GaussianShapeAlignmentStartGenerator | Abstract base class for generators of starting transformations used to seed Gaussian-shape overlap optimization |
| CCDPL.Shape.PrincipalAxesAlignmentStartGenerator | Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape |
| CCDPL.Shape.GaussianShapeFunction | Function representation of a Gaussian shape, used to evaluate the shape's density, volume, surface area and related quantities at arbitrary 3D positions |
| CCDPL.Shape.GaussianShapeFunctionAlignment | Driver for the alignment of one Shape.GaussianShapeFunction (the aligned shape) against a fixed reference Shape.GaussianShapeFunction |
| CCDPL.Shape.GaussianShapeFunctionAlignment.Result | A single alignment result: rigid-body transformation plus shape and color overlap values |
| CCDPL.Shape.GaussianShapeGenerator | Generates Shape.GaussianShape instances from molecular graphs |
| ►CCDPL.Shape.GaussianShapeOverlapFunction | Abstract base class for functions evaluating the overlap between two Gaussian shape functions |
| CCDPL.Shape.ExactGaussianShapeOverlapFunction | Shape.GaussianShapeOverlapFunction implementation that evaluates the overlap analytically using the full Gaussian-product expansion (no approximations) |
| CCDPL.Shape.FastGaussianShapeOverlapFunction | Shape.GaussianShapeOverlapFunction implementation that uses two approximation techniques to trade some accuracy for a substantial speedup compared to Shape.ExactGaussianShapeOverlapFunction |
| CCDPL.Shape.GaussianShapeSet | Data structure storing a set of (shared) Gaussian shapes |
| CCDPL.Shape.ReferenceColorTverskyScore | Functor wrapping Shape.calcReferenceColorTverskyScore() |
| CCDPL.Shape.ReferenceShapeTverskyScore | Functor wrapping Shape.calcReferenceShapeTverskyScore() |
| CCDPL.Shape.ReferenceTotalOverlapTverskyScore | Functor wrapping Shape.calcReferenceTotalOverlapTverskyScore() |
| CCDPL.Shape.ReferenceTverskyComboScore | Functor wrapping Shape.calcReferenceTverskyComboScore() |
| CCDPL.Shape.ScreeningProcessor | High-level driver for shape-based virtual screening of molecular databases |
| CCDPL.Shape.ScreeningSettings | Bundle of configuration parameters for Shape.ScreeningProcessor |
| CCDPL.Shape.ShapeTanimotoScore | Functor wrapping Shape.calcShapeTanimotoScore() |
| CCDPL.Shape.ShapeTverskyScore | Functor wrapping Shape.calcShapeTverskyScore() |
| CCDPL.Shape.SymmetryClass | Provides constants for the rotational symmetry class of a Gaussian shape |
| CCDPL.Shape.TanimotoComboScore | Functor wrapping Shape.calcTanimotoComboScore() |
| CCDPL.Shape.TotalOverlapTanimotoScore | Functor wrapping Shape.calcTotalOverlapTanimotoScore() |
| CCDPL.Shape.TotalOverlapTverskyScore | Functor wrapping Shape.calcTotalOverlapTverskyScore() |
| CCDPL.Shape.TverskyComboScore | Functor wrapping Shape.calcTverskyComboScore() |
| CCDPL.Shape.Vector7D | |
| CCDPL.Shape.VoidMolecularGraph2AlignmentResultFunctor | |
| CCDPL.Util.BitSet | Dynamic bitset class |
| CCDPL.Util.BitSetArray | Array storing Util.BitSet objects |
| CCDPL.Util.BronKerboschAlgorithm | Implementation of the Bron-Kerbosch clique-detection algorithm [BKA] |
| CCDPL.Util.DArray | Array storing floating-point values of type double |
| CCDPL.Util.DG2DCoordinatesGenerator | |
| CCDPL.Util.DG2DCoordinatesGenerator.DistanceConstraint | |
| CCDPL.Util.DG2DCoordinatesGenerator.DistanceConstraintList | |
| CCDPL.Util.DG3DCoordinatesGenerator | Convenience alias for the 3D coordinates generator with double-precision values |
| CCDPL.Util.DG3DCoordinatesGenerator.DistanceConstraint | |
| CCDPL.Util.DG3DCoordinatesGenerator.DistanceConstraintList | |
| CCDPL.Util.DG3DCoordinatesGenerator.VolumeConstraint | |
| CCDPL.Util.DG3DCoordinatesGenerator.VolumeConstraintList | |
| CCDPL.Util.LArray | Array storing integers of type long |
| CCDPL.Util.SArray | Array storing std::string objects |
| CCDPL.Util.STArray | Array storing unsigned integers of type std::size_t |
| CCDPL.Util.STPair | Pair of unsigned integers of type std::size_t |
| CCDPL.Util.STPairArray | Array storing pairs of unsigned integers of type std::size_t |
| CCDPL.Util.UIArray | Array storing unsigned integers of type unsigned int |
| CCDPL.Vis.Alignment | Provides flags that are used to specify the 2D alignment of graphical objects within a bounded rectangular area |
| CCDPL.Vis.ArrowStyle | Provides constants for the specification of reaction arrow styles in 2D depictions of chemical reactions |
| CCDPL.Vis.AtomProperty | Provides keys for built-in Chem.Atom properties |
| CCDPL.Vis.AtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CCDPL.Vis.BondProperty | Provides keys for built-in Chem.Bond properties |
| CCDPL.Vis.BondPropertyDefault | Provides default values for built-in Chem.Bond properties |
| CCDPL.Vis.Brush | Specifies the fill pattern and fill color of shapes |
| CCDPL.Vis.Color | Specifies a color in terms of its red, green and blue components and an alpha-channel for transparency |
| ►CCDPL.Vis.ColorTable | Container for the storage and lookup of Vis.Color objects that are associated with a numeric identifier |
| CCDPL.Vis.DefaultAtomColorTable | Provides default colors for the element dependent coloring of atom labels in 2D depictions of chemical structures |
| CCDPL.Vis.DefaultFeatureColorTable | Provides default colors for the type dependent coloring of chemical features in 3D visualizations of pharmacophores |
| CCDPL.Vis.ControlParameter | Provides keys for built-in control-parameters |
| CCDPL.Vis.ControlParameterDefault | Provides default values for built-in control-parameters |
| CCDPL.Vis.DataFormat | Provides preinitialized Base.DataFormat objects for all supported image output formats |
| CCDPL.Vis.Font | Specifies a font for drawing text |
| ►CCDPL.Vis.FontMetrics | Interface providing methods for querying information about the metrics of a font |
| CCDPL.Vis.CairoBackend.CairoFontMetrics | Implements the FontMetrics interface for the Cairo rendering backend |
| CCDPL.Vis.QtBackend.QtFontMetrics | Implements the FontMetrics interface for the Qt rendering backend |
| ►CCDPL.Vis.GraphicsPrimitive2D | The abstract base class of all 2D graphics primitives |
| CCDPL.Vis.ClipPathPrimitive2D | 2D graphics primitive representing a clipping region in 2D space |
| CCDPL.Vis.EllipsePrimitive2D | 2D graphics primitive representing an ellipse |
| CCDPL.Vis.LinePrimitive2D | 2D graphics primitive representing a single line |
| CCDPL.Vis.LineSegmentListPrimitive2D | 2D graphics primitive representing a list of disjoint line segments |
| CCDPL.Vis.PathPrimitive2D | 2D graphics primitive representing an arbitrary path in 2D space |
| CCDPL.Vis.PointListPrimitive2D | 2D graphics primitive representing a list of points |
| CCDPL.Vis.PolygonPrimitive2D | 2D graphics primitive representing a polygon |
| CCDPL.Vis.PolylinePrimitive2D | 2D graphics primitive representing a set of connected line segments |
| CCDPL.Vis.TextBlockPrimitive2D | 2D graphics primitive representing a block of styled text |
| CCDPL.Vis.TextLabelPrimitive2D | 2D graphics primitive representing a text label |
| CCDPL.Vis.LayoutDirection | Provides constants that are used to specify the main direction of object layouts |
| CCDPL.Vis.LayoutStyle | Provides constants that are used to specify the layout of a set of graphical objects |
| ►CCDPL.Vis.Line2D | Specifies a line segment in 2D space |
| CCDPL.Vis.LinePrimitive2D | 2D graphics primitive representing a single line |
| CCDPL.Vis.Material | Defines material properties of Vis.Object3D instances |
| CCDPL.Vis.MolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CCDPL.Vis.MolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CCDPL.Vis.Object3DInputHandler | |
| ►CCDPL.Vis.Object3DOutputHandler | |
| CCDPL.Vis.PLYObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the Polygon File Format [PLYFMT] |
| CCDPL.Vis.R3DObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the Raster3D [R3DFMT] format |
| CCDPL.Vis.STLObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the STL [STLFMT] format |
| CCDPL.Vis.VRMLObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the VRML [VRML97] format |
| CCDPL.Vis.Object3DProperty | Provides keys for built-in Vis.Object3D properties |
| CCDPL.Vis.Object3DPropertyDefault | Provides default values for built-in Vis.Object3D properties |
| ►CCDPL.Vis.Path2D | Provides a container for painting operations, enabling arbitrary graphical shapes to be constructed and reused |
| CCDPL.Vis.ClipPathPrimitive2D | 2D graphics primitive representing a clipping region in 2D space |
| CCDPL.Vis.PathPrimitive2D | 2D graphics primitive representing an arbitrary path in 2D space |
| CCDPL.Vis.Path2DConverter | Provides an interface for classes that implement the conversion of Vis.Path2D objects into rendering backend specific path descriptions or drawing operations |
| CCDPL.Vis.Pen | Specifies how to draw lines and outlines of shapes |
| CCDPL.Vis.ReactionProperty | Provides keys for built-in Chem.Reaction properties |
| CCDPL.Vis.ReactionPropertyDefault | Provides default values for built-in Chem.Reaction properties |
| CCDPL.Vis.Rectangle2D | Specifies an axis aligned rectangular area in 2D space |
| ►CCDPL.Vis.Renderer2D | Interface providing methods for low level 2D drawing operations |
| CCDPL.Vis.CairoBackend.CairoRenderer2D | Implements the Renderer2D interface on top of the Cairo 2D Graphics Library |
| CCDPL.Vis.QtBackend.QtRenderer2D | Implements the Renderer2D interface on top of the Qt Toolkit |
| ►CCDPL.Vis.Shape3D | The abstract base of all classes describing the geometric shape of 3D objects |
| ►CCDPL.Vis.TriangleMesh3D | Data structure for describing the geometric shape of 3D objects by means of a triangle mesh |
| CCDPL.Vis.IcosahedronMesh3D | A pre-defined triangle mesh providing the vertices and faces of a regular icosahedron |
| CCDPL.Vis.RightFrustumMesh3D | A pre-defined triangle mesh providing the vertices and faces of a right frustum specified by the contructor arguments |
| CCDPL.Vis.TorusMesh3D | Pre-defined triangle mesh providing the vertices and faces of a torus specified by the contructor arguments |
| CCDPL.Vis.Shape3DVisitor | The base of all Vis.Shape3D visitor implementations [VPTN] |
| CCDPL.Vis.SizeAdjustment | Provides constants that are used to specify the size adjustment policy for graphical objects within a bounded rectangular area |
| CCDPL.Vis.SizeSpecification | Specifies the value and type of a size attribute and defines how the value may change during processing steps |
| CCDPL.Vis.StructureGridView2D.Cell | Data structure storing the contents of a grid cell |
| ►Cbuiltins.Exception | |
| ►CCDPL.Base.Exception | The root of the CDPL exception hierarchy |
| CCDPL.Base.BadCast | Thrown to indicate that a cast or conversion from a given source type to a requested target type is not possible |
| CCDPL.Base.ItemNotFound | Thrown to indicate that some requested data item could not be found |
| ►CCDPL.Base.OperationFailed | Thrown to indicate that some requested operation has failed (e.g |
| CCDPL.Base.CalculationFailed | Thrown to indicate that some requested calculation has failed |
| CCDPL.Base.IOError | Thrown to indicate that an I/O operation has failed because of physical (e.g |
| ►CCDPL.Base.ValueError | Thrown to indicate errors caused by some invalid value |
| CCDPL.Base.NullPointerException | Thrown when an operation requires or expects a valid reference but a None reference was provided |
| ►CCDPL.Base.RangeError | Thrown to indicate that a value is out of range |
| CCDPL.Base.IndexError | Thrown to indicate that an index is out of range |
| CCDPL.Base.SizeError | Thrown to indicate that the size of a (multidimensional) array is not correct |
| ►CCDPL.ForceField.Error | Base class of the ForceField subsystem exception hierarchy |
| CCDPL.ForceField.ParameterizationFailed | Thrown when force field parameterization has failed |
| ►Cbuiltins.IndexError | |
| CCDPL.Base.IndexError | Thrown to indicate that an index is out of range |
| ►Cbuiltins.object | |
| CCDPL.Util.PropertyValue | Unary functor that retrieves the value of a given property from the Base.PropertyContainer instance provided as argument |
| CCDPL.Util.PropertyValueProduct | Binary functor that calculates the product of two property values retrieved from a pair of Base.PropertyContainer instances passed as argument |
| CCDPL.Vis.QtBackend.QtObjectFactory | Provides methods for the creation of QFont, QColor, QPen and QBrush objects from Font, Color, Pen and Brush instances |
| ►Cbuiltins.OSError | |
| CCDPL.Base.IOError | Thrown to indicate that an I/O operation has failed because of physical (e.g |
| ►Cbuiltins.ValueError | |
| CCDPL.Base.ValueError | Thrown to indicate errors caused by some invalid value |
1.9.1