▼ N CDPL The namespace of the Chemical Data Processing Library ► N Base Contains core framework classes and functions C Any A safe, type checked container for arbitrary data of variable type C BadCast Thrown to indicate that a cast or conversion from a given source type to a requested target type is not possible C CalculationFailed Thrown to indicate that some requested calculation has failed C ControlParameterContainer A class providing methods for the storage and lookup of control-parameter values C ControlParameterList A data structure for the storage and lookup of control-parameter values ► C DataFormat Provides meta-information about a particular data storage format C FileExtensionSequence C DataIOBase Provides infrastructure for the registration of I/O callback functions C Exception The root of the CDPL C FileIOStream C IOError Thrown to indicate that an I/O operation has failed because of physical (e.g ► C IOStream C OpenMode C IStream C IndexError Thrown to indicate that an index is out of range C ItemNotFound Thrown to indicate that some requested data item could not be found C LookupKey An unique lookup key for control-parameter and property values C NullPointerException Thrown when an operation requires or expects a valid reference but a None reference was provided C OStream C OperationFailed Thrown to indicate that some requested operation has failed (e.g C PropertyContainer A class providing methods for the storage and lookup of object properties C RangeError Thrown to indicate that a value is out of range C SizeError Thrown to indicate that the size of a (multidimensional) array is not correct C StringIOStream C ValueError Thrown to indicate errors caused by some invalid value C VoidDataIOBaseFunctor C VoidFunctor C VoidLookupKeyAnyFunctor C VoidLookupKeyFunctor ► N Biomol Contains classes and functions related to biological macromolecules C AtomProperty Provides keys for built-in Biomol.Atom properties C AtomPropertyDefault Provides default values for built-in Chem.Atom properties C AtomPropertyFlag Provides flags for the specification of basic Chem.Atom properties C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters C DataFormat Provides preinitialized Base.DataFormat objects for all supported biopolymer data formats C FileMMCIFBZ2MolecularGraphWriter C FileMMCIFBZ2MoleculeReader C FileMMCIFGZMolecularGraphWriter C FileMMCIFGZMoleculeReader C FileMMCIFMolecularGraphWriter C FileMMCIFMoleculeReader C FileMMTFBZ2MolecularGraphWriter C FileMMTFBZ2MoleculeReader C FileMMTFGZMolecularGraphWriter C FileMMTFGZMoleculeReader C FileMMTFMolecularGraphWriter C FileMMTFMoleculeReader C FilePDBBZ2MolecularGraphWriter C FilePDBBZ2MoleculeReader C FilePDBGZMolecularGraphWriter C FilePDBGZMoleculeReader C FilePDBMolecularGraphWriter C FilePDBMoleculeReader C HierarchyView A data structure allowing a hierarchical view on biological macromolecules C HierarchyViewChain HierarchyViewChain C HierarchyViewFragment HierarchyViewFragment C HierarchyViewModel HierarchyViewModel C HierarchyViewNode HierarchyViewNode C MMCIFBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the MMCIF format C MMCIFBZ2MolecularGraphWriter C MMCIFBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the MMCIF format C MMCIFBZ2MoleculeReader ► C MMCIFData A data structure for the storage of imported MMCIF data (see [MMCIF ]) C Category C Item C MMCIFDataProcessingFunction A generic wrapper class used to store a user-defined function for the processing of Biomol.MMCIFData instances C MMCIFGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the MMCIF format C MMCIFGZMolecularGraphWriter C MMCIFGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the MMCIF format C MMCIFGZMoleculeReader C MMCIFMolecularGraphOutputHandler A handler for the output of molecular graph data in the MMCIF format C MMCIFMolecularGraphWriter C MMCIFMoleculeInputHandler A handler for the input of molecule data in the MMCIF format C MMCIFMoleculeReader C MMTFBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF ] C MMTFBZ2MolecularGraphWriter C MMTFBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF ] format C MMTFBZ2MoleculeReader C MMTFGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF ] C MMTFGZMolecularGraphWriter C MMTFGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF ] format C MMTFGZMoleculeReader C MMTFMolecularGraphOutputHandler A handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF ] format C MMTFMolecularGraphWriter A writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF ] C MMTFMoleculeInputHandler A handler for the input of molecule data in the Macromolecular Transmission Format (MMTF)y [MMTF ] C MMTFMoleculeReader A reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF ] C MolecularGraphPointerStringFunctor C MolecularGraphProperty Provides keys for built-in Biomol.MolecularGraph properties C MolecularGraphPropertyDefault Provides default values for built-in Chem.MolecularGraph properties C PDBBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBBZ2MolecularGraphWriter C PDBBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBBZ2MoleculeReader ► C PDBData A data structure for the storage of imported PDB data records (see [CTFILE ]) C RecordType C PDBFormatVersion Provides constants for the specification of the Brookhaven Protein Data Bank (PDB) [PDB ] format version C PDBGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBGZMolecularGraphWriter C PDBGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBGZMoleculeReader C PDBMolecularGraphOutputHandler A handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBMolecularGraphWriter A writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBMoleculeInputHandler A handler for the input of molecule data in the Brookhaven Protein Data Bank (PDB) [PDB ] format C PDBMoleculeReader A reader for molecule data in the Brookhaven Protein Data Bank (PDB) [PDB ] format ► C ResidueDictionary A global dictionary for the lookup of meta-data associated with the residues in biological macromolecules C Entry C ResidueList Implements the extraction of residues in biological macromolecules C ResidueType ► N Chem Contains classes and functions related to chemistry C ANDAtomMatchExpressionList ANDAtomMatchExpressionList C ANDBondMatchExpressionList ANDBondMatchExpressionList C ANDMolecularGraphMatchExpressionList ANDMolecularGraphMatchExpressionList C ANDReactionMatchExpressionList ANDReactionMatchExpressionList C AmideImidicAcidTautomerization AmideImidicAcidTautomerizationRule C AromaticRingSet Implements the perception of aromatic rings in a molecular graph C AromaticSSSRSubset Implements the extraction of the aromatic rings in the SSSR of a molecular graph C AromaticSubstructure Implements the perception of aromatic atoms and bonds in a molecular graph ► C Atom Atom C AtomSequence C BondSequence C Atom2DCoordinatesCalculator Atom2DCoordinatesCalculator C Atom3DCoordinatesFunction A generic wrapper class used to store a user-defined Chem.Atom 3D-coordinates function C Atom3DCoordinatesFunctor Atom3DCoordinatesFunctor C AtomArray3DCoordinatesFunctor AtomArray3DCoordinatesFunctor C AtomBondMapping A data structure for the common storage of related atom to atom and bond to bond mappings C AtomConfiguration Provides constants that are used to specify the R/S configuration of atoms C AtomConfigurationMatchExpression AtomConfigurationMatchExpression C AtomConformer3DCoordinatesFunctor AtomConformer3DCoordinatesFunctor C AtomContainer A common interface for data-structures that support a random access to stored Chem.Atom instances ► C AtomDictionary A global dictionary for the lookup of data associated with the atom types defined in namespace Chem.AtomType C Entry C AtomEnvironmentMatchExpression AtomEnvironmentMatchExpression C AtomMapping A data type for the storage and lookup of arbitrary atom to atom mappings C AtomMatchConstraint Provides numerical identifiers for built-in Chem.Atom matching constraints C AtomMatchExpression A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C AtomMatchExpressionList A container for the storage and evaluation of logical match expression lists C AtomMatchExpressionPtrAtomFunctor C AtomPredicate A generic wrapper class used to store a user-defined atom predicate C AtomProperty Provides keys for built-in Chem.Atom properties C AtomPropertyDefault Provides default values for built-in Chem.Atom properties C AtomPropertyFlag Provides flags for the specification of basic Chem.Atom properties C AtomType Provides constants for the specification of the chemical element or generic type of an atom C AtomTypeMatchExpression AtomTypeMatchExpression C AutomorphismGroupSearch AutomorphismGroupSearch C BRICSAtomLabel Provides constants for the labeling of atoms in bonds matched by a BRICS fragmentation rule C BRICSFragmentGenerator BRICSFragmentGenerator C BRICSRuleID Provides constants for the identification of BRICS fragmentation rules C BasicAtom BasicAtom C BasicBond BasicBond C BasicMolecule BasicMolecule C BasicReaction BasicReaction C BemisMurckoAnalyzer BemisMurckoAnalyzer ► C Bond Bond C AtomSequence C BondConfiguration Provides constants that are used to specify the cis/trans configuration of bonds C BondConfigurationMatchExpression BondConfigurationMatchExpression C BondContainer A common interface for data-structures that support a random access to stored Chem.Bond instances C BondDirection Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings C BondDirectionMatchExpression BondDirectionMatchExpression C BondMapping A data type for the storage and lookup of arbitrary bond to bond mappings C BondMatchConstraint Provides numerical identifiers for built-in Chem.Bond matching constraints and flags for the specification of bond orders C BondMatchExpression A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C BondMatchExpressionList A container for the storage and evaluation of logical match expression lists C BondMatchExpressionPtrBondFunctor C BondOrderCalculator BondOrderCalculator C BondPredicate A generic wrapper class used to store a user-defined bond predicate C BondProperty Provides keys for built-in Chem.Bond properties C BondPropertyDefault Provides default values for built-in Chem.Bond properties C BondPropertyFlag Provides flags for the specification of basic Chem.Bond properties C BondReactionCenterStatusMatchExpression BondReactionCenterStatusMatchExpression C BondStereoFlag Provides constants for the specification of stereo bonds in 2D depictions of chemical structures C BondStereoFlagCalculator BondStereoFlagCalculator C BondSubstituentDirectionMatchExpression BondSubstituentDirectionMatchExpression C BoolAtom2Functor C BoolAtom4Functor C BoolAtomMappingFunctor C BoolBond2Functor C BoolConstMolecularGraphFunctor C BoolEntity3D2Functor C BoolEntity3D4Functor C BoolEntity3DMappingFunctor C BoolMolecularGraphAtomBondMappingFunctor C BoolMolecularGraphFunctor C BoolSTPairArrayFunctor C CDFBZ2MolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL C CDFBZ2MolecularGraphWriter C CDFBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL C CDFBZ2MoleculeReader C CDFBZ2ReactionInputHandler A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL C CDFBZ2ReactionOutputHandler A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL C CDFBZ2ReactionReader C CDFBZ2ReactionWriter C CDFGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL C CDFGZMolecularGraphWriter C CDFGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL C CDFGZMoleculeReader C CDFGZReactionInputHandler A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL C CDFGZReactionOutputHandler A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL C CDFGZReactionReader C CDFGZReactionWriter C CDFMolecularGraphOutputHandler A handler for the output of molecular graph data in the native I/O format of the CDPL C CDFMolecularGraphWriter A writer for molecular graph data in the native I/O format of the CDPL C CDFMoleculeInputHandler A handler for the input of molecule data in the native I/O format of the CDPL C CDFMoleculeReader A reader for molecule data in the native I/O format of the CDPL C CDFReactionInputHandler A handler for the input of reaction data in the native I/O format of the CDPL C CDFReactionOutputHandler A handler for the output of reaction data in the native I/O format of the CDPL C CDFReactionReader A reader for reaction data in the native I/O format of the CDPL C CDFReactionWriter A writer for molecular graph data in the native I/O format of the CDPL C CIPConfigurationLabeler CIPConfigurationLabeler C CIPDescriptor Provides constants for the specification of stereogenic atom/bond configurations determined by the CIP sequence rules C CIPPriorityCalculator CIPPriorityCalculator C CMLBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML ] format C CMLBZ2MolecularGraphWriter C CMLBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML ] format C CMLBZ2MoleculeReader C CMLGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML ] format C CMLGZMolecularGraphWriter C CMLGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML ] format C CMLGZMoleculeReader C CMLMolecularGraphOutputHandler A handler for the output of molecular graph data in the Chemical Markup Language [CML ] format C CMLMolecularGraphWriter A writer for molecular graph data in the Chemical Markup Language [CML ] format C CMLMoleculeInputHandler A handler for the input of molecule data in the Chemical Markup Language [CML ] format C CMLMoleculeReader A Reader for molecule data in the Chemical Markup Language [CML ] format C CanonicalNumberingCalculator CanonicalNumberingCalculator ► C ChEMBLStandardizer Implementation of the ChEMBL structure preprocessing pipeline C ChangeFlags C CommonConnectedSubstructureSearch CommonConnectedSubstructureSearch C CompleteRingSet Implements the exhaustive perception of rings in a molecular graph C ComponentSet Implements the perception of molecular graph components C CompoundMoleculeReader CompoundDataReader C CompoundReactionReader CompoundDataReader C ConnectedSubstructureSet ConnectedSubstructureSet C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters C CyclicSubstructure Implements the perception of ring atoms and bonds in a molecular graph C DataFormat Provides preinitialized Base.DataFormat objects for all supported chemical data formats C DefaultMultiConfMoleculeInputProcessor MultiConfMoleculeInputProcessor C DefaultTautomerGenerator DefaultTautomerGenerator C DoubleAtom2Functor C DoubleAtom2UInt2Functor C DoubleAtom2UIntFunctor C DoubleAtomFunctor C DoubleDVectorFunctor C DoubleEntity3D2Functor C DoubleEntity3DFunctor C DoubleVector3D2AtomFunctor C ElectronSystem Describes an electron system of a molecule in terms of involved atoms and their electron contributions C ElectronSystemList A data type for the storage of Chem.ElectronSystem objects C Entity3D Entity3D C Entity3DContainer A common interface for data-structures that support a random access to stored Chem.Entity3D instances C Entity3DMapping A data type for the storage and lookup of arbitrary entity to entity mappings C Entity3DProperty Provides keys for built-in Chem.Entity3D properties C ExtendedSSSR Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph C FileCDFBZ2MolecularGraphWriter C FileCDFBZ2MoleculeReader C FileCDFBZ2ReactionReader C FileCDFBZ2ReactionWriter C FileCDFGZMolecularGraphWriter C FileCDFGZMoleculeReader C FileCDFGZReactionReader C FileCDFGZReactionWriter C FileCDFMolecularGraphWriter C FileCDFMoleculeReader C FileCDFReactionReader C FileCDFReactionWriter C FileCMLBZ2MolecularGraphWriter C FileCMLBZ2MoleculeReader C FileCMLGZMolecularGraphWriter C FileCMLGZMoleculeReader C FileCMLMolecularGraphWriter C FileCMLMoleculeReader C FileINCHIMolecularGraphWriter C FileINCHIMoleculeReader C FileJMEMolecularGraphWriter C FileJMEMoleculeReader C FileJMEReactionReader C FileJMEReactionWriter C FileMOL2BZ2MolecularGraphWriter C FileMOL2BZ2MoleculeReader C FileMOL2GZMolecularGraphWriter C FileMOL2GZMoleculeReader C FileMOL2MolecularGraphWriter C FileMOL2MoleculeReader C FileMOLMolecularGraphWriter C FileMOLMoleculeReader C FileRDFBZ2ReactionReader C FileRDFBZ2ReactionWriter C FileRDFGZReactionReader C FileRDFGZReactionWriter C FileRDFReactionReader C FileRDFReactionWriter C FileRXNReactionWriter C FileSDFBZ2MolecularGraphWriter C FileSDFBZ2MoleculeReader C FileSDFGZMolecularGraphWriter C FileSDFGZMoleculeReader C FileSDFMolecularGraphWriter C FileSDFMoleculeReader C FileSMARTSMolecularGraphWriter C FileSMARTSMoleculeReader C FileSMARTSReactionReader C FileSMARTSReactionWriter C FileSMILESBZ2MolecularGraphWriter C FileSMILESBZ2MoleculeReader C FileSMILESBZ2ReactionReader C FileSMILESBZ2ReactionWriter C FileSMILESGZMolecularGraphWriter C FileSMILESGZMoleculeReader C FileSMILESGZReactionReader C FileSMILESGZReactionWriter C FileSMILESMolecularGraphWriter C FileSMILESMoleculeReader C FileSMILESReactionReader C FileSMILESReactionWriter C FileXYZBZ2MolecularGraphWriter C FileXYZBZ2MoleculeReader C FileXYZGZMolecularGraphWriter C FileXYZGZMoleculeReader C FileXYZMolecularGraphWriter C FileXYZMoleculeReader ► C Fragment Fragment C AtomSequence C BondSequence ► C FragmentGenerator FragmentGenerator C ExcludePattern C FragmentationRule C FragmentLink C FragmentList A data type for the storage of Chem.Fragment objects C GenericHydrogen13ShiftTautomerization GenericHydrogen13ShiftTautomerizationRule C GenericHydrogen15ShiftTautomerization GenericHydrogen15ShiftTautomerizationRule ► C HashCodeCalculator HashCodeCalculator C DefAtomHashSeedFunctor The default functor for the generation of atom hash seeds C DefBondHashSeedFunctor The default functor for the generation of bond hash seeds C HybridizationState Provides constants for the specification of atom hybridization states C Hydrogen3DCoordinatesCalculator Hydrogen3DCoordinatesCalculator C INCHIMolecularGraphOutputHandler A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C INCHIMolecularGraphWriter A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C INCHIMoleculeInputHandler A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C INCHIMoleculeReader A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI ] format C INCHIReturnCode Provides constants that are used to describe the status of an InChI [INCHI ] output or input operation C ImineEnamineTautomerization ImineEnamineTautomerizationRule C JMEMolecularGraphOutputHandler A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEMolecularGraphWriter A writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEMoleculeInputHandler A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEMoleculeReader A reader for molecule data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionInputHandler A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionOutputHandler A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionReader A reader for reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C JMEReactionWriter A writer for reaction data in the native I/O format of the JME Molecular Editor [JME ] java applet C KekuleStructureCalculator KekuleStructureCalculator C KeteneYnolTautomerization KeteneYnolTautomerizationRule C KetoEnolTautomerization KetoEnolTautomerizationRule C LactamLactimTautomerization LactamLactimTautomerizationRule C MDLDataFormatVersion Provides constants that are used to specify the connection table and Rxn-File version for the I/O of molecular graphs and reactions in MDL format [CTFILE ] C MDLParity Provides constants that are used to specify the MDL stereo parity of atoms C MOL2BZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format C MOL2BZ2MolecularGraphWriter C MOL2BZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format C MOL2BZ2MoleculeReader C MOL2ChargeType Provides constants for the specification of the atom charge type in Tripos MOL2 files C MOL2GZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format C MOL2GZMolecularGraphWriter C MOL2GZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format C MOL2GZMoleculeReader C MOL2MolecularGraphOutputHandler A handler for the output of molecular graph data in the Sybyl MOL2 format C MOL2MolecularGraphWriter C MOL2MoleculeInputHandler A handler for the input of molecule data in the Sybyl MOL2 format C MOL2MoleculeReader C MOL2MoleculeType Provides constants for the specification of the molecule type in Tripos MOL2 files C MOLMolecularGraphOutputHandler A handler for the output of molecular graph data in the MDL Mol-File [CTFILE ] format C MOLMolecularGraphWriter A writer for molecular graph data in the MDL Mol-File [CTFILE ] format C MOLMoleculeInputHandler A handler for the input of molecule data in the MDL Mol-File [CTFILE ] format C MOLMoleculeReader A reader for molecule data in the MDL Mol-File [CTFILE ] format ► C MatchConstraint MatchConstraint C Relation Defines constants for the specification of relational constraints on the values of query/target attribute pairs ► C MatchConstraintList MatchConstraintList C Type Defines constants that describe the logical type of the match constraint list C MaxCommonAtomSubstructureSearch MaxCommonAtomSubstructureSearch C MaxCommonBondSubstructureSearch MaxCommonBondSubstructureSearch C MolGraphMatchExpressionPtrMolGraphFunctor ► C MolecularGraph MolecularGraph C AtomSequence C BondSequence C MolecularGraphComponentGroupingMatchExpression MolecularGraphComponentGroupingMatchExpression ► C MolecularGraphIOManager A singleton class that serves as a global registry for Chem.MolecularGraphInputHandler and Chem.MolecularGraphOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C MolecularGraphInputHandler C MolecularGraphMatchConstraint Provides numerical identifiers for built-in Chem.MolecularGraph matching constraints C MolecularGraphMatchExpression A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C MolecularGraphMatchExpressionList C MolecularGraphOutputHandler A factory interface providing methods for the creation of Chem.MolecularGraphWriterBase instances for data output in a particular storage format C MolecularGraphProperty Provides keys for built-in Chem.MolecularGraph properties C MolecularGraphPropertyDefault Provides default values for built-in Chem.MolecularGraph properties C MolecularGraphWriter Writer for molecule data in any supported format C MolecularGraphWriterBase An interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink ► C Molecule Molecule C AtomSequence C BondSequence ► C MoleculeIOManager A singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C MoleculeInputHandler A factory interface providing methods for the creation of Chem.MoleculeReaderBase instances for reading data provided in a particular storage format C MoleculeOutputHandler C MoleculeReader Reader for molecule data in any supported format C MoleculeReaderBase An interface for reading data objects of type Chem.Molecule from an arbitrary data source C MorganNumberingCalculator MorganNumberingCalculator C MultiConfMoleculeInputProcessor MultiConfMoleculeInputProcessor C MultiSubstructureSearch MultiSubstructureSearch C NOTAtomMatchExpression NOTAtomMatchExpression C NOTBondMatchExpression NOTBondMatchExpression C NOTMolecularGraphMatchExpression NOTMolecularGraphMatchExpression C NOTReactionMatchExpression NOTReactionMatchExpression C NitroAciTautomerization NitroAciTautomerizationRule C NitrosoOximeTautomerization NitrosoOximeTautomerizationRule C ORAtomMatchExpressionList ORAtomMatchExpressionList C ORBondMatchExpressionList ORBondMatchExpressionList C ORMolecularGraphMatchExpressionList ORMolecularGraphMatchExpressionList C ORReactionMatchExpressionList ORReactionMatchExpressionList ► C PatternAtomTyper PatternAtomTyper C Pattern ► C PatternBasedTautomerizationRule PatternBasedTautomerizationRule C BondOrderChange C PhosphinicAcidTautomerization PhosphinicAcidTautomerizationRule C PiElectronSystemList Implements the perception of all pi electron systems present in a molecule ► C ProtonationStateStandardizer Sets the protation state of molecules according to desired objectives C Flavor C RDFBZ2ReactionInputHandler A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE ] format C RDFBZ2ReactionOutputHandler A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE ] format C RDFBZ2ReactionReader C RDFBZ2ReactionWriter C RDFGZReactionInputHandler A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE ] format C RDFGZReactionOutputHandler A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE ] format C RDFGZReactionReader C RDFGZReactionWriter C RDFReactionInputHandler A handler for the input of reaction data in the MDL RD-File [CTFILE ] format C RDFReactionOutputHandler A handler for the output of reaction data in the MDL RD-File [CTFILE ] format C RDFReactionReader A reader for reaction data in the MDL RD-File [CTFILE ] format C RDFReactionWriter A writer for reaction data in the MDL RD-File [CTFILE ] format C RECAPAtomLabel Provides constants for the labeling of atoms in bonds matched by a RECAP fragmentation rule C RECAPFragmentGenerator RECAPFragmentGenerator C RECAPRuleID Provides constants for the identification of RECAP fragmentation rules C RXNReactionInputHandler A handler for the input of reaction data in the MDL Rxn-File [CTFILE ] format C RXNReactionOutputHandler A handler for the output of reaction data in the MDL Rxn-File [CTFILE ] format C RXNReactionReader A reader for reaction data in the MDL Rxn-File [CTFILE ] format C RXNReactionWriter A writer for reaction data in the MDL Rxn-File [CTFILE ] format C RadicalType Provides constants that are used to specify the degeneracy of the electronic state of radical atoms ► C Reaction Reaction C ComponentSequence C ReactionAtomMappingMatchExpression ReactionAtomMappingMatchExpression C ReactionCenterStatus Provides flags that are used to describe state changes of atoms and bonds in a reaction center C ReactionComponentGroupingMatchExpression ReactionComponentGroupingMatchExpression ► C ReactionIOManager A singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C ReactionInputHandler A factory interface providing methods for the creation of Chem.ReactionReaderBase instances for reading data provided in a particular storage format C ReactionMatchConstraint Provides numerical identifiers for built-in Chem.Reaction matching constraints C ReactionMatchExpression A generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms C ReactionMatchExpressionList C ReactionOutputHandler A factory interface providing methods for the creation of Chem.ReactionWriterBase instances for data output in a particular storage format C ReactionProperty Provides keys for built-in Chem.Reaction properties C ReactionPropertyDefault Provides default values for built-in Chem.Reaction properties C ReactionReader Reader for reaction data in any supported format C ReactionReaderBase An interface for reading data objects of type Chem.Reaction from an arbitrary data source C ReactionRole Provides constants that are used to specify the role of molecules (components) in a chemical reaction C ReactionSubstructureSearch ReactionSubstructureSearch C ReactionWriter Writer for reaction data in any supported format C ReactionWriterBase An interface for writing data objects of type Chem.Reaction to an arbitrary data sink C Reactor Reactor ► C ResonanceStructureGenerator ResonanceStructureGenerator C StructureData C SDFBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE ] format C SDFBZ2MolecularGraphWriter C SDFBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE ] format C SDFBZ2MoleculeReader C SDFGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE ] format C SDFGZMolecularGraphWriter C SDFGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE ] format C SDFGZMoleculeReader C SDFMolecularGraphOutputHandler A handler for the output of molecular graph data in the MDL SD-File [CTFILE ] format C SDFMolecularGraphWriter A writer for molecular graph data in the MDL Mol-File [CTFILE ] format C SDFMoleculeInputHandler A handler for the input of molecule data in the MDL SD-File [CTFILE ] format C SDFMoleculeReader A Reader for molecule data in the MDL SD-File [CTFILE ] format C SMARTSMolecularGraphOutputHandler A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS ] format C SMARTSMolecularGraphWriter A writer for molecular graph data in the Daylight SMARTS [SMARTS ] format C SMARTSMoleculeInputHandler A handler for the input of molecule data in the Daylight SMARTS [SMARTS ] format C SMARTSMoleculeReader A reader for molecule data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionInputHandler A handler for the input of reaction data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionOutputHandler A handler for the output of reaction data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionReader A reader for reaction data in the Daylight SMARTS [SMARTS ] format C SMARTSReactionWriter A writer for reaction data in the Daylight SMARTS [SMARTS ] format C SMILESBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES ] format C SMILESBZ2MolecularGraphWriter C SMILESBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES ] format C SMILESBZ2MoleculeReader C SMILESBZ2ReactionInputHandler A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES ] format C SMILESBZ2ReactionOutputHandler A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES ] format C SMILESBZ2ReactionReader C SMILESBZ2ReactionWriter C SMILESGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES ] format C SMILESGZMolecularGraphWriter C SMILESGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES ] format C SMILESGZMoleculeReader C SMILESGZReactionInputHandler A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES ] format C SMILESGZReactionOutputHandler A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES ] format C SMILESGZReactionReader C SMILESGZReactionWriter C SMILESMolecularGraphOutputHandler A handler for the output of molecular graph data in the Daylight SMILES [SMILES ] format C SMILESMolecularGraphWriter A writer for molecular graph data in the Daylight SMILES [SMILES ] format C SMILESMoleculeInputHandler A handler for the input of molecule data in the Daylight SMILES [SMILES ] format C SMILESMoleculeReader A reader for molecule data in the Daylight SMILES [SMILES ] format C SMILESReactionInputHandler A handler for the input of reaction data in the Daylight SMILES [SMILES ] format C SMILESReactionOutputHandler A handler for the output of reaction data in the Daylight SMILES [SMILES ] format C SMILESReactionReader A reader for reaction data in the Daylight SMILES [SMILES ] format C SMILESReactionWriter A writer for reaction data in the Daylight SMILES [SMILES ] format C SizeTypeAtomFunctor C SizeTypeAtomMolecularGraphFunctor C SmallestSetOfSmallestRings Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs C SpatialAtomAlignment C SpatialEntity3DAlignment ► C StereoDescriptor A data structure for the storage and retrieval of stereochemical information about atoms and bonds C ReferenceAtomArray ► C StereoisomerGenerator StereoisomerGenerator C StereoDescriptorArray C StringDataBlock An array of Chem.StringDataBlockEntry objects used to store the structure or reaction data block of a STRING SD- or RD-File data record (see [CTFILE ]) C StringDataBlockEntry Represents a data item in the structure or reaction data block of a MDL SD- or RD-File data record (see [CTFILE ]) ► C SubstructureHistogramCalculator SubstructureHistogramCalculator C Pattern C SubstructureSearch SubstructureSearch C SulfenicAcidTautomerization SulfenicAcidTautomerizationRule C SurfaceAtomExtractor SurfaceAtomExtractor C SybylAtomType Provides constants for the specification of the Tripos Sybyl atom type C SybylBondType Provides constants for the specification of the Tripos Sybyl bond type C SymmetryClassCalculator SymmetryClassCalculator ► C TautomerGenerator TautomerGenerator C Mode C TautomerScore TautomerScore C TautomerizationRule TautomerizationRule C TautomerizationType Provides constants serving as identifiers for built-in Chem.TautomerizationRule implementations C TopologicalAtomAlignment C TopologicalEntity3DAlignment C UInt64AtomFunctor C UInt64AtomMolecularGraphFunctor C UInt64BondFunctor C Vector2DAtomFunctor C Vector3DEntity3DFunctor C VoidMolecularGraphFunctor C VoidMoleculeMolecularGraphFunctor C XYZBZ2MolecularGraphOutputHandler A handler for the output of bzip2-compressed molecular graph data in the XYZ format C XYZBZ2MolecularGraphWriter C XYZBZ2MoleculeInputHandler A handler for the input of bzip2-compressed molecule data in the XYZ format C XYZBZ2MoleculeReader C XYZGZMolecularGraphOutputHandler A handler for the output of gzip-compressed molecular graph data in the XYZ format C XYZGZMolecularGraphWriter C XYZGZMoleculeInputHandler A handler for the input of gzip-compressed molecule data in the XYZ format C XYZGZMoleculeReader C XYZMolecularGraphOutputHandler A handler for the output of molecular graph data in the XYZ format C XYZMolecularGraphWriter C XYZMoleculeInputHandler A handler for the input of molecule data in the XYZ format C XYZMoleculeReader ► N ConfGen Contains classes and functions related to conformer ensemble generation C CFLMoleculeInputHandler A handler for the input of molecule data from conformer generator fragment libraries C CFLMoleculeReader A reader for molecule data in the native I/O format of the CDPL C CallbackFunction A generic wrapper class used to store a user-defined callback functions (see [FUNWRP ]) ► C CanonicalFragment CanonicalFragment C AtomMapping C ConformerData C ConformerGenerator C ConformerGeneratorSettings C ConformerSamplingMode Provides constants used to specify the employed conformer sampling method C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters ► C DGConstraintGenerator C StereoCenterData C DGConstraintGeneratorSettings C DGStructureGenerator C DGStructureGeneratorSettings C DataFormat Provides preinitialized Base.DataFormat objects for all supported data formats C FileCFLMoleculeReader C ForceFieldType Provides constants that are used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations C FragmentAssembler C FragmentAssemblerSettings C FragmentConformerGenerator ► C FragmentConformerGeneratorSettings C FragmentSettings C FragmentLibrary C FragmentLibraryEntry FragmentLibraryEntry C FragmentLibraryGenerator FragmentLibraryGenerator C FragmentType Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models C LogMessageCallbackFunction A generic wrapper class used to store a user-defined callback functions C NitrogenEnumerationMode Provides constants that are used to specify the mode of invertible nitrogen enumeration C RMSDConformerSelector C ReturnCode Provides constants that are used to describe the result of operations related to conformer generation C StructureGenerationMode Provides constants used to specify the employed structure generation method C StructureGenerator C StructureGeneratorSettings ► C TorsionCategory C CategorySequence C RuleSequence C TorsionDriver C TorsionDriverSettings C TorsionLibrary ► C TorsionRule C AngleEntry ► C TorsionRuleMatch C AtomArray C TorsionRuleMatcher ► N Descr Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors C AtomAutoCorrelation3DVectorCalculator AtomAutoCorrelation3DVectorCalculator C AtomRDFCodeCalculator AtomRDFCodeCalculator C AutoCorrelation2DVectorCalculator AutoCorrelation2DVectorCalculator C BCUTDescriptorCalculator BCUTDescriptorCalculator C BitSetBulkSimilarityCalculator C BurdenMatrixGenerator BurdenMatrixGenerator ► C CircularFingerprintGenerator CircularFingerprintGenerator C DefAtomIdentifierFunctor The functor for the generation of ECFP atom identifiers C DefBondIdentifierFunctor The default functor for the generation of bond identifiers C CosineSimilarity Functor class for calculating Cosine Similarities [WCOS ] of bitsets and vectors C DVectorBulkSimilarityCalculator C DiceSimilarity Functor class for calculating the Dice Similarity [GSIM ] of bitsets C DoubleBitSet2Functor C DoubleDVector2Functor C DoubleFVector2Functor C DoubleLVector2Functor C DoubleULVector2Functor C EuclideanDistance Functor class for calculating the Euclidean Distance [CITB ] between bitsets and vectors C EuclideanSimilarity Functor class for calculating the Euclidean Similarity [GSIM ] of bitsets C FVectorBulkSimilarityCalculator C FeatureAutoCorrelation3DVectorCalculator FeatureAutoCorrelation3DVectorCalculator C FeatureRDFCodeCalculator FeatureRDFCodeCalculator C HammingDistance Functor class for calculating the Hamming Distance [WHAM , CITB ] between bitsets C LVectorBulkSimilarityCalculator C MACCSFingerprintGenerator Generation of 166 bit MACCS key fingerprints C ManhattanDistance Functor class for calculating the Manhattan Distance [MADI ] between bitsets and vectors C ManhattanSimilarity Functor class for calculating the Manhattan Similarity [GSIM ] of bitsets C MolecularComplexityCalculator MolecularComplexityCalculator ► C MoleculeAutoCorr2DDescriptorCalculator MoleculeAutoCorr2DDescriptorCalculator C Mode C MoleculeAutoCorr3DDescriptorCalculator MoleculeAutoCorr3DDescriptorCalculator C MoleculeRDFDescriptorCalculator MoleculeRDFDescriptorCalculator ► C NPoint2DPharmacophoreFingerprintGenerator NPoint2DPharmacophoreFingerprintGenerator C FeatureDistanceType C NPoint3DPharmacophoreFingerprintGenerator NPoint3DPharmacophoreFingerprintGenerator C NPointPharmacophoreFingerprintGenerator NPointPharmacophoreFingerprintGenerator ► C PathFingerprintGenerator PathFingerprintGenerator C DefAtomDescriptorFunctor The default functor for the generation of atom descriptors C DefBondDescriptorFunctor The default functor for the generation of bond descriptors C PharmacophoreAutoCorr3DDescriptorCalculator PharmacophoreAutoCorr3DDescriptorCalculator C PharmacophoreRDFDescriptorCalculator PharmacophoreRDFDescriptorCalculator C PubChemFingerprintGenerator Generation of 881 bit PubChem fingerprints C TanimotoSimilarity Functor class for calculating Tanimoto Similarities [CITB ] of bitsets and vectors C TverskySimilarity Functor class for calculating the Tversky Similarity [GSIM ] of bitsets C ULVectorBulkSimilarityCalculator ► N ForceField Contains classes and functions related to molecular force fields C AtomProperty Provides keys for built-in Chem.Atom properties C BondProperty Provides keys for built-in Chem.Bond properties C ElasticPotential C ElasticPotentialList C Error C InteractionFilterFunction2 C InteractionFilterFunction3 C InteractionFilterFunction4 C InteractionType Provides flags for the specification of a set of force field interaction types C MMFF94AngleBendingInteraction C MMFF94AngleBendingInteractionList C MMFF94AngleBendingInteractionParameterizer ► C MMFF94AngleBendingParameterTable C Entry ► C MMFF94AromaticAtomTypeDefinitionTable C Entry C MMFF94AromaticSSSRSubset Implements the extraction of all rings in the SSSR of a molecular graph that are aromatic according to MMFF94 conventions C MMFF94AtomChargeFunction A generic wrapper class used to store a user-defined MMFF94 partial atom charge function ► C MMFF94AtomTypePropertyTable C Entry C MMFF94AtomTyper ► C MMFF94BondChargeIncrementTable C Entry C MMFF94BondStretchingInteraction C MMFF94BondStretchingInteractionList C MMFF94BondStretchingInteractionParameterizer ► C MMFF94BondStretchingParameterTable C Entry ► C MMFF94BondStretchingRuleParameterTable C Entry C MMFF94BondTypeIndexFunction A generic wrapper class used to store a user-defined MMFF94 bond type index function C MMFF94BondTyper C MMFF94ChargeCalculator ► C MMFF94DefaultStretchBendParameterTable C Entry C MMFF94ElectrostaticInteraction C MMFF94ElectrostaticInteractionList C MMFF94ElectrostaticInteractionParameterizer C MMFF94EnergyCalculator ► C MMFF94FormalAtomChargeDefinitionTable C Entry C MMFF94GradientCalculator ► C MMFF94HeavyToHydrogenAtomTypeMap C Entry C MMFF94InteractionData C MMFF94InteractionParameterizer C MMFF94NumericAtomTypeFunction A generic wrapper class used to store a user-defined numeric MMFF94 atom type function C MMFF94OutOfPlaneBendingInteraction C MMFF94OutOfPlaneBendingInteractionList C MMFF94OutOfPlaneBendingInteractionParameterizer ► C MMFF94OutOfPlaneBendingParameterTable C Entry C MMFF94ParameterSet Provides flags for the specification of the MMFF94 parameter set to use ► C MMFF94PartialBondChargeIncrementTable C Entry ► C MMFF94PrimaryToParameterAtomTypeMap C Entry C MMFF94RingSetFunction A generic wrapper class used to store a user-defined MMFF94 ring set function C MMFF94StretchBendInteraction C MMFF94StretchBendInteractionList C MMFF94StretchBendInteractionParameterizer ► C MMFF94StretchBendParameterTable C Entry C MMFF94SymbolicAtomTypeFunction A generic wrapper class used to store a user-defined symbolic MMFF94 atom type function ► C MMFF94SymbolicAtomTypePatternTable C Entry ► C MMFF94SymbolicToNumericAtomTypeMap C Entry C MMFF94TorsionInteraction C MMFF94TorsionInteractionList C MMFF94TorsionInteractionParameterizer ► C MMFF94TorsionParameterTable C Entry C MMFF94VanDerWaalsAtomParameters ► C MMFF94VanDerWaalsInteraction C HDonorAcceptorType C MMFF94VanDerWaalsInteractionList C MMFF94VanDerWaalsInteractionParameterizer ► C MMFF94VanDerWaalsParameterTable C Entry C MolecularGraphProperty Provides keys for built-in Chem.MolecularGraph properties C ParameterizationFailed C TopologicalAtomDistanceFunction A generic wrapper class used to store a user-defined topological atom-pair distance function C UFFAtomType Provides constants for the specification of Universal Force Field (UFF) atom types ► C UFFAtomTypePropertyTable C Entry ► N GRAIL Contains classes and functions related to the GRAIL method [GRAIL ] C AtomDensityGridCalculator AtomDensityGridCalculator C AttributedGridProperty Provides keys for built-in Grid.AttributedGrid properties C AttributedGridPropertyDefault Provides default values for built-in Grid.AttributedGrid properties ► C BindingAffinityCalculator BindingAffinityCalculator C AffinityMeasure C BuriednessGridCalculator BuriednessGridCalculator C BuriednessScore BuriednessScore C DoubleVector3DFeatureFunctor ► C FeatureInteractionScoreGridCalculator FeatureInteractionScoreGridCalculator C MaxScoreFunctor C ScoreSumFunctor C FeatureType Provides constants for the specification of pharmacophore feature types with extensions for H-bond acceptors and donors C GRAILDataSetGenerator GRAILDataSetGenerator ► C GRAILDescriptorCalculator GRAILDescriptorCalculator C ElementIndex ► C GRAILXDescriptorCalculator GRAILXDescriptorCalculator C ElementIndex C GeneralizedBellAtomDensity GeneralizedBellAtomDensity C VoidPharmacophoreFunctor ► N Grid Contains classes and functions related to grid based data representation and processing C AttributedGrid AttributedGrid C AttributedGridProperty Provides keys for built-in Grid.AttributedGrid properties C AttributedGridPropertyDefault Provides default values for built-in Grid.AttributedGrid properties C CDFBZ2DRegularGridInputHandler A handler for the input of bzip2-compressed spatial regular grid data in the native I/O format of the CDPL C CDFBZ2DRegularGridOutputHandler A handler for the output of bzip2-compressed spatial regular grid data in the native I/O format of the CDPL C CDFBZ2DRegularGridReader C CDFBZ2DRegularGridSetInputHandler A handler for the input of bzip2-compressed spatial regular grid set data in the native I/O format of the CDPL C CDFBZ2DRegularGridSetOutputHandler A handler for the output of bzip2-compressed spatial regular grid set data in the native I/O format of the CDPL C CDFBZ2DRegularGridSetReader C CDFBZ2DRegularGridSetWriter C CDFBZ2DRegularGridWriter C CDFDRegularGridInputHandler A handler for the input of spatial regular grid data in the native I/O format of the CDPL C CDFDRegularGridOutputHandler A handler for the output of spatial regular grid data in the native I/O format of the CDPL C CDFDRegularGridReader A reader for spatial regular grid data in the native I/O format of the CDPL C CDFDRegularGridSetInputHandler A handler for the input of spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridSetOutputHandler A handler for the output of spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridSetReader A reader for spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridSetWriter A writer for spatial regular grid set data in the native I/O format of the CDPL C CDFDRegularGridWriter A writer for spatial regular grid data in the native I/O format of the CDPL C CDFGZDRegularGridInputHandler A handler for the input of gzip-compressed spatial regular grid data in the native I/O format of the CDPL C CDFGZDRegularGridOutputHandler A handler for the output of gzip-compressed spatial regular grid data in the native I/O format of the CDPL C CDFGZDRegularGridReader C CDFGZDRegularGridSetInputHandler A handler for the input of gzip-compressed spatial regular grid set data in the native I/O format of the CDPL C CDFGZDRegularGridSetOutputHandler A handler for the output of gzip-compressed spatial regular grid set data in the native I/O format of the CDPL C CDFGZDRegularGridSetReader C CDFGZDRegularGridSetWriter C CDFGZDRegularGridWriter C CompoundDRegularGridReader CompoundDataReader C CompoundDRegularGridSetReader CompoundDataReader C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters C DRegularGrid RegularGrid ► C DRegularGridIOManager A singleton class that serves as a global registry for Grid.DRegularGridInputHandler and Grid.DRegularGridOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C DRegularGridInputHandler A factory interface providing methods for the creation of Grid.DRegularGridReaderBase instances for reading data provided in a particular storage format C DRegularGridOutputHandler A factory interface providing methods for the creation of Grid.DRegularGridWriterBase instances for data output in a particular storage format C DRegularGridReader Reader for grid data of type Grid.DRegularGrid in any supported format C DRegularGridReaderBase An interface for reading data objects of type Grid.DRegularGrid from an arbitrary data source C DRegularGridSet RegularGridSet ► C DRegularGridSetIOManager A singleton class that serves as a global registry for Grid.DRegularGridSetInputHandler and Grid.DRegularGridSetOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C DRegularGridSetInputHandler A factory interface providing methods for the creation of Grid.DRegularGridSetReaderBase instances for reading data provided in a particular storage format C DRegularGridSetOutputHandler A factory interface providing methods for the creation of Grid.DRegularGridSetWriterBase instances for data output in a particular storage format C DRegularGridSetReader Reader for grid set data of type Grid.DRegularGridSet in any supported format C DRegularGridSetReaderBase An interface for reading data objects of type Grid.DRegularGridSet from an arbitrary data source C DRegularGridSetWriter Writer for grid set data of type Grid.DRegularGridSet in any supported format C DRegularGridSetWriterBase An interface for writing data objects of type Grid.DRegularGridSet to an arbitrary data sink C DRegularGridWriter Writer for grid data of type Grid.DRegularGrid in any supported format C DRegularGridWriterBase An interface for writing data objects of type Grid.DRegularGrid to an arbitrary data sink C DSpatialGrid SpatialGrid C DataFormat Provides preinitialized Base.DataFormat objects for all supported data formats C FRegularGrid RegularGrid C FRegularGridSet RegularGridSet C FSpatialGrid SpatialGrid C FileCDFBZ2DRegularGridReader C FileCDFBZ2DRegularGridSetReader C FileCDFBZ2DRegularGridSetWriter C FileCDFBZ2DRegularGridWriter C FileCDFDRegularGridReader C FileCDFDRegularGridSetReader C FileCDFDRegularGridSetWriter C FileCDFDRegularGridWriter C FileCDFGZDRegularGridReader C FileCDFGZDRegularGridSetReader C FileCDFGZDRegularGridSetWriter C FileCDFGZDRegularGridWriter ► N Math Contains classes and functions related to mathematics C ConstDGridExpression C ConstDHomogenousCoordsAdapter C ConstDMatrixColumn C ConstDMatrixExpression C ConstDMatrixRange C ConstDMatrixRow C ConstDMatrixSlice C ConstDMatrixTranspose C ConstDQuaternionExpression C ConstDQuaternionVectorAdapter C ConstDVectorExpression C ConstDVectorQuaternionAdapter C ConstDVectorRange C ConstDVectorSlice C ConstFGridExpression C ConstFHomogenousCoordsAdapter C ConstFMatrixColumn C ConstFMatrixExpression C ConstFMatrixRange C ConstFMatrixRow C ConstFMatrixSlice C ConstFMatrixTranspose C ConstFQuaternionExpression C ConstFQuaternionVectorAdapter C ConstFVectorExpression C ConstFVectorQuaternionAdapter C ConstFVectorRange C ConstFVectorSlice C ConstLHomogenousCoordsAdapter C ConstLMatrixColumn C ConstLMatrixExpression C ConstLMatrixRange C ConstLMatrixRow C ConstLMatrixSlice C ConstLMatrixTranspose C ConstLQuaternionExpression C ConstLQuaternionVectorAdapter C ConstLVectorExpression C ConstLVectorQuaternionAdapter C ConstLVectorRange C ConstLVectorSlice C ConstLowerTriangularDMatrixAdapter C ConstLowerTriangularFMatrixAdapter C ConstLowerTriangularLMatrixAdapter C ConstLowerTriangularULMatrixAdapter C ConstULHomogenousCoordsAdapter C ConstULMatrixColumn C ConstULMatrixExpression C ConstULMatrixRange C ConstULMatrixRow C ConstULMatrixSlice C ConstULMatrixTranspose C ConstULQuaternionExpression C ConstULQuaternionVectorAdapter C ConstULVectorExpression C ConstULVectorQuaternionAdapter C ConstULVectorRange C ConstULVectorSlice C ConstUnitLowerTriangularDMatrixAdapter C ConstUnitLowerTriangularFMatrixAdapter C ConstUnitLowerTriangularLMatrixAdapter C ConstUnitLowerTriangularULMatrixAdapter C ConstUnitUpperTriangularDMatrixAdapter C ConstUnitUpperTriangularFMatrixAdapter C ConstUnitUpperTriangularLMatrixAdapter C ConstUnitUpperTriangularULMatrixAdapter C ConstUpperTriangularDMatrixAdapter C ConstUpperTriangularFMatrixAdapter C ConstUpperTriangularLMatrixAdapter C ConstUpperTriangularULMatrixAdapter C DGrid An unbounded dense grid holding floating point values of type double C DGridExpression C DHomogenousCoordsAdapter C DIdentityMatrix C DKabschAlgorithm C DMLRModel Performs Multiple Linear Regression [WLIREG ] on a set of data points C DMatrix An unbounded dense matrix holding floating point values of type double C DMatrixColumn C DMatrixExpression C DMatrixRange C DMatrixRow C DMatrixSlice C DMatrixTranspose C DQuaternion C DQuaternionExpression C DQuaternionVectorAdapter C DRealQuaternion ► C DRegularSpatialGrid An unbounded dense regular grid in 3D space holding floating point values of type double C DataMode C DRotationMatrix C DScalarGrid C DScalarMatrix C DScalarVector C DScalingMatrix C DTranslationMatrix C DUnitVector C DVector An unbounded dense vector holding floating point values of type double ► C DVectorBFGSMinimizer Fletcher's implementation of the BFGS method C Status C DVectorExpression C DVectorQuaternionAdapter C DVectorRange C DVectorSlice C DZeroGrid C DZeroMatrix C DZeroVector C DoubleDVector2Functor C DoubleDVectorFunctor C DoubleVector2DArray2Functor C DoubleVector2DArrayFunctor C DoubleVector3DArray2Functor C DoubleVector3DArrayFunctor C FGrid An unbounded dense grid holding floating point values of type float C FGridExpression C FHomogenousCoordsAdapter C FIdentityMatrix C FKabschAlgorithm C FMLRModel Performs Multiple Linear Regression [WLIREG ] on a set of data points C FMatrix An unbounded dense matrix holding floating point values of type float C FMatrixColumn C FMatrixExpression C FMatrixRange C FMatrixRow C FMatrixSlice C FMatrixTranspose C FQuaternion C FQuaternionExpression C FQuaternionVectorAdapter C FRealQuaternion ► C FRegularSpatialGrid An unbounded dense regular grid in 3D space holding floating point values of type float C DataMode C FRotationMatrix C FScalarGrid C FScalarMatrix C FScalarVector C FScalingMatrix C FTranslationMatrix C FUnitVector C FVector An unbounded dense vector holding floating point values of type float ► C FVectorBFGSMinimizer Fletcher's implementation of the BFGS method C Status C FVectorExpression C FVectorQuaternionAdapter C FVectorRange C FVectorSlice C FZeroGrid C FZeroMatrix C FZeroVector C FloatFVector2Functor C FloatFVectorFunctor C FloatVector2FArray2Functor C FloatVector2FArrayFunctor C FloatVector3FArray2Functor C FloatVector3FArrayFunctor C LHomogenousCoordsAdapter C LIdentityMatrix C LMatrix An unbounded dense matrix holding signed integers of type long C LMatrixColumn C LMatrixExpression C LMatrixRange C LMatrixRow C LMatrixSlice C LMatrixTranspose C LQuaternion C LQuaternionExpression C LQuaternionVectorAdapter C LRealQuaternion C LRotationMatrix C LScalarMatrix C LScalarVector C LScalingMatrix C LTranslationMatrix C LUnitVector C LVector An unbounded dense vector holding signed integers of type long C LVectorExpression C LVectorQuaternionAdapter C LVectorRange C LVectorSlice C LZeroMatrix C LZeroVector C Lower C Matrix2D A bounded 2x2 matrix holding floating point values of type double C Matrix2F A bounded 2x2 matrix holding floating point values of type float C Matrix2L A bounded 2x2 matrix holding signed integers of type long C Matrix2UL A bounded 2x2 matrix holding unsigned integers of type unsigned long C Matrix3D A bounded 3x3 matrix holding floating point values of type double C Matrix3F A bounded 3x3 matrix holding floating point values of type float C Matrix3L A bounded 3x3 matrix holding signed integers of type long C Matrix3UL A bounded 3x3 matrix holding unsigned integers of type unsigned long C Matrix4D A bounded 4x4 matrix holding floating point values of type double C Matrix4F A bounded 4x4 matrix holding floating point values of type float C Matrix4L A bounded 4x4 matrix holding signed integers of type long C Matrix4UL A bounded 4x4 matrix holding unsigned integers of type unsigned long C Range C Slice C SparseDMatrix An unbounded sparse matrix holding floating point values of type double C SparseDVector An unbounded sparse vector holding floating point values of type double C SparseFMatrix An unbounded sparse matrix holding floating point values of type float C SparseFVector An unbounded sparse vector holding floating point values of type float C SparseLMatrix An unbounded sparse matrix holding signed integers of type long C SparseLVector An unbounded sparse vector holding signed integers of type long C SparseULMatrix An unbounded sparse matrix holding unsigned integers of type unsigned long C SparseULVector An unbounded sparse vector holding unsigned integers of type unsigned long C ULHomogenousCoordsAdapter C ULIdentityMatrix C ULMatrix An unbounded dense matrix holding unsigned integers of type unsigned long C ULMatrixColumn C ULMatrixExpression C ULMatrixRange C ULMatrixRow C ULMatrixSlice C ULMatrixTranspose C ULQuaternion C ULQuaternionExpression C ULQuaternionVectorAdapter C ULRealQuaternion C ULRotationMatrix C ULScalarMatrix C ULScalarVector C ULScalingMatrix C ULTranslationMatrix C ULUnitVector C ULVector An unbounded dense vector holding unsigned integers of type unsigned long C ULVectorExpression C ULVectorQuaternionAdapter C ULVectorRange C ULVectorSlice C ULZeroMatrix C ULZeroVector C UnitLower C UnitUpper C Upper C Vector2D A bounded 2 element vector holding floating point values of type double C Vector2DArray An array of Math.Vector2D objects C Vector2DArrayAlignmentCalculator ► C Vector2DArrayBFGSMinimizer C Status C Vector2F A bounded 2 element vector holding floating point values of type float C Vector2FArray An array of Math.Vector2F objects C Vector2FArrayAlignmentCalculator ► C Vector2FArrayBFGSMinimizer C Status C Vector2L A bounded 2 element vector holding signed integers of type long C Vector2LArray An array of Math.Vector2L objects C Vector2UL A bounded 2 element vector holding unsigned integers of type unsigned long C Vector2ULArray An array of Math.Vector2UL objects C Vector3D A bounded 3 element vector holding floating point values of type double C Vector3DArray An array of Math.Vector3D objects C Vector3DArrayAlignmentCalculator ► C Vector3DArrayBFGSMinimizer C Status C Vector3F A bounded 3 element vector holding floating point values of type float C Vector3FArray An array of Math.Vector3F objects C Vector3FArrayAlignmentCalculator ► C Vector3FArrayBFGSMinimizer C Status C Vector3L A bounded 3 element vector holding signed integers of type long C Vector3LArray An array of Math.Vector3L objects C Vector3UL A bounded 3 element vector holding unsigned integers of type unsigned long C Vector3ULArray An array of Math.Vector3UL objects C Vector4D A bounded 4 element vector holding floating point values of type double C Vector4F A bounded 4 element vector holding floating point values of type float C Vector4L A bounded 4 element vector holding signed integers of type long C Vector4UL A bounded 4 element vector holding unsigned integers of type unsigned long C Vector7D A bounded 7 element vector holding floating point values of type double ► N MolProp Contains classes and functions related to the calculation/preciction of physicochemical molecular properties C AtomHydrophobicityCalculator Implements Greene's algorithm [CATA ] for the calculation of atom hydrophobicities C AtomProperty Provides keys for built-in MolProp.Atom properties C AtomPropertyDefault Provides default values for built-in Chem.Atom properties C BondProperty Provides keys for built-in MolProp.Bond properties C CoordinationGeometry Provides constants used to specify the spatial geometry of atom arrangements around a common central atom C ElementHistogram A data type for the storage of element histograms of chemical compounds C HBondAcceptorAtomType Provides constants used to specify the structural class of H-bond acceptor atoms C HBondAcceptorAtomTyper C HBondDonorAtomType Provides constants used to specify the structural class of H-bond donor atoms C HBondDonorAtomTyper C LogSCalculator LogSCalculator C MHMOPiChargeCalculator MHMOPiChargeCalculator C MassComposition A data type for the storage of mass percent compositions of chemical compounds C PEOESigmaChargeCalculator PEOESigmaChargeCalculator C TPSACalculator TPSACalculator C XLogPCalculator XLogPCalculator ► N Pharm Contains classes and functions related to pharmacophore perception and pharmacophore applications C AromaticFeatureGenerator AromaticFeatureGenerator C BasicFeature BasicFeature C BasicPharmacophore BasicPharmacophore C BoolDoubleFunctor C BoolFeature2Functor C BoolFeature2Matrix4DFunctor C BoolFeature4Functor C BoolFeatureFunctor C BoolSearchHitDoubleFunctor C BoolSizeType2Functor C CDFBZ2FeatureContainerOutputHandler A handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL C CDFBZ2FeatureContainerWriter C CDFBZ2PharmacophoreInputHandler A handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL C CDFBZ2PharmacophoreReader C CDFFeatureContainerOutputHandler A handler for the output of feature container data in the native I/O format of the CDPL C CDFFeatureContainerWriter A writer for feature container data in the native I/O format of the CDPL C CDFGZFeatureContainerOutputHandler A handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL C CDFGZFeatureContainerWriter C CDFGZPharmacophoreInputHandler A handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL C CDFGZPharmacophoreReader C CDFPharmacophoreInputHandler A handler for the input of pharmacophore data in the native I/O format of the CDPL C CDFPharmacophoreReader A reader for pharmacophore data in the native I/O format of the CDPL C CationPiInteractionConstraint CationPiInteractionConstraint C CationPiInteractionScore CationPiInteractionScore C CompoundPharmacophoreReader CompoundDataReader C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters C DataFormat Provides preinitialized Base.DataFormat objects for all supported data formats C DefaultInteractionAnalyzer DefaultInteractionAnalyzer ► C DefaultPharmacophoreGenerator DefaultPharmacophoreGenerator C Configuration Flags controlling feature generation C DoubleDouble2Functor C DoubleDoubleFunctor C DoubleFeature2Functor C DoubleFeature2Matrix4DFunctor C DoubleFeature2UIntFunctor C DoubleFeatureFunctor C DoubleSearchHitFunctor C Feature Feature C Feature3DCoordinatesFunction A generic wrapper class used to store a user-defined Pharm.Feature 3D-coordinates function C FeatureContainer FeatureContainer ► C FeatureContainerIOManager A singleton class that serves as a global registry for Pharm.FeatureContainerInputHandler and Pharm.FeatureContainerOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C FeatureContainerOutputHandler A factory interface providing methods for the creation of Pharm.FeatureContainerWriterBase instances for data output in a particular storage format C FeatureContainerProperty Provides keys for built-in Pharm.FeatureContainer properties C FeatureContainerPropertyDefault Provides default values for built-in Pharm.FeatureContainer properties C FeatureContainerWriter Writer for pharmacophore data in any supported format C FeatureContainerWriterBase An interface for writing data objects of type Pharm.FeatureContainer to an arbitrary data sink C FeatureDistanceConstraint FeatureDistanceConstraint C FeatureDistanceScore FeatureDistanceScore C FeatureGenerator FeatureGenerator C FeatureGeometry Provides constants for the specification of the generic geometry of a pharmacophore feature C FeatureGeometryMatchFunctor FeatureGeometryMatchFunctor C FeatureInteractionScore FeatureInteractionScore C FeatureInteractionScoreCombiner FeatureInteractionScoreCombiner C FeatureMapping A data type for the storage and lookup of arbitrary feature to feature mappings C FeaturePairDistanceMatchFunctor FeaturePairDistanceMatchFunctor C FeaturePositionMatchFunctor FeaturePositionMatchFunctor C FeatureProperty Provides keys for built-in Pharm.Feature properties C FeaturePropertyDefault Provides default values for built-in Pharm.Feature properties C FeatureSet FeatureSet C FeatureType Provides constants for the specification of the generic type of a pharmacophore feature C FeatureTypeHistogram A data type for the storage of feature type histograms of pharmacophores C FeatureTypeMatchFunctor FeatureTypeMatchFunctor C FileCDFBZ2FeatureContainerWriter C FileCDFBZ2PharmacophoreReader C FileCDFFeatureContainerWriter C FileCDFGZFeatureContainerWriter C FileCDFGZPharmacophoreReader C FileCDFPharmacophoreReader C FilePMLFeatureContainerWriter C FilePMLPharmacophoreReader C FileScreeningHitCollector FileScreeningHitCollector C HBondAcceptorFeatureGenerator HBondAcceptorFeatureGenerator C HBondDonorFeatureGenerator HBondDonorFeatureGenerator C HBondingInteractionConstraint HBondingInteractionConstraint C HBondingInteractionScore HBondingInteractionScore C HydrophobicAtomFeatureGenerator HydrophobicAtomFeatureGenerator C HydrophobicFeatureGenerator HydrophobicFeatureGenerator C HydrophobicInteractionConstraint HydrophobicInteractionConstraint C HydrophobicInteractionScore HydrophobicInteractionScore C InteractionAnalyzer InteractionAnalyzer C InteractionConstraintConnector InteractionConstraintConnector C InteractionPharmacophoreGenerator InteractionPharmacophoreGenerator C IonicInteractionConstraint IonicInteractionConstraint C IonicInteractionScore IonicInteractionScore C NegIonizableFeatureGenerator NegIonizableFeatureGenerator C OrthogonalPiPiInteractionConstraint OrthogonalPiPiInteractionConstraint C OrthogonalPiPiInteractionScore OrthogonalPiPiInteractionScore C PMLFeatureContainerOutputHandler A handler for the output of pharmacophore data in the native I/O format of LigandScout C PMLFeatureContainerWriter A writer for feature container data in the native I/O format of LigandScout C PMLPharmacophoreInputHandler A handler for the input of pharmacophore data in the native I/O format of LigandScout C PMLPharmacophoreReader A reader for pharmacophore data in the native I/O format of LigandScout C PSDMolecularGraphOutputHandler A handler for the output of molecular graph dara in the PSD-format of the CDPL C PSDMolecularGraphWriter A writer for molecular graph data in the PSD-format of the CDPL C PSDMoleculeInputHandler A handler for the input of molecule data in the PSD-format of the CDPL C PSDMoleculeReader A reader for molecule data in the PSD-format of the CDPL C PSDPharmacophoreInputHandler A handler for the input of pharmacophore data in the PSD-format of the CDPL C PSDPharmacophoreReader A reader for pharmacophore data in the PSD-format of the CDPL C PSDScreeningDBAccessor A class for accessing pharmacophore screening databases in the built-in optimized format C PSDScreeningDBCreator A class for the creation of optimized pharmacophore screening databases C ParallelPiPiInteractionConstraint ParallelPiPiInteractionConstraint C ParallelPiPiInteractionScore ParallelPiPiInteractionScore ► C PatternBasedFeatureGenerator PatternBasedFeatureGenerator C PatternAtomLabelFlag C Pharmacophore Pharmacophore C PharmacophoreAlignment PharmacophoreAlignment C PharmacophoreFitScore PharmacophoreFitScore C PharmacophoreFitScreeningScore PharmacophoreFitScreeningScore C PharmacophoreGenerator PharmacophoreGenerator ► C PharmacophoreIOManager A singleton class that serves as a global registry for Pharm.PharmacophoreInputHandler and Pharm.PharmacophoreOutputHandler implementation instances C InputHandlerSequence C OutputHandlerSequence C PharmacophoreInputHandler A factory interface providing methods for the creation of Pharm.PharmacophoreReaderBase instances for reading data provided in a particular storage format C PharmacophoreReader Reader for pharmacophore data in any supported format C PharmacophoreReaderBase An interface for reading data objects of type Pharm.Pharmacophore from an arbitrary data source C PosIonizableFeatureGenerator PosIonizableFeatureGenerator C ScreeningDBAccessor A class for accessing the data stored in pharmacophore screening databases ► C ScreeningDBCreator A class for the creation of optimized pharmacophore screening databases C Mode ► C ScreeningProcessor ScreeningProcessor C HitReportMode C SearchHit C SpatialFeatureAlignment C SpatialFeatureMapping SpatialFeatureMapping C TopologicalFeatureAlignment C XBondAcceptorFeatureGenerator XBondAcceptorFeatureGenerator C XBondDonorFeatureGenerator XBondDonorFeatureGenerator C XBondingInteractionConstraint XBondingInteractionConstraint C XBondingInteractionScore XBondingInteractionScore ► N Shape Contains classes and functions related to molecular shape representation and processing C AlignedColorTverskyScore C AlignedShapeTverskyScore C AlignedTotalOverlapTverskyScore C AlignedTverskyComboScore C AlignmentResult C AlignmentResultSelectionMode C BoolAlignmentResult2Functor C BoolSizeType2Functor C BoolSizeTypeFunctor C ColorTanimotoScore C ColorTverskyScore C DoubleAlignmentResultFunctor C ExactGaussianShapeOverlapFunction C FastGaussianShapeAlignment C FastGaussianShapeOverlapFunction ► C GaussianShape A data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions C Element C GaussianShapeAlignment C GaussianShapeAlignmentStartGenerator C GaussianShapeFunction ► C GaussianShapeFunctionAlignment C Result C GaussianShapeGenerator C GaussianShapeOverlapFunction C GaussianShapeSet C PrincipalAxesAlignmentStartGenerator C ReferenceColorTverskyScore C ReferenceShapeTverskyScore C ReferenceTotalOverlapTverskyScore C ReferenceTverskyComboScore C ScreeningProcessor ► C ScreeningSettings C AlignmentMode C ColorFeatureType C ScreeningMode C ShapeTanimotoScore C ShapeTverskyScore C SymmetryClass C TanimotoComboScore C TotalOverlapTanimotoScore C TotalOverlapTverskyScore C TverskyComboScore C Vector7D C VoidMolecularGraph2AlignmentResultFunctor ► N Util Contains general purpose algorithms, containers, functors and other classes C BZip2IOStream C BZip2IStream C BZip2OStream C BitSet A dynamic bitset class C BitSetArray An array of Util.BitSet C BronKerboschAlgorithm Implementation of the Bron-Kerbosch clique-detection algorithm [BKA ] C DArray An array of double precision floating-point numbers ► C DG2DCoordinatesGenerator C DistanceConstraint C DistanceConstraintList ► C DG3DCoordinatesGenerator C DistanceConstraint C DistanceConstraintList C VolumeConstraint C VolumeConstraintList C GZipIOStream C GZipIStream C GZipOStream C LArray An array of unsigned integers of type long C PropertyValue An unary functor that retrieves the value of a given property from the Base.PropertyContainer instance provided as argument C PropertyValueProduct A binary functor that calculates the product of two property values retrieved from a pair of Base.PropertyContainer instances passed as argument C SArray An array of std::string objects C STArray An array of unsigned integers of type std::size_t C STPair A pair of unsigned integers of type std::size_t C STPairArray An array of pairs of unsigned integers of type std::size_t C UIArray An array of unsigned integers ► N Vis Contains classes and functions related to data visualization ► N CairoBackend Contains classes related to the implementation of CDPL.Vis interfaces on top of the Cairo 2D Graphics Library [CAIRO ] C CairoFontMetrics Implements the FontMetrics interface for the Cairo rendering backend C CairoRenderer2D Implements the Renderer2D interface on top of the Cairo 2D Graphics Library ► N QtBackend Contains classes related to the implementation of CDPL.Vis interfaces on top of the Qt Toolkit [QTDOC ] C QtFontMetrics Implements the FontMetrics interface for the Qt rendering backend C QtObjectFactory Provides methods for the creation of QFont, QColor, QPen and QBrush objects from Font , Color , Pen and Brush instances C QtRenderer2D Implements the Renderer2D interface on top of the Qt Toolkit C Alignment Provides flags that are used to specify the 2D alignment of graphical objects within a bounded rectangular area C ArrowStyle Provides constants for the specification of reaction arrow styles in 2D depictions of chemical reactions C AtomColorTable Provides preinitialized color tables for the visualization of atomic properties C AtomProperty Provides keys for built-in Chem.Atom properties C AtomPropertyDefault Provides default values for built-in Vis.Atom properties C BondProperty Provides keys for built-in Chem.Bond properties C BondPropertyDefault Provides default values for built-in Vis.Bond properties ► C Brush Specifies the fill pattern and fill color of shapes C Style Defines constants for supported fill pattern styles C ClipPathPrimitive2D A graphics primitive representing a clipping region in 2D space C Color Specifies a color in terms of its red, green and blue components and an alpha-channel for transparency C ColorTable A container for the storage and lookup of Vis.Color objects that are associated with a numeric identifier C ControlParameter Provides keys for built-in control-parameters C ControlParameterDefault Provides default values for built-in control-parameters C DataFormat Provides preinitialized Base.DataFormat objects for all supported image output formats C EllipsePrimitive2D A graphics primitive representing a ellipse C FilePDFMolecularGraphWriter C FilePDFReactionWriter C FilePNGMolecularGraphWriter C FilePNGReactionWriter C FilePSMolecularGraphWriter C FilePSReactionWriter C FileSVGMolecularGraphWriter C FileSVGReactionWriter C Font Specifies a font for drawing text C FontMetrics An interface class with methods that provide information about the metrics of a font C GraphicsPrimitive2D The abstract base class of all 2D graphics primitives C LayoutDirection Provides constants that are used to specify the main direction of object layouts C LayoutStyle Provides constants that are used to specify the layout of a set of graphical objects C Line2D Specifies a line segment in 2D space C LinePrimitive2D A graphics primitive representing a single line C LineSegmentListPrimitive2D A graphics primitive representing a list of disjoint line segments C MolecularGraphProperty Provides keys for built-in Chem.MolecularGraph properties C MolecularGraphPropertyDefault Provides default values for built-in Chem.MolecularGraph properties C PDFMolecularGraphOutputHandler A handler for the output of 2D depictions of chemical structures in the Portable Document Format (PDF) [WPDF ] C PDFMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Portable Document Format (PDF) [WPDF ] C PDFReactionOutputHandler A handler for the output of 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF ] C PDFReactionWriter Creates 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF ] C PNGMolecularGraphOutputHandler A handler for the output of 2D depictions of chemical structures in the Portable Network Graphics (PNG) [WPNG ] format C PNGMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Portable Network Graphics (PNG) [WPNG ] format C PNGReactionOutputHandler A handler for the output of 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG ] format C PNGReactionWriter Creates 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG ] format C PSMolecularGraphOutputHandler A handler for the output of 2D depictions of chemical structures in the PostScript (PS) [WPS ] format C PSMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the PostScript (PS) [WPS ] format C PSReactionOutputHandler A handler for the output of 2D depictions of chemical reactions in the PostScript (PS) [WPS ] format C PSReactionWriter Creates 2D depictions of chemical reactions in the PostScript (PS) [WPS ] format ► C Path2D Provides a container for painting operations, enabling arbitrary graphical shapes to be constructed and reused C FillRule Specifies which method to use for filling closed shapes described by the Path2D C Path2DConverter Provides an interface for classes that implement the conversion of Vis.Path2D objects into rendering backend specific path descriptions or drawing operations C PathPrimitive2D A graphics primitive representing an arbitrary path in 2D space ► C Pen Specifies how to draw lines and outlines of shapes C CapStyle Defines constants for supported line cap styles C JoinStyle Defines constants for supported line join styles C LineStyle Defines constants for supported line styles C PointArray2D Stores a set of points in 2D space C PointListPrimitive2D A graphics primitive representing a list of points C PolygonPrimitive2D A graphics primitive representing a polygon C PolylinePrimitive2D A graphics primitive representing a set of connected line segments C ReactionProperty Provides keys for built-in Chem.Reaction properties C ReactionPropertyDefault Provides default values for built-in Vis.Reaction properties C ReactionView2D Implements the 2D visualization of chemical reactions C Rectangle2D Specifies an axis aligned rectangular area in 2D space C Renderer2D An interface that provides methods for low level 2D drawing operations C SVGMolecularGraphOutputHandler A handler for the output of 2D depictions of chemical structures in the Scalable Vector Graphics (SVG) [WSVG ] format C SVGMolecularGraphWriter Creates 2D structure diagrams of molecular graphs in the Scalable Vector Graphics (SVG) [WSVG ] format C SVGReactionOutputHandler A handler for the output of 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG ] format C SVGReactionWriter Creates 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG ] format C SizeAdjustment Provides constants that are used to specify the size adjustment policy for graphical objects within a bounded rectangular area C SizeSpecification Specifies the value and type of a size attribute and defines how the value may change during processing steps ► C StructureGridView2D Implements the 2D visualization of multiple chemical structures arranged in a grid C Cell Data structure storing the contents of a grid cell C StructureView2D Implements the 2D visualization of chemical structures C TextBlockPrimitive2D A graphics primitive representing a block of styled text C TextLabelPrimitive2D A graphics primitive representing a text label C View2D The abstract base of classes implementing the 2D visualization of data objects 
1.9.1
