| ▼NCDPL | The namespace of the Chemical Data Processing Library |
| ►NBase | Contains core framework classes and functions |
| CAny | Safe, type checked container for arbitrary data of variable type |
| CBadCast | Thrown to indicate that a cast or conversion from a given source type to a requested target type is not possible |
| CCalculationFailed | Thrown to indicate that some requested calculation has failed |
| CControlParameterContainer | Base class providing methods for the storage and lookup of control-parameter values |
| CControlParameterList | Data structure for the storage and lookup of control-parameter values |
| ►CDataFormat | Provides meta-information about a particular data storage format |
| CFileExtensionSequence | |
| CDataIOBase | Provides infrastructure for the registration of I/O callback functions |
| CException | The root of the CDPL exception hierarchy |
| CFileIOStream | |
| CIOError | Thrown to indicate that an I/O operation has failed because of physical (e.g |
| ►CIOStream | |
| COpenMode | |
| CIStream | |
| CIndexError | Thrown to indicate that an index is out of range |
| CItemNotFound | Thrown to indicate that some requested data item could not be found |
| CLookupKey | Unique lookup key for control-parameter and property values |
| CNullPointerException | Thrown when an operation requires or expects a valid reference but a None reference was provided |
| COStream | |
| COperationFailed | Thrown to indicate that some requested operation has failed (e.g |
| CPropertyContainer | Base class providing methods for the storage and lookup of object properties |
| CRangeError | Thrown to indicate that a value is out of range |
| CSizeError | Thrown to indicate that the size of a (multidimensional) array is not correct |
| CStringIOStream | |
| CValueError | Thrown to indicate errors caused by some invalid value |
| CVoidDataIOBaseFunctor | |
| CVoidFunctor | |
| CVoidLookupKeyAnyFunctor | |
| CVoidLookupKeyFunctor | |
| ►NBiomol | Contains classes and functions related to biological macromolecules |
| CAtomProperty | Provides keys for built-in Chem.Atom properties |
| CAtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CAtomPropertyFlag | Provides flags for the specification of basic Chem.Atom properties |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported biopolymer data formats |
| CFileMMCIFBZ2MolecularGraphWriter | |
| CFileMMCIFBZ2MoleculeReader | |
| CFileMMCIFGZMolecularGraphWriter | |
| CFileMMCIFGZMoleculeReader | |
| CFileMMCIFMolecularGraphWriter | |
| CFileMMCIFMoleculeReader | |
| CFileMMTFBZ2MolecularGraphWriter | |
| CFileMMTFBZ2MoleculeReader | |
| CFileMMTFGZMolecularGraphWriter | |
| CFileMMTFGZMoleculeReader | |
| CFileMMTFMolecularGraphWriter | |
| CFileMMTFMoleculeReader | |
| CFilePDBBZ2MolecularGraphWriter | |
| CFilePDBBZ2MoleculeReader | |
| CFilePDBGZMolecularGraphWriter | |
| CFilePDBGZMoleculeReader | |
| CFilePDBMolecularGraphWriter | |
| CFilePDBMoleculeReader | |
| CHierarchyView | Data structure providing a hierarchical view on biological macromolecules |
| CHierarchyViewChain | Data structure for the representation of biological macromolecule chains |
| CHierarchyViewFragment | Data structure for the representation of a single contiguous fragment of a biological macromolecule chain |
| CHierarchyViewModel | Data structure for the representation of individual biological macromolecule models |
| CHierarchyViewNode | Abstract base class for nodes of the Biomol.HierarchyView tree (models, chains, residues) |
| CMMCIFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| ►CMMCIFData | Data structure for the storage of imported MMCIF data (see [MMCIF]) |
| CCategory | A single mmCIF data category, holding an ordered list of data items (columns) |
| CItem | A single data item (column) of an mmCIF category, holding an ordered list of string values |
| CMMCIFDataProcessingFunction | Generic wrapper class used to store a user-defined function for the processing of Biomol.MMCIFData instances |
| CMMCIFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFGZMoleculeReader | Reader for molecule data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFMolecularGraphWriter | Writer for molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFMoleculeInputHandler | Handler for the input of molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMCIFMoleculeReader | Reader for molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format |
| CMMTFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CMMTFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CMMTFGZMoleculeReader | Reader for molecule data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] format |
| CMMTFMolecularGraphWriter | Writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFMoleculeInputHandler | Handler for the input of molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CMMTFMoleculeReader | Reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] |
| CMolecularGraphPointerStringFunctor | |
| CMolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CMolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CPDBBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| ►CPDBData | Data structure for the storage of data records found in PDB formatted data [PDB] |
| CRecordType | Identifies the type of PDB data record |
| CPDBFormatVersion | Provides constants for the specification of the Brookhaven Protein Data Bank (PDB) [PDB] format version |
| CPDBGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBGZMoleculeReader | Reader for molecule data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBMolecularGraphWriter | Writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBMoleculeInputHandler | Handler for the input of molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| CPDBMoleculeReader | Reader for molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format |
| ►CResidueDictionary | Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules |
| CEntry | A single residue dictionary entry |
| CResidueList | Data structure for the storage of residues extracted from biological macromolecules |
| CResidueType | Provides constants for the specification of the type of a chemical component (residue) |
| ►NChem | Contains classes and functions related to chemistry |
| CANDAtomMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CANDBondMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CANDMolecularGraphMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CANDReactionMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical conjunction (AND) |
| CAmideImidicAcidTautomerization | Implementation of the amide ↔ imidic-acid tautomerization rule |
| CAromaticRingSet | Implements the perception of aromatic rings in a molecular graph |
| CAromaticSSSRSubset | Implements the extraction of the aromatic rings in the SSSR of a molecular graph |
| CAromaticSubstructure | Implements the perception of aromatic atoms and bonds in a molecular graph |
| ►CAtom | Abstract base class representing a chemical atom and its bonded neighborhood |
| CAtomSequence | |
| CBondSequence | |
| CAtom2DCoordinatesCalculator | Generates 2D coordinates for the atoms of a molecular graph using a layout algorithm that combines ring-system templates, chain extension, and substituent placement |
| CAtom3DCoordinatesFunction | Generic wrapper class used to store a user-defined Chem.Atom 3D-coordinates function |
| CAtom3DCoordinatesFunctor | Helper-functor for retrieving the 3D coordinates of an atom (via the Chem.AtomProperty.COORDINATES_3D property) |
| CAtomArray3DCoordinatesFunctor | 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 |
| CAtomBondMapping | Data structure for the common storage of related atom to atom and bond to bond mappings |
| CAtomConfiguration | Provides constants that are used to specify the configuration of stereogenic atoms |
| CAtomConfigurationMatchExpression | Chem.MatchExpression that constrains target atoms by their stereo configuration relative to a query atom |
| CAtomConformer3DCoordinatesFunctor | Helper-functor for retrieving the 3D coordinates of an atom for a specific conformer (via the Chem.AtomProperty.CONFORMER_COORDINATES_3D conformer-array property) |
| CAtomContainer | Common interface for data structures that support a random access to stored Chem.Atom instances |
| ►CAtomDictionary | A global dictionary for the lookup of data associated with the atom types defined in namespace Chem.AtomType |
| CEntry | A single dictionary entry describing the properties of an (atom type, isotope) pair |
| CAtomEnvironmentMatchExpression | Chem.MatchExpression that constrains target atoms by the structural environment encoded as a SMARTS substructure pattern |
| CAtomMapping | Data type for the storage and lookup of arbitrary atom to atom mappings |
| CAtomMatchConstraint | Provides numerical identifiers for built-in Chem.Atom matching constraints |
| CAtomMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CAtomMatchExpressionList | Container for the storage and evaluation of logical match expression lists |
| CAtomMatchExpressionPtrAtomFunctor | |
| CAtomPredicate | Generic wrapper class used to store a user-defined atom predicate |
| CAtomProperty | Provides keys for built-in Chem.Atom properties |
| CAtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CAtomPropertyFlag | Provides flags for the specification of basic Chem.Atom properties |
| CAtomType | Provides constants for the specification of the chemical element or generic type of an atom |
| CAtomTypeMatchExpression | MatchExpression that checks the atom type of a target atom against a query atom type |
| CAutomorphismGroupSearch | Enumerates the atom/bond automorphisms of a molecular graph |
| CBRICSAtomLabel | Provides constants for the labeling of atoms of bonds matched by a BRICS fragmentation rule |
| CBRICSFragmentGenerator | Chem.FragmentGenerator preconfigured with the 16 BRICS bond-cleavage rules and the associated exclude patterns for combinatorial fragmentation of organic molecules |
| CBRICSRuleID | Provides constants for the identification of BRICS fragmentation rules |
| CBasicAtom | Concrete Chem.Atom implementation used as the atom type of Chem.BasicMolecule |
| CBasicBond | Default implementation of the Chem.Bond interface |
| CBasicMolecule | Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances |
| CBasicReaction | Default concrete implementation of the Chem.Reaction abstract interface |
| CBemisMurckoAnalyzer | Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains |
| ►CBond | Abstract base class representing a chemical bond between two Chem.Atom instances |
| CAtomSequence | |
| CBondConfiguration | Provides constants that are used to specify the cis/trans configuration of bonds |
| CBondConfigurationMatchExpression | Chem.MatchExpression that constrains target bonds by their stereo configuration relative to a query bond |
| CBondContainer | Common interface for data structures that support a random access to stored Chem.Bond instances |
| CBondDirection | Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings |
| CBondDirectionMatchExpression | Chem.MatchExpression that constrains target bonds by their SMILES/SMARTS bond direction |
| CBondMapping | Data type for the storage and lookup of arbitrary bond to bond mappings |
| CBondMatchConstraint | Provides numerical identifiers for built-in Chem.Bond matching constraints and flags for the specification of bond orders |
| CBondMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CBondMatchExpressionList | Container for the storage and evaluation of logical match expression lists |
| CBondMatchExpressionPtrBondFunctor | |
| CBondOrderCalculator | Perceives bond orders of a molecular graph from its 3D structure and atom connectivity |
| CBondPredicate | Generic wrapper class used to store a user-defined bond predicate |
| CBondProperty | Provides keys for built-in Chem.Bond properties |
| CBondPropertyDefault | Provides default values for built-in Chem.Bond properties |
| CBondPropertyFlag | Provides flags for the specification of basic Chem.Bond properties |
| CBondReactionCenterStatusMatchExpression | Chem.MatchExpression that constrains target bonds by their reaction-center status (see Chem.ReactionCenterStatus) |
| CBondStereoFlag | Provides constants for the specification of stereo bonds in 2D depictions of chemical structures |
| CBondStereoFlagCalculator | Calculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph |
| CBondSubstituentDirectionMatchExpression | 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) |
| CBoolAtom2Functor | |
| CBoolAtom4Functor | |
| CBoolAtomMappingFunctor | |
| CBoolBond2Functor | |
| CBoolConstMolecularGraphFunctor | |
| CBoolEntity3D2Functor | |
| CBoolEntity3D4Functor | |
| CBoolEntity3DMappingFunctor | |
| CBoolMolecularGraphAtomBondMappingFunctor | |
| CBoolMolecularGraphFunctor | |
| CBoolSTPairArrayFunctor | |
| CCDFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL |
| CCDFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL |
| CCDFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL |
| CCDFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed native I/O format of the CDPL |
| CCDFBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL |
| CCDFBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL |
| CCDFBZ2ReactionReader | Reader for reaction data in the bzip2-compressed native I/O format of the CDPL |
| CCDFBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed native I/O format of the CDPL |
| CCDFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL |
| CCDFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed native I/O format of the CDPL |
| CCDFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL |
| CCDFGZMoleculeReader | Reader for molecule data in the gzip-compressed native I/O format of the CDPL |
| CCDFGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL |
| CCDFGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL |
| CCDFGZReactionReader | Reader for reaction data in the gzip-compressed native I/O format of the CDPL |
| CCDFGZReactionWriter | Writer for reaction data in the gzip-compressed native I/O format of the CDPL |
| CCDFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the native I/O format of the CDPL |
| CCDFMolecularGraphWriter | Writer for molecular graph data in the native I/O format of the CDPL |
| CCDFMoleculeInputHandler | Handler for the input of molecule data in the native I/O format of the CDPL |
| CCDFMoleculeReader | Reader for molecule data in the native I/O format of the CDPL |
| CCDFReactionInputHandler | Handler for the input of reaction data in the native I/O format of the CDPL |
| CCDFReactionOutputHandler | Handler for the output of reaction data in the native I/O format of the CDPL |
| CCDFReactionReader | Reader for reaction data in the native I/O format of the CDPL |
| CCDFReactionWriter | Writer for reaction data in the native I/O format of the CDPL |
| CCIPConfigurationLabeler | Assigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph |
| CCIPDescriptor | Provides constants for the specification of stereogenic atom/bond configurations determined by the Cahn-Ingold-Prelog (CIP) sequence rules |
| CCIPPriorityCalculator | Computes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph |
| CCMLBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format |
| CCMLBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format |
| CCMLBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format |
| CCMLBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format |
| CCMLGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format |
| CCMLGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format |
| CCMLGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format |
| CCMLGZMoleculeReader | Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format |
| CCMLMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Chemical Markup Language [CML] format |
| CCMLMolecularGraphWriter | Writer for molecular graph data in the Chemical Markup Language [CML] format |
| CCMLMoleculeInputHandler | Handler for the input of molecule data in the Chemical Markup Language [CML] format |
| CCMLMoleculeReader | Reader for molecule data in the Chemical Markup Language [CML] format |
| CCanonicalNumberingCalculator | Calculation of canonical atom numberings for molecular graphs using McKay's algorithm |
| ►CChEMBLStandardizer | Implementation of the ChEMBL structure preprocessing pipeline |
| CChangeFlags | Bitwise-OR-combined flags reporting which standardization steps modified the input molecule |
| CCommonConnectedSubstructureSearch | Enumerates all maximal common connected substructures shared between a query and a target molecular graph |
| CCompleteRingSet | Implements the exhaustive perception of rings in a molecular graph |
| CComponentSet | Implements the perception of molecular graph components |
| CCompoundMoleculeReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCompoundReactionReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CConjugatedRingBondPatternSwitching | Chem.TautomerizationRule implementation that enumerates tautomers obtained by switching the single/double bond pattern of conjugated rings (e.g |
| CConnectedSubstructureSet | Enumerates the connected substructures of a molecular graph of a specified bond count |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| CCyclicSubstructure | Implements the perception of ring atoms and bonds in a molecular graph |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported chemical data formats |
| CDefaultMultiConfMoleculeInputProcessor | Default Chem.MultiConfMoleculeInputProcessor implementation that detects multi-conformer input by comparing atom and bond properties (and optionally molecule names) between successive input molecules |
| CDefaultTautomerGenerator | Chem.TautomerGenerator preconfigured with the standard CDPKit tautomerization rules |
| CDoubleAtom2Functor | |
| CDoubleAtom2UInt2Functor | |
| CDoubleAtom2UIntFunctor | |
| CDoubleAtomFunctor | |
| CDoubleDVectorFunctor | |
| CDoubleEntity3D2Functor | |
| CDoubleEntity3DFunctor | |
| CDoubleVector3D2AtomFunctor | |
| CElectronSystem | Describes an electron system of a molecule in terms of involved atoms and their electron contributions |
| CElectronSystemList | Data type for the storage of Chem.ElectronSystem objects |
| CEntity3D | Base class for objects that have a position in 3D space (e.g |
| CEntity3DContainer | Common interface for data structures that support a random access to stored Chem.Entity3D instances |
| CEntity3DMapping | Data type for the storage and lookup of arbitrary entity to entity mappings |
| CEntity3DProperty | Provides keys for built-in Chem.Entity3D properties |
| CExtendedSSSR | Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph |
| CFileCDFBZ2MolecularGraphWriter | |
| CFileCDFBZ2MoleculeReader | |
| CFileCDFBZ2ReactionReader | |
| CFileCDFBZ2ReactionWriter | |
| CFileCDFGZMolecularGraphWriter | |
| CFileCDFGZMoleculeReader | |
| CFileCDFGZReactionReader | |
| CFileCDFGZReactionWriter | |
| CFileCDFMolecularGraphWriter | |
| CFileCDFMoleculeReader | |
| CFileCDFReactionReader | |
| CFileCDFReactionWriter | |
| CFileCMLBZ2MolecularGraphWriter | |
| CFileCMLBZ2MoleculeReader | |
| CFileCMLGZMolecularGraphWriter | |
| CFileCMLGZMoleculeReader | |
| CFileCMLMolecularGraphWriter | |
| CFileCMLMoleculeReader | |
| CFileINCHIMolecularGraphWriter | |
| CFileINCHIMoleculeReader | |
| CFileJMEMolecularGraphWriter | |
| CFileJMEMoleculeReader | |
| CFileJMEReactionReader | |
| CFileJMEReactionWriter | |
| CFileMOL2BZ2MolecularGraphWriter | |
| CFileMOL2BZ2MoleculeReader | |
| CFileMOL2GZMolecularGraphWriter | |
| CFileMOL2GZMoleculeReader | |
| CFileMOL2MolecularGraphWriter | |
| CFileMOL2MoleculeReader | |
| CFileMOLMolecularGraphWriter | |
| CFileMOLMoleculeReader | |
| CFileRDFBZ2ReactionReader | |
| CFileRDFBZ2ReactionWriter | |
| CFileRDFGZReactionReader | |
| CFileRDFGZReactionWriter | |
| CFileRDFReactionReader | |
| CFileRDFReactionWriter | |
| CFileRXNReactionWriter | |
| CFileSDFBZ2MolecularGraphWriter | |
| CFileSDFBZ2MoleculeReader | |
| CFileSDFGZMolecularGraphWriter | |
| CFileSDFGZMoleculeReader | |
| CFileSDFMolecularGraphWriter | |
| CFileSDFMoleculeReader | |
| CFileSMARTSMolecularGraphWriter | |
| CFileSMARTSMoleculeReader | |
| CFileSMARTSReactionReader | |
| CFileSMARTSReactionWriter | |
| CFileSMILESBZ2MolecularGraphWriter | |
| CFileSMILESBZ2MoleculeReader | |
| CFileSMILESBZ2ReactionReader | |
| CFileSMILESBZ2ReactionWriter | |
| CFileSMILESGZMolecularGraphWriter | |
| CFileSMILESGZMoleculeReader | |
| CFileSMILESGZReactionReader | |
| CFileSMILESGZReactionWriter | |
| CFileSMILESMolecularGraphWriter | |
| CFileSMILESMoleculeReader | |
| CFileSMILESReactionReader | |
| CFileSMILESReactionWriter | |
| CFileXYZBZ2MolecularGraphWriter | |
| CFileXYZBZ2MoleculeReader | |
| CFileXYZGZMolecularGraphWriter | |
| CFileXYZGZMoleculeReader | |
| CFileXYZMolecularGraphWriter | |
| CFileXYZMoleculeReader | |
| ►CFragment | Concrete Chem.MolecularGraph implementation that stores references to a selectable subset of atoms and bonds (typically of a parent Chem.Molecule) |
| CAtomSequence | |
| CBondSequence | |
| ►CFragmentGenerator | Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules |
| CExcludePattern | A pattern descriptor specifying bonds that shall not be cleaved |
| CFragmentationRule | A single fragmentation rule, consisting of a bond substructure match pattern and a numeric rule ID |
| CFragmentLink | Records the connectivity between two fragments produced by a single bond cleavage |
| CFragmentList | Data type for the storage of Chem.Fragment objects |
| CGenericHydrogen13ShiftTautomerization | 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) |
| CGenericHydrogen15ShiftTautomerization | 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) |
| ►CHashCodeCalculator | Computes a 64-bit hash code that identifies a molecular graph up to a configurable set of atom and bond properties |
| CDefAtomHashSeedFunctor | The default functor for the generation of atom hash seeds |
| CDefBondHashSeedFunctor | The default functor for the generation of bond hash seeds |
| CHybridizationState | Provides constants for the specification of atom hybridization states |
| CHydrogen3DCoordinatesCalculator | Generates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors |
| CINCHIMolecularGraphOutputHandler | Handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CINCHIMolecularGraphWriter | Writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CINCHIMoleculeInputHandler | Handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CINCHIMoleculeReader | Reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format |
| CINCHIReturnCode | Provides constants that are used to describe the status of an InChI [INCHI] output or input operation |
| CImineEnamineTautomerization | Chem.TautomerizationRule implementation that enumerates the imine/enamine tautomers of an \( R_2C=N{-}CHR_2 \rightleftharpoons R_2CH{-}N=CR_2 \) system |
| CJMEMolecularGraphOutputHandler | Handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEMolecularGraphWriter | Writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEMoleculeInputHandler | Handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEMoleculeReader | Reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEReactionInputHandler | Handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEReactionOutputHandler | Handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEReactionReader | Reader for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CJMEReactionWriter | Writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet |
| CKekuleStructureCalculator | 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) |
| CKeteneYnolTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates ketene/ynol tautomers (Chem.TautomerizationType.KETENE_YNOL) |
| CKetoEnolTautomerization | Chem.TautomerizationRule implementation that enumerates the keto/enol tautomers of an \( R_2C{-}C(=O)R' \rightleftharpoons RC=C(OH)R' \) system |
| CLactamLactimTautomerization | Chem.TautomerizationRule implementation that enumerates the lactam/lactim tautomers of a cyclic amide \( {-}NH{-}C(=O){-} \rightleftharpoons {-}N=C(OH){-} \) system |
| CMDLDataFormatVersion | 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 |
| CMDLParity | Provides constants that are used to specify the MDL stereo parity of atoms |
| CMOL2BZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format |
| CMOL2BZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format |
| CMOL2BZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format |
| CMOL2BZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Sybyl MOL2 format |
| CMOL2ChargeType | Provides constants for the specification of the atom charge type in Sybyl MOL2 files |
| CMOL2GZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format |
| CMOL2GZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format |
| CMOL2GZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format |
| CMOL2GZMoleculeReader | Reader for molecule data in the gzip-compressed Sybyl MOL2 format |
| CMOL2MolecularGraphOutputHandler | Handler for the output of molecular graph data in the Sybyl MOL2 format |
| CMOL2MolecularGraphWriter | Writer for molecular graph data in the Sybyl MOL2 format |
| CMOL2MoleculeInputHandler | Handler for the input of molecule data in the Sybyl MOL2 format |
| CMOL2MoleculeReader | Reader for molecule data in the Sybyl MOL2 format |
| CMOL2MoleculeType | Provides constants for the specification of the molecule type in Sybyl MOL2 files |
| CMOLMolecularGraphOutputHandler | Handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format |
| CMOLMolecularGraphWriter | Writer for molecular graph data in the MDL Mol-File [CTFILE] format |
| CMOLMoleculeInputHandler | Handler for the input of molecule data in the MDL Mol-File [CTFILE] format |
| CMOLMoleculeReader | Reader for molecule data in the MDL Mol-File [CTFILE] format |
| ►CMatchConstraint | Describes a single attribute-comparison constraint between a query and a target object used by molecular graph matching algorithms |
| CRelation | Defines constants for the specification of relational constraints on the values of query/target attribute pairs |
| ►CMatchConstraintList | 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 |
| CType | Defines constants that describe the logical type of the match constraint list |
| CMaxCommonAtomSubstructureSearch | 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 |
| CMaxCommonBondSubstructureSearch | 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 |
| CMolGraphMatchExpressionPtrMolGraphFunctor | |
| ►CMolecularGraph | Abstract base class for representations of a chemical structure as a graph of bonded atoms |
| CAtomSequence | |
| CBondSequence | |
| CMolecularGraphComponentGroupingMatchExpression | 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) |
| ►CMolecularGraphIOManager | Singleton class that serves as a global registry for Chem.MolecularGraphInputHandler and Chem.MolecularGraphOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CMolecularGraphInputHandler | |
| CMolecularGraphMatchConstraint | Provides numerical identifiers for built-in Chem.MolecularGraph matching constraints |
| CMolecularGraphMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CMolecularGraphMatchExpressionList | |
| CMolecularGraphOutputHandler | Factory interface providing methods for the creation of Chem.MolecularGraphWriterBase instances for data output in a particular storage format |
| CMolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CMolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CMolecularGraphWriter | Writer for molecule data in any supported format |
| CMolecularGraphWriterBase | Interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink |
| ►CMolecule | Abstract base class representing a mutable molecular graph that owns its atoms and bonds |
| CAtomSequence | |
| CBondSequence | |
| ►CMoleculeIOManager | Singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CMoleculeInputHandler | Factory interface providing methods for the creation of Chem.MoleculeReaderBase instances for reading data provided in a particular storage format |
| CMoleculeOutputHandler | |
| CMoleculeReader | Reader for molecule data in any supported format |
| CMoleculeReaderBase | Interface for reading data objects of type Chem.Molecule from an arbitrary data source |
| CMorganNumberingCalculator | Computes a canonical atom numbering of a molecular graph using a modified Morgan algorithm |
| CMultiConfMoleculeInputProcessor | Abstract base interface for processors that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules |
| CMultiSubstructureSearch | Evaluates a boolean expression over multiple substructure queries against a target molecular graph |
| CNOTAtomMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CNOTBondMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CNOTMolecularGraphMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CNOTReactionMatchExpression | Chem.MatchExpression decorator that negates the result of a wrapped Chem.MatchExpression instance |
| CNitroAciTautomerization | Implementation of the nitro ↔ aci-nitro tautomerization rule |
| CNitrosoOximeTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates nitroso/oxime tautomers (Chem.TautomerizationType.NITROSO_OXIME) |
| CORAtomMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CORBondMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CORMolecularGraphMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| CORReactionMatchExpressionList | Chem.MatchExpressionList specialization that evaluates the stored expressions as a logical disjunction (OR) |
| ►CPatternAtomTyper | Assigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns |
| CPattern | Stores a single substructure query molecular graph, its atom label value, its priority and match-handling flags |
| ►CPatternBasedTautomerizationRule | Match pattern-based implementation of the Chem.TautomerizationRule interface |
| CBondOrderChange | Encodes a single bond order change between two pattern atoms applied when the parent transformation pattern matches |
| CPhosphinicAcidTautomerization | Chem.PatternBasedTautomerizationRule implementation that enumerates phosphinic-acid tautomers (Chem.TautomerizationType.PHOSPHINIC_ACID) |
| CPiElectronSystemList | Implements the perception of all π-electron systems present in a molecule |
| ►CProtonationStateStandardizer | Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives |
| CFlavor | Selects the objective driving the protonation-state adjustment |
| CRDFBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format |
| CRDFBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format |
| CRDFBZ2ReactionReader | Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format |
| CRDFBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format |
| CRDFGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format |
| CRDFGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format |
| CRDFGZReactionReader | Reader for reaction data in the gzip-compressed MDL RD-File [CTFILE] format |
| CRDFGZReactionWriter | Writer for reaction data in the gzip-compressed MDL RD-File [CTFILE] format |
| CRDFReactionInputHandler | Handler for the input of reaction data in the MDL RD-File [CTFILE] format |
| CRDFReactionOutputHandler | Handler for the output of reaction data in the MDL RD-File [CTFILE] format |
| CRDFReactionReader | Reader for reaction data in the MDL RD-File [CTFILE] format |
| CRDFReactionWriter | Writer for reaction data in the MDL RD-File [CTFILE] format |
| CRECAPAtomLabel | Provides constants for the labeling of atoms of bonds matched by a RECAP fragmentation rule |
| CRECAPFragmentGenerator | Chem.FragmentGenerator implementation applying the RECAP [RECAP] cleavage rules (see Chem.RECAPRuleID) to produce a set of fragment building blocks from a molecular graph |
| CRECAPRuleID | Provides constants for the identification of RECAP fragmentation rules |
| CRXNReactionInputHandler | Handler for the input of reaction data in the MDL Rxn-File [CTFILE] format |
| CRXNReactionOutputHandler | Handler for the output of reaction data in the MDL Rxn-File [CTFILE] format |
| CRXNReactionReader | Reader for reaction data in the MDL Rxn-File [CTFILE] format |
| CRXNReactionWriter | Writer for reaction data in the MDL Rxn-File [CTFILE] format |
| CRadicalType | Provides constants that are used to specify the degeneracy of the electronic state of radical atoms |
| ►CReaction | Abstract base class for chemical reactions composed of role-tagged Chem.Molecule components |
| CComponentSequence | |
| CReactionAtomMappingMatchExpression | Chem.MatchExpression that constrains reaction substructure matches by a required reactant-to-product atom mapping |
| CReactionCenterStatus | Provides flags that are used to describe state changes of atoms and bonds in a reaction center |
| CReactionComponentGroupingMatchExpression | 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) |
| ►CReactionIOManager | Singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CReactionInputHandler | Factory interface providing methods for the creation of Chem.ReactionReaderBase instances for reading data provided in a particular storage format |
| CReactionMatchConstraint | Provides numerical identifiers for built-in Chem.Reaction matching constraints |
| CReactionMatchExpression | Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms |
| CReactionMatchExpressionList | |
| CReactionOutputHandler | Factory interface providing methods for the creation of Chem.ReactionWriterBase instances for data output in a particular storage format |
| CReactionProperty | Provides keys for built-in Chem.Reaction properties |
| CReactionPropertyDefault | Provides default values for built-in Chem.Reaction properties |
| CReactionReader | Reader for reaction data in any supported format |
| CReactionReaderBase | Interface for reading data objects of type Chem.Reaction from an arbitrary data source |
| CReactionRole | Provides constants that are used to specify the role of molecules (components) in a chemical reaction |
| CReactionSubstructureSearch | Reaction-level analogue of Chem.SubstructureSearch that locates atom/bond mappings of a query reaction pattern in a target reaction |
| CReactionWriter | Writer for reaction data in any supported format |
| CReactionWriterBase | Interface for writing data objects of type Chem.Reaction to an arbitrary data sink |
| CReactor | Applies a Chem.Reaction template to the reactant components of a target Chem.Reaction to generate the corresponding product molecules |
| ►CResonanceStructureGenerator | Enumerates the resonance structures of a molecular graph by redistributing π-electrons across the resonance-active bonds |
| CStructureData | Holds the per-atom formal charges and per-bond orders that define a single resonance structure |
| CSDFBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format |
| CSDFBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format |
| CSDFBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format |
| CSDFBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format |
| CSDFGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format |
| CSDFGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format |
| CSDFGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format |
| CSDFGZMoleculeReader | Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format |
| CSDFMolecularGraphOutputHandler | Handler for the output of molecular graph data in the MDL SD-File [CTFILE] format |
| CSDFMolecularGraphWriter | Writer for molecular graph data in the MDL SD-File [CTFILE] format |
| CSDFMoleculeInputHandler | Handler for the input of molecule data in the MDL SD-File [CTFILE] format |
| CSDFMoleculeReader | Reader for molecule data in the MDL SD-File [CTFILE] format |
| CSMARTSMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format |
| CSMARTSMolecularGraphWriter | Writer for molecular graph data in the Daylight SMARTS [SMARTS] format |
| CSMARTSMoleculeInputHandler | Handler for the input of molecule data in the Daylight SMARTS [SMARTS] format |
| CSMARTSMoleculeReader | Reader for molecule data in the Daylight SMARTS [SMARTS] format |
| CSMARTSReactionInputHandler | Handler for the input of reaction data in the Daylight SMARTS [SMARTS] format |
| CSMARTSReactionOutputHandler | Handler for the output of reaction data in the Daylight SMARTS [SMARTS] format |
| CSMARTSReactionReader | Reader for reaction data in the Daylight SMARTS [SMARTS] format |
| CSMARTSReactionWriter | Writer for reaction data in the Daylight SMARTS [SMARTS] format |
| CSMILESBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format |
| CSMILESBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CSMILESBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format |
| CSMILESBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CSMILESBZ2ReactionInputHandler | Handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format |
| CSMILESBZ2ReactionOutputHandler | Handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format |
| CSMILESBZ2ReactionReader | Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CSMILESBZ2ReactionWriter | Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format |
| CSMILESGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format |
| CSMILESGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format |
| CSMILESGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format |
| CSMILESGZMoleculeReader | Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format |
| CSMILESGZReactionInputHandler | Handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format |
| CSMILESGZReactionOutputHandler | Handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format |
| CSMILESGZReactionReader | Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format |
| CSMILESGZReactionWriter | Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format |
| CSMILESMolecularGraphOutputHandler | Handler for the output of molecular graph data in the Daylight SMILES [SMILES] format |
| CSMILESMolecularGraphWriter | Writer for molecular graph data in the Daylight SMILES [SMILES] format |
| CSMILESMoleculeInputHandler | Handler for the input of molecule data in the Daylight SMILES [SMILES] format |
| CSMILESMoleculeReader | Reader for molecule data in the Daylight SMILES [SMILES] format |
| CSMILESReactionInputHandler | Handler for the input of reaction data in the Daylight SMILES [SMILES] format |
| CSMILESReactionOutputHandler | Handler for the output of reaction data in the Daylight SMILES [SMILES] format |
| CSMILESReactionReader | Reader for reaction data in the Daylight SMILES [SMILES] format |
| CSMILESReactionWriter | Writer for reaction data in the Daylight SMILES [SMILES] format |
| CSizeTypeAtomFunctor | |
| CSizeTypeAtomMolecularGraphFunctor | |
| CSmallestSetOfSmallestRings | Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs |
| CSpatialAtomAlignment | |
| CSpatialEntity3DAlignment | |
| ►CStereoDescriptor | Data structure for the storage and retrieval of stereochemical information about atoms and bonds |
| CReferenceAtomArray | |
| ►CStereoisomerGenerator | Enumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters |
| CStereoDescriptorArray | Array of StereoDescriptor values (one per atom or one per bond of the input molecular graph) |
| CStringDataBlock | Array of Chem.StringDataBlockEntry objects |
| CStringDataBlockEntry | Represents a data item consisting of a header and a data payload |
| CSubstructureEditor | 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 |
| ►CSubstructureHistogramCalculator | Counts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container |
| CPattern | Stores a single substructure query molecular graph, its histogram ID, its priority and match-handling flags |
| CSubstructureSearch | Subgraph-isomorphism search of a query molecular graph against a target molecular graph, implemented after the VF2 algorithm |
| CSulfenicAcidTautomerization | Chem.TautomerizationRule implementation that enumerates the sulfenic-acid tautomers of an \( R{-}S{-}OH \rightleftharpoons R{-}S(=O)H \) system |
| CSurfaceAtomExtractor | Extracts the solvent-accessible surface atoms of a set of atoms |
| CSybylAtomType | Provides constants for the specification of the Tripos Sybyl atom type |
| CSybylBondType | Provides constants for the specification of the Tripos Sybyl bond type |
| CSymmetryClassCalculator | Perceives topological-symmetry classes of the atoms in a molecular graph |
| ►CTautomerGenerator | 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 |
| CMode | Constants specifying the output tautomer filtering strategy |
| CTautomerScore | Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph |
| CTautomerizationRule | Abstract base class for all tautomerization rule implementations used by the Chem.TautomerGenerator |
| CTautomerizationType | Provides constants serving as identifiers for built-in Chem.TautomerizationRule implementations |
| CTopologicalAtomAlignment | |
| CTopologicalEntity3DAlignment | |
| CUInt64AtomFunctor | |
| CUInt64AtomMolecularGraphFunctor | |
| CUInt64BondFunctor | |
| CVector2DAtomFunctor | |
| CVector3DEntity3DFunctor | |
| CVoidMolecularGraphFunctor | |
| CVoidMoleculeMolecularGraphFunctor | |
| CXYZBZ2MolecularGraphOutputHandler | Handler for the output of bzip2-compressed molecular graph data in the XYZ format |
| CXYZBZ2MolecularGraphWriter | Writer for molecular graph data in the bzip2-compressed XYZ format |
| CXYZBZ2MoleculeInputHandler | Handler for the input of bzip2-compressed molecule data in the XYZ format |
| CXYZBZ2MoleculeReader | Reader for molecule data in the bzip2-compressed XYZ format |
| CXYZGZMolecularGraphOutputHandler | Handler for the output of gzip-compressed molecular graph data in the XYZ format |
| CXYZGZMolecularGraphWriter | Writer for molecular graph data in the gzip-compressed XYZ format |
| CXYZGZMoleculeInputHandler | Handler for the input of gzip-compressed molecule data in the XYZ format |
| CXYZGZMoleculeReader | Reader for molecule data in the gzip-compressed XYZ format |
| CXYZMolecularGraphOutputHandler | Handler for the output of molecular graph data in the XYZ format |
| CXYZMolecularGraphWriter | Writer for molecular graph data in XYZ format to an output stream |
| CXYZMoleculeInputHandler | Handler for the input of molecule data in the XYZ format |
| CXYZMoleculeReader | Reader for molecule data in XYZ format from an input stream |
| ►NConfGen | Contains classes and functions related to conformer ensemble generation |
| CCFLMoleculeInputHandler | Handler for the input of molecule fragments stored in the CDPL Conformer Generator Fragment Library (CFL) format |
| CCFLMoleculeReader | Reader for molecule fragment data stored in the CDPL Conformer Generator Fragment Library (CFL) format |
| CCallbackFunction | Generic wrapper for storing user-defined callback functions returning a bool status flag (see [FUNWRP]) |
| ►CCanonicalFragment | Data structure representing a canonicalized molecular fragment |
| CAtomMapping | Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph |
| CConformerData | Container for the 3D coordinates of a generated conformer plus its associated energy value |
| CConformerGenerator | High-level driver for the generation of low-energy conformer ensembles of molecular graphs |
| CConformerGeneratorSettings | Bundle of configuration parameters for conformer ensemble generation via class ConfGen.ConformerGenerator |
| CConformerSamplingMode | Provides constants used to specify the employed conformer sampling method |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| ►CDGConstraintGenerator | Constructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation |
| CStereoCenterData | Pair holding an atom or bond index plus the associated stereo descriptor |
| CDGConstraintGeneratorSettings | Bundle of configuration parameters for distance-geometry constraint generation via class ConfGen.DGConstraintGenerator |
| CDGStructureGenerator | Distance-geometry-based generation of raw 3D structures for molecular graphs |
| CDGStructureGeneratorSettings | Bundle of configuration parameters for raw coordinates generation via class ConfGen.DGStructureGenerator |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CFileCFLMoleculeReader | |
| CForceFieldType | Provides constants used to specify the forcefield that shall be used for 3D coordinates refinement and energy calculations |
| CFragmentAssembler | Driver for the fragment-based generation of 3D starting conformers |
| CFragmentAssemblerSettings | Bundle of configuration parameters for fragment conformer assembly via class ConfGen.FragmentAssembler |
| CFragmentConformerGenerator | Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle) |
| ►CFragmentConformerGeneratorSettings | Bundle of configuration parameters for fragment conformer ensemble generation via class ConfGen.FragmentConformerGenerator |
| CFragmentSettings | Per-fragment-class settings (separate parameters for chain, small ring system and macrocycle fragments) |
| CFragmentLibrary | Data structure representing a library of pre-generated molecular fragment conformer ensembles |
| CFragmentLibraryEntry | Data structure representing a single entry of a conformer generation fragment library |
| CFragmentLibraryGenerator | Driver for populating a ConfGen.FragmentLibrary with conformers of canonicalized molecular fragments |
| CFragmentType | Provides constants that are used to describe the nature of fragments used to build-up molecule 3D models |
| CLogMessageCallbackFunction | Generic wrapper for storing user-defined log message callback functions (see [FUNWRP]) |
| CNitrogenEnumerationMode | Provides constants for specifying the mode of invertible nitrogen enumeration |
| CRMSDConformerSelector | Greedy RMSD-based conformer-diversity filter |
| CReturnCode | Provides constants that are used to describe the result of operations related to conformer generation |
| CStructureGenerationMode | Provides constants used to specify the 3D structure generation method that shall be employed |
| CStructureGenerator | High-level driver for the generation of a single low-energy 3D structure from a molecular graph |
| CStructureGeneratorSettings | Bundle of configuration parameters for single 3D structure generation via class ConfGen.StructureGenerator |
| ►CTorsionCategory | Represents a node of a hierarchical torsion library |
| CCategorySequence | |
| CRuleSequence | |
| CTorsionDriver | 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 |
| CTorsionDriverSettings | Bundle of configuration parameters for systematic conformer enumeration via class ConfGen.TorsionDriver |
| CTorsionLibrary | Data structure representing a hierarchical library of torsion rules organized into categories |
| ►CTorsionRule | Data structure for the representation of single torsion library rules |
| CAngleEntry | One preferred torsion angle for a rule, characterized by its value, the two tolerance bands and a score |
| ►CTorsionRuleMatch | A single match of a ConfGen.TorsionRule against a rotatable bond: the rule, the bond and the four atoms that span the torsion |
| CAtomArray | |
| CTorsionRuleMatcher | Finds torsion rules from a ConfGen.TorsionLibrary instance that match a given rotatable bond |
| ►NDescr | Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors |
| CAtomAutoCorrelation3DVectorCalculator | AutoCorrelation3DVectorCalculator implementation for the calculation of atom-centered 3D auto-correlation vectors of chemical structures |
| CAtomRDFCodeCalculator | RDFCodeCalculator implementation for the calculation of atom-centered radial distribution function (RDF) codes of chemical structures |
| CAutoCorrelation2DVectorCalculator | Calculation of the topological (2D) auto-correlation vector of a molecular graph |
| CBCUTDescriptorCalculator | Calculation of the BCUT (Burden-CAS-University-of-Texas) descriptor of a molecular graph |
| CBitSetBulkSimilarityCalculator | |
| CBurdenMatrixGenerator | Calculation of the Burden matrix of a molecular graph |
| ►CCircularFingerprintGenerator | Generation of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP) |
| CDefAtomIdentifierFunctor | The functor for the generation of ECFP atom identifiers |
| CDefBondIdentifierFunctor | The default functor for the generation of bond identifiers |
| CCosineSimilarity | Functor class for calculating Cosine Similarities [WCOS] of bitsets and vectors |
| CDVectorBulkSimilarityCalculator | |
| CDiceSimilarity | Functor class for calculating the Dice Similarity [GSIM] of bitsets |
| CDoubleBitSet2Functor | |
| CDoubleDVector2Functor | |
| CDoubleFVector2Functor | |
| CDoubleLVector2Functor | |
| CDoubleULVector2Functor | |
| CEuclideanDistance | Functor class for calculating the Euclidean Distance [CITB] between bitsets and vectors |
| CEuclideanSimilarity | Functor class for calculating the Euclidean Similarity [GSIM] of bitsets |
| CFVectorBulkSimilarityCalculator | |
| CFeatureAutoCorrelation3DVectorCalculator | AutoCorrelation3DVectorCalculator specialization for feature-centered 3D auto-correlation vectors of pharmacophores |
| CFeatureRDFCodeCalculator | RDFCodeCalculator implementation for the calculation of feature-centered radial distribution function (RDF) codes of pharmacophores |
| CHammingDistance | Functor class for calculating the Hamming Distance [WHAM, CITB] between bitsets |
| CKuvekPocketDescriptorCalculator | Implements the algorithm devised by Kuvek et al |
| CLVectorBulkSimilarityCalculator | |
| CMACCSFingerprintGenerator | Generation of 166 bit MACCS key fingerprints |
| CManhattanDistance | Functor class for calculating the Manhattan Distance [MADI] between bitsets and vectors |
| CManhattanSimilarity | Functor class for calculating the Manhattan Similarity [GSIM] of bitsets |
| CMolecularComplexityCalculator | Calculation of the molecular complexity of a molecular graph after Hendrickson, Huang and Toczko |
| ►CMoleculeAutoCorr2DDescriptorCalculator | Calculation of a topological (2D) auto-correlation descriptor of a molecular graph partitioned by specific atom types |
| CMode | Specifies how the descriptor is partitioned by atom types |
| CMoleculeAutoCorr3DDescriptorCalculator | Calculation of a 3D auto-correlation descriptor of a molecular graph partitioned by specific atom types |
| CMoleculeRDFDescriptorCalculator | Calculation of an RDF descriptor of a molecular graph partitioned by specific atom types |
| ►CNPoint2DPharmacophoreFingerprintGenerator | N-point pharmacophore fingerprint generator that uses topological feature distances |
| CFeatureDistanceType | Specifies how the topological distance between two features is derived from the topological distances between their underlying atoms |
| CNPoint3DPharmacophoreFingerprintGenerator | N-point pharmacophore fingerprint generator that uses spatial 3D feature distances |
| CNPointPharmacophoreFingerprintGenerator | Abstract base for N-point pharmacophore fingerprint generators |
| ►CPathFingerprintGenerator | Generation of Daylight-style path fingerprints of molecular graphs |
| CDefAtomDescriptorFunctor | The default functor for the generation of atom descriptors |
| CDefBondDescriptorFunctor | The default functor for the generation of bond descriptors |
| CPharmacophoreAutoCorr3DDescriptorCalculator | Calculation of a 3D auto-correlation descriptor of a pharmacophore partitioned by specific feature types |
| CPharmacophoreRDFDescriptorCalculator | Calculation of an RDF descriptor of a pharmacophore partitioned by specific feature types |
| CPubChemFingerprintGenerator | Generation of 881 bit PubChem fingerprints |
| CTanimotoSimilarity | Functor class for calculating Tanimoto Similarities [CITB] of bitsets and vectors |
| CTverskySimilarity | Functor class for calculating the Tversky Similarity [GSIM] of bitsets |
| CULVectorBulkSimilarityCalculator | |
| ►NForceField | Contains classes and functions related to molecular force fields |
| CAtomProperty | Provides keys for built-in Chem.Atom properties |
| CBondProperty | Provides keys for built-in Chem.Bond properties |
| CElasticPotential | Stores parameters for an elastic potential (harmonic distance restraint) between a pair of atoms |
| CElasticPotentialList | Data structure for the storage of elastic potential parameter set records |
| CError | Base class of the ForceField subsystem exception hierarchy |
| CInteractionFilterFunction3 | Generic wrapper for storing user-defined three-atom interaction filtering functions (see [FUNWRP]) |
| CInteractionFilterFunction4 | Generic wrapper for storing user-defined four-atom interaction filtering functions (see [FUNWRP]) |
| CInteractionType | Provides flags for the specification of a set of force field interaction types |
| CMMFF94AngleBendingInteraction | Stores parameters for a single MMFF94 angle-bending interaction defined over an atom triplet |
| CMMFF94AngleBendingInteractionList | Data structure for the storage of MMFF94 angle-bending interaction parameter records |
| CMMFF94AngleBendingInteractionParameterizer | Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph |
| ►CMMFF94AngleBendingParameterTable | Data structure for the storage and lookup of MMFF94 angle-bending interaction parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| ►CMMFF94AromaticAtomTypeDefinitionTable | Data structure for the storage and lookup of MMFF94 aromatic atom type definitions |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94AromaticSSSRSubset | Implements the extraction of all rings in the SSSR of a molecular graph that are considered aromatic according to the MMFF94 aromaticity model |
| CMMFF94AtomChargeFunction | Generic wrapper class used to store a user-defined MMFF94 partial atom charge retrieval function |
| ►CMMFF94AtomTypePropertyTable | Data structure for the storage and lookup of structural and chemical property data associated with numeric MMFF94 atom types |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94AtomTyper | Assigns MMFF94 symbolic and numeric atom types to the atoms of a molecular graph |
| ►CMMFF94BondChargeIncrementTable | Data structure for the storage and lookup of MMFF94 bond charge increments |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94BondStretchingInteraction | Stores parameters for a single MMFF94 bond-stretching interaction between two bonded atoms |
| CMMFF94BondStretchingInteractionList | Data structure for the storage of MMFF94 bond-stretching interaction parameter records |
| CMMFF94BondStretchingInteractionParameterizer | Detects and parameterizes the MMFF94 bond-stretching interactions of a molecular graph |
| ►CMMFF94BondStretchingParameterTable | Data structure for the storage and lookup of MMFF94 bond-stretching interaction parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| ►CMMFF94BondStretchingRuleParameterTable | Data structure for the storage and lookup of MMFF94 bond-stretching interaction fallback parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94BondTypeIndexFunction | Generic wrapper class used to store a user-defined MMFF94 bond type index retrieval function |
| CMMFF94BondTyper | Assigns MMFF94 bond type indices to the bonds of a molecular graph |
| CMMFF94ChargeCalculator | Calculator for the MMFF94 partial atomic charges of a molecular graph |
| ►CMMFF94DefaultStretchBendParameterTable | Data structure for the storage and lookup of MMFF94 stretch-bend interaction fallback parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94ElectrostaticInteraction | Stores parameters for a single MMFF94 electrostatic interaction between two non-bonded atoms |
| CMMFF94ElectrostaticInteractionList | Data structure for the storage of MMFF94 electrostatic interaction parameter records |
| CMMFF94ElectrostaticInteractionParameterizer | Detects and parameterizes the MMFF94 electrostatic interactions of a molecular graph |
| CMMFF94EnergyCalculator | Calculates the total MMFF94 force field energy for a set of atom 3D coordinates |
| ►CMMFF94FormalAtomChargeDefinitionTable | Data structure for the storage and lookup of formal charge definitions used by the MMFF94 charge model |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94GradientCalculator | Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates |
| ►CMMFF94HeavyToHydrogenAtomTypeMap | Data structure for the storage and lookup of heavy-to-hydrogen symbolic MMFF94 atom type mappings |
| CEntry | The type of the map entries |
| CMMFF94InteractionData | Container holding the full set of MMFF94 interaction parameter records for a molecular graph |
| CMMFF94InteractionParameterizer | Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization |
| CMMFF94NumericAtomTypeFunction | Generic wrapper class used to store a user-defined numeric MMFF94 atom type retrieval function |
| CMMFF94OutOfPlaneBendingInteraction | Stores parameters for a single MMFF94 out-of-plane bending interaction at a trigonal center |
| CMMFF94OutOfPlaneBendingInteractionList | Data structure for the storage of MMFF94 out-of-plane bending interaction parameter records |
| CMMFF94OutOfPlaneBendingInteractionParameterizer | Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph |
| ►CMMFF94OutOfPlaneBendingParameterTable | Data structure for the storage and lookup of MMFF94 out-of-plane bending interaction force constants |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94ParameterSet | Provides constants for the specification of a MMFF94 parameter set variant |
| ►CMMFF94PartialBondChargeIncrementTable | Data structure for the storage and lookup of MMFF94 per-atom partial bond charge increment and formal charge adjustment factors |
| CEntry | Data structure for the storage of values associated with a single table entry |
| ►CMMFF94PrimaryToParameterAtomTypeMap | Data structure for the storage and lookup of primary numeric MMFF94 atom type to fallback parameter atom type list mappings |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94RingSetFunction | Generic wrapper class used to store a user-defined MMFF94 ring set retrieval function |
| CMMFF94StretchBendInteraction | Stores paramters for a single MMFF94 stretch-bend coupling interaction |
| CMMFF94StretchBendInteractionList | Data structure for the storage of MMFF94 stretch-bend coupling interaction parameter records |
| CMMFF94StretchBendInteractionParameterizer | Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph |
| ►CMMFF94StretchBendParameterTable | Data structure for the storage and lookup of MMFF94 stretch-bend interaction parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94SymbolicAtomTypeFunction | Generic wrapper class used to store a user-defined symbolic MMFF94 atom type retrieval function |
| ►CMMFF94SymbolicAtomTypePatternTable | Data structure storing SMARTS substructure patterns used to assign symbolic MMFF94 atom types during atom typing |
| CEntry | A single atom type pattern record |
| ►CMMFF94SymbolicToNumericAtomTypeMap | Lookup table mapping each symbolic MMFF94 atom type to its corresponding numeric MMFF94 atom type |
| CEntry | The map entry type (a (symbolic type, numeric type) key/value pair) |
| CMMFF94TorsionInteraction | Stores parameters for a single MMFF94 torsion interaction over an atom quadruplet i-j-k-l |
| CMMFF94TorsionInteractionList | Data structure for the storage of MMFF94 torsion interaction parameter records |
| CMMFF94TorsionInteractionParameterizer | Detects and parameterizes the MMFF94 torsion interactions of a molecular graph |
| ►CMMFF94TorsionParameterTable | Data structure for the storage and lookup of MMFF94 torsion interaction parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMMFF94VanDerWaalsAtomParameters | |
| ►CMMFF94VanDerWaalsInteraction | Stores parameters for a single MMFF94 Van der Waals interaction between two non-bonded atoms |
| CHDonorAcceptorType | MMFF94 hydrogen-bond donor/acceptor classification of an atom |
| CMMFF94VanDerWaalsInteractionList | Data structure for the storage of MMFF94 Van der Waals interaction parameter records |
| CMMFF94VanDerWaalsInteractionParameterizer | Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph |
| ►CMMFF94VanDerWaalsParameterTable | Data structure for the storage and lookup of MMFF94 interaction parameters |
| CEntry | Data structure for the storage of values associated with a single table entry |
| CMolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CParameterizationFailed | Thrown when force field parameterization has failed |
| CTopologicalAtomDistanceFunction | Generic wrapper class used to store a user-defined topological atom-pair distance function |
| CUFFAtomType | Provides constants for the specification of numeric Universal Force Field (UFF) atom types |
| ►CUFFAtomTypePropertyTable | Data structure for the storage and lookup of various properties associated with numeric UFF atom types |
| CEntry | Data structure for the storage of values associated with a single table entry |
| ►NGRAIL | Contains classes and functions related to the GRAIL method [GRAIL, GRADE] |
| CAtomDensityGridCalculator | Calculator that fills a spatial grid with combined per-atom density contributions |
| CAttributedGridProperty | Provides keys for built-in Grid.AttributedGrid properties |
| CAttributedGridPropertyDefault | Provides default values for built-in Grid.AttributedGrid properties |
| ►CBindingAffinityCalculator | Predicts the binding affinity of a ligand pose from its GRAIL descriptor vector |
| CAffinityMeasure | Specifies the affinity measure the prediction targets |
| CBuriednessGridCalculator | Calculator that fills a spatial grid with per-cell buriedness scores derived from GRAIL.BuriednessScore |
| CBuriednessScore | Functor for the calculation of the buriedness of a 3D query position with respect to the surrounding atoms |
| CDoubleVector3DFeatureFunctor | |
| ►CFeatureInteractionScoreGridCalculator | Calculator that fills a spatial grid with per-cell feature-interaction scores against a set of target pharmacophore features |
| CMaxScoreFunctor | Score-combination functor returning the maximum (infinity norm) of the per-feature scores |
| CScoreSumFunctor | Score-combination functor returning the sum of the per-feature scores |
| CFeatureType | 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 |
| CGRAILDataSetGenerator | 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 |
| ►CGRAILDescriptorCalculator | Calculation of GRAIL descriptors for protein-ligand complexes |
| CElementIndex | Indices of the individual elements of the GRAIL descriptor vector |
| ►CGRAILXDescriptorCalculator | Calculation of the extended GRAIL-X descriptor for protein-ligand complexes |
| CElementIndex | Indices of the individual elements of the extended GRAIL-X descriptor vector |
| CGeneralizedBellAtomDensity | Functor for the evaluation of the generalized-bell atom density contribution of an atom at a query position |
| CVoidPharmacophoreFunctor | |
| ►NGrid | Contains classes and functions related to grid based data representation and processing |
| CAttributedGrid | Abstract base class for grid types that also carry generic key/value properties |
| CAttributedGridProperty | Provides keys for built-in Grid.AttributedGrid properties |
| CAttributedGridPropertyDefault | Provides default values for built-in Grid.AttributedGrid properties |
| CCDFBZ2DRegularGridInputHandler | Handler for the input of bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridOutputHandler | Handler for the output of bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridReader | Reader for bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridSetInputHandler | Handler for the input of bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridSetOutputHandler | Handler for the output of bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridSetReader | Reader for bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridSetWriter | Writer for bzip2-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFBZ2DRegularGridWriter | Writer for bzip2-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFDRegularGridInputHandler | Handler for the input of regular spatial grid data in the native I/O format of the CDPL |
| CCDFDRegularGridOutputHandler | Handler for the output of regular spatial grid data in the native I/O format of the CDPL |
| CCDFDRegularGridReader | Reader for regular spatial grid data in the native I/O format of the CDPL |
| CCDFDRegularGridSetInputHandler | Handler for the input of regular spatial grid set data in the native I/O format of the CDPL |
| CCDFDRegularGridSetOutputHandler | Handler for the output of regular spatial grid set data in the native I/O format of the CDPL |
| CCDFDRegularGridSetReader | Reader for regular spatial grid set data in the native I/O format of the CDPL |
| CCDFDRegularGridSetWriter | Writer for regular spatial grid set data in the native I/O format of the CDPL |
| CCDFDRegularGridWriter | Writer for regular spatial grid data in the native I/O format of the CDPL |
| CCDFGZDRegularGridInputHandler | Handler for the input of gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFGZDRegularGridOutputHandler | Handler for the output of gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFGZDRegularGridReader | Reader for gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCDFGZDRegularGridSetInputHandler | Handler for the input of gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFGZDRegularGridSetOutputHandler | Handler for the output of gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFGZDRegularGridSetReader | Reader for gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFGZDRegularGridSetWriter | Writer for gzip-compressed regular spatial grid set data in the native I/O format of the CDPL |
| CCDFGZDRegularGridWriter | Writer for gzip-compressed regular spatial grid data in the native I/O format of the CDPL |
| CCUBEDRegularGridInputHandler | Handler for the input of regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCUBEDRegularGridOutputHandler | Handler for the output of regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCUBEDRegularGridReader | Reader for regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCUBEDRegularGridWriter | Writer for regular spatial grid data in the Gaussian CUBE [CUBE] format |
| CCompoundDRegularGridReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CCompoundDRegularGridSetReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| CDRegularGrid | A regular spatial grid storing double-precision floating-point values |
| ►CDRegularGridIOManager | Singleton class that serves as a global registry for Grid.DRegularGridInputHandler and Grid.DRegularGridOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CDRegularGridInputHandler | Factory interface providing methods for the creation of Grid.DRegularGridReaderBase instances for reading data provided in a particular storage format |
| CDRegularGridOutputHandler | Factory interface providing methods for the creation of Grid.DRegularGridWriterBase instances for data output in a particular storage format |
| CDRegularGridReader | Reader for regular spatial grid data of type Grid.DRegularGrid in any supported format |
| CDRegularGridReaderBase | Interface for reading data objects of type Grid.DRegularGrid from an arbitrary data source |
| CDRegularGridSet | Convenience alias for the double-precision regular spatial grid sets |
| ►CDRegularGridSetIOManager | Singleton class that serves as a global registry for Grid.DRegularGridSetInputHandler and Grid.DRegularGridSetOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CDRegularGridSetInputHandler | Factory interface providing methods for the creation of Grid.DRegularGridSetReaderBase instances for reading data provided in a particular storage format |
| CDRegularGridSetOutputHandler | Factory interface providing methods for the creation of Grid.DRegularGridSetWriterBase instances for data output in a particular storage format |
| CDRegularGridSetReader | Reader for regular spatial grid set data of type Grid.DRegularGridSet in any supported format |
| CDRegularGridSetReaderBase | Interface for reading data objects of type Grid.DRegularGridSet from an arbitrary data source |
| CDRegularGridSetWriter | Writer for regular spatial grid set data of type Grid.DRegularGridSet in any supported format |
| CDRegularGridSetWriterBase | Interface for writing data objects of type Grid.DRegularGridSet to an arbitrary data sink |
| CDRegularGridWriter | Writer for grid data of type Grid.DRegularGrid in any supported format |
| CDRegularGridWriterBase | Interface for writing data objects of type Grid.DRegularGrid to an arbitrary data sink |
| CDSpatialGrid | Convenience alias for the double-precision spatial-grid abstract base |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CFRegularGrid | A regular spatial grid storing single-precision floating-point values |
| CFRegularGridSet | Convenience alias for the single-precision regular spatial grid sets |
| CFSpatialGrid | Convenience alias for the single-precision spatial-grid abstract base |
| CFileCDFBZ2DRegularGridReader | |
| CFileCDFBZ2DRegularGridSetReader | |
| CFileCDFBZ2DRegularGridSetWriter | |
| CFileCDFBZ2DRegularGridWriter | |
| CFileCDFDRegularGridReader | |
| CFileCDFDRegularGridSetReader | |
| CFileCDFDRegularGridSetWriter | |
| CFileCDFDRegularGridWriter | |
| CFileCDFGZDRegularGridReader | |
| CFileCDFGZDRegularGridSetReader | |
| CFileCDFGZDRegularGridSetWriter | |
| CFileCDFGZDRegularGridWriter | |
| CFileCUBEDRegularGridReader | |
| CFileCUBEDRegularGridWriter | |
| ►NMath | Contains classes and functions related to mathematics |
| CConstDGridExpression | |
| CConstDHomogenousCoordsAdapter | |
| CConstDMatrixColumn | |
| CConstDMatrixExpression | |
| CConstDMatrixRange | |
| CConstDMatrixRow | |
| CConstDMatrixSlice | |
| CConstDMatrixTranspose | |
| CConstDQuaternionExpression | |
| CConstDQuaternionVectorAdapter | |
| CConstDVectorExpression | |
| CConstDVectorQuaternionAdapter | |
| CConstDVectorRange | |
| CConstDVectorSlice | |
| CConstFGridExpression | |
| CConstFHomogenousCoordsAdapter | |
| CConstFMatrixColumn | |
| CConstFMatrixExpression | |
| CConstFMatrixRange | |
| CConstFMatrixRow | |
| CConstFMatrixSlice | |
| CConstFMatrixTranspose | |
| CConstFQuaternionExpression | |
| CConstFQuaternionVectorAdapter | |
| CConstFVectorExpression | |
| CConstFVectorQuaternionAdapter | |
| CConstFVectorRange | |
| CConstFVectorSlice | |
| CConstLHomogenousCoordsAdapter | |
| CConstLMatrixColumn | |
| CConstLMatrixExpression | |
| CConstLMatrixRange | |
| CConstLMatrixRow | |
| CConstLMatrixSlice | |
| CConstLMatrixTranspose | |
| CConstLQuaternionExpression | |
| CConstLQuaternionVectorAdapter | |
| CConstLVectorExpression | |
| CConstLVectorQuaternionAdapter | |
| CConstLVectorRange | |
| CConstLVectorSlice | |
| CConstLowerTriangularDMatrixAdapter | |
| CConstLowerTriangularFMatrixAdapter | |
| CConstLowerTriangularLMatrixAdapter | |
| CConstLowerTriangularULMatrixAdapter | |
| CConstULHomogenousCoordsAdapter | |
| CConstULMatrixColumn | |
| CConstULMatrixExpression | |
| CConstULMatrixRange | |
| CConstULMatrixRow | |
| CConstULMatrixSlice | |
| CConstULMatrixTranspose | |
| CConstULQuaternionExpression | |
| CConstULQuaternionVectorAdapter | |
| CConstULVectorExpression | |
| CConstULVectorQuaternionAdapter | |
| CConstULVectorRange | |
| CConstULVectorSlice | |
| CConstUnitLowerTriangularDMatrixAdapter | |
| CConstUnitLowerTriangularFMatrixAdapter | |
| CConstUnitLowerTriangularLMatrixAdapter | |
| CConstUnitLowerTriangularULMatrixAdapter | |
| CConstUnitUpperTriangularDMatrixAdapter | |
| CConstUnitUpperTriangularFMatrixAdapter | |
| CConstUnitUpperTriangularLMatrixAdapter | |
| CConstUnitUpperTriangularULMatrixAdapter | |
| CConstUpperTriangularDMatrixAdapter | |
| CConstUpperTriangularFMatrixAdapter | |
| CConstUpperTriangularLMatrixAdapter | |
| CConstUpperTriangularULMatrixAdapter | |
| CDGrid | Unbounded dense grid storing floating-point values of type double |
| CDGridExpression | |
| CDHomogenousCoordsAdapter | |
| CDIdentityMatrix | Memory-efficient immutable identity matrix with element values of type double |
| CDKabschAlgorithm | |
| CDMLRModel | Performs Multiple Linear Regression [WLIREG] on a set of data points \( (y_i, \vec{X}_i) \) |
| CDMatrix | Unbounded dense matrix holding floating-point values of type double |
| CDMatrixColumn | |
| CDMatrixExpression | |
| CDMatrixRange | |
| CDMatrixRow | |
| CDMatrixSlice | |
| CDMatrixTranspose | |
| CDQuaternion | General 4-component quaternion with component values of type double |
| CDQuaternionExpression | |
| CDQuaternionVectorAdapter | |
| CDRealQuaternion | A memory-efficient pure-real quaternion with component values of type double |
| CDRegularSpatialGrid | Unbounded dense regular grid storing floating-point values of type double |
| CDRotationMatrix | Rotation matrix holding floating-point values of type double |
| CDScalarGrid | Immutable grid where all elements have the same value of type double |
| CDScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type double |
| CDScalarVector | Memory-efficient immutable vector where all elements have the same value of type double |
| CDScalingMatrix | Scaling matrix holding floating-point values of type double |
| CDTranslationMatrix | Translation matrix holding floating-point values of type double |
| CDUnitVector | Memory-efficient immutable unit vector with element values of type double |
| CDVector | Unbounded dense vector holding floating-point values of type double |
| ►CDVectorBFGSMinimizer | Implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for solving unconstrained nonlinear optimization problems |
| CStatus | Status bitmask reported by minimize() and getStatus() |
| CDVectorExpression | |
| CDVectorQuaternionAdapter | |
| CDVectorRange | |
| CDVectorSlice | |
| CDZeroGrid | Immutable grid where all elements have the value zero of type double |
| CDZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type double |
| CDZeroVector | Memory-efficient immutable vector where all elements have the value zero of type double |
| CDoubleDVector2Functor | |
| CDoubleDVectorFunctor | |
| CDoubleVector2DArray2Functor | |
| CDoubleVector2DArrayFunctor | |
| CDoubleVector3DArray2Functor | |
| CDoubleVector3DArrayFunctor | |
| CFGrid | Unbounded dense grid storing floating-point values of type float |
| CFGridExpression | |
| CFHomogenousCoordsAdapter | |
| CFIdentityMatrix | Memory-efficient immutable identity matrix with element values of type float |
| CFKabschAlgorithm | |
| CFMLRModel | Performs Multiple Linear Regression [WLIREG] on a set of data points \( (y_i, \vec{X}_i) \) |
| CFMatrix | Unbounded dense matrix holding floating-point values of type float |
| CFMatrixColumn | |
| CFMatrixExpression | |
| CFMatrixRange | |
| CFMatrixRow | |
| CFMatrixSlice | |
| CFMatrixTranspose | |
| CFQuaternion | General 4-component quaternion with component values of type float |
| CFQuaternionExpression | |
| CFQuaternionVectorAdapter | |
| CFRealQuaternion | A memory-efficient pure-real quaternion with component values of type float |
| CFRegularSpatialGrid | Unbounded dense regular grid storing floating-point values of type float |
| CFRotationMatrix | Rotation matrix holding floating-point values of type float |
| CFScalarGrid | Immutable grid where all elements have the same value of type float |
| CFScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type float |
| CFScalarVector | Memory-efficient immutable vector where all elements have the same value of type float |
| CFScalingMatrix | Scaling matrix holding floating-point values of type float |
| CFTranslationMatrix | Translation matrix holding floating-point values of type float |
| CFUnitVector | Memory-efficient immutable unit vector with element values of type float |
| CFVector | Unbounded dense vector holding floating-point values of type float |
| ►CFVectorBFGSMinimizer | Implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for solving unconstrained nonlinear optimization problems |
| CStatus | Status bitmask reported by minimize() and getStatus() |
| CFVectorExpression | |
| CFVectorQuaternionAdapter | |
| CFVectorRange | |
| CFVectorSlice | |
| CFZeroGrid | Immutable grid where all elements have the value zero of type float |
| CFZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type float |
| CFZeroVector | Memory-efficient immutable vector where all elements have the value zero of type float |
| CFloatFVector2Functor | |
| CFloatFVectorFunctor | |
| CFloatVector2FArray2Functor | |
| CFloatVector2FArrayFunctor | |
| CFloatVector3FArray2Functor | |
| CFloatVector3FArrayFunctor | |
| CLHomogenousCoordsAdapter | |
| CLIdentityMatrix | Memory-efficient immutable identity matrix with element values of type long |
| CLMatrix | Unbounded dense matrix holding signed integers of type long |
| CLMatrixColumn | |
| CLMatrixExpression | |
| CLMatrixRange | |
| CLMatrixRow | |
| CLMatrixSlice | |
| CLMatrixTranspose | |
| CLQuaternion | General 4-component quaternion with component values of type long |
| CLQuaternionExpression | |
| CLQuaternionVectorAdapter | |
| CLRealQuaternion | A memory-efficient pure-real quaternion with component values of type long |
| CLRotationMatrix | Rotation matrix holding integer values of type long |
| CLScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type long |
| CLScalarVector | Memory-efficient immutable vector where all elements have the same value of type long |
| CLScalingMatrix | Scaling matrix holding integer values of type long |
| CLTranslationMatrix | Translation matrix holding integer values of type long |
| CLUnitVector | Memory-efficient immutable unit vector with element values of type long |
| CLVector | Unbounded dense vector holding signed integers of type long |
| CLVectorExpression | |
| CLVectorQuaternionAdapter | |
| CLVectorRange | |
| CLVectorSlice | |
| CLZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type long |
| CLZeroVector | Memory-efficient immutable vector where all elements have the value zero of type long |
| CLower | Tag selecting the lower-triangular view (entries strictly above the diagonal read as zero) for Math.TriangularAdapter |
| CMatrix2D | Bounded 2x2 matrix holding floating-point values of type double |
| CMatrix2F | Bounded 2x2 matrix holding floating-point values of type float |
| CMatrix2L | Bounded 2x2 matrix holding signed integers of type long |
| CMatrix2UL | Bounded 2x2 matrix holding unsigned integers of type unsigned long |
| CMatrix3D | Bounded 3x3 matrix holding floating-point values of type double |
| CMatrix3F | Bounded 3x3 matrix holding floating-point values of type float |
| CMatrix3L | Bounded 3x3 matrix holding signed integers of type long |
| CMatrix3UL | Bounded 3x3 matrix holding unsigned integers of type unsigned long |
| CMatrix4D | Bounded 4x4 matrix holding floating-point values of type double |
| CMatrix4F | Bounded 4x4 matrix holding floating-point values of type float |
| CMatrix4L | Bounded 4x4 matrix holding signed integers of type long |
| CMatrix4UL | Bounded 4x4 matrix holding unsigned integers of type unsigned long |
| CRange | Half-open index range \( [start, stop) \) used for slicing vector and matrix expressions |
| CSlice | Index slice ( \( start, stride, size \)) used for strided slicing of vector and matrix expressions |
| CSparseDMatrix | Unbounded sparse matrix holding floating-point values of type double |
| CSparseDVector | Unbounded sparse vector holding floating-point values of type double |
| CSparseFMatrix | Unbounded sparse matrix holding floating-point values of type float |
| CSparseFVector | Unbounded sparse vector holding floating-point values of type float |
| CSparseLMatrix | Unbounded sparse matrix holding signed integers of type long |
| CSparseLVector | Unbounded sparse vector holding signed integers of type long |
| CSparseULMatrix | Unbounded sparse matrix holding unsigned integers of type unsigned long |
| CSparseULVector | Unbounded sparse vector holding unsigned integers of type unsigned long |
| CULHomogenousCoordsAdapter | |
| CULIdentityMatrix | Memory-efficient immutable identity matrix with element values of type unsigned long |
| CULMatrix | Unbounded dense matrix holding unsigned integers of type unsigned long |
| CULMatrixColumn | |
| CULMatrixExpression | |
| CULMatrixRange | |
| CULMatrixRow | |
| CULMatrixSlice | |
| CULMatrixTranspose | |
| CULQuaternion | General 4-component quaternion with component values of type unsigned long |
| CULQuaternionExpression | |
| CULQuaternionVectorAdapter | |
| CULRealQuaternion | A memory-efficient pure-real quaternion with component values of type unsigned long |
| CULRotationMatrix | Rotation matrix holding unsigned integer values of type unsigned long |
| CULScalarMatrix | Memory-efficient immutable matrix where all elements have the same value of type unsigned long |
| CULScalarVector | Memory-efficient immutable vector where all elements have the same value of type unsigned long |
| CULScalingMatrix | Scaling matrix holding unsigned integer values of type unsigned long |
| CULTranslationMatrix | Translation matrix holding unsigned integer values of type unsigned long |
| CULUnitVector | Memory-efficient immutable unit vector with element values of type unsigned long |
| CULVector | Unbounded dense vector holding unsigned integers of type unsigned long |
| CULVectorExpression | |
| CULVectorQuaternionAdapter | |
| CULVectorRange | |
| CULVectorSlice | |
| CULZeroMatrix | Memory-efficient immutable matrix where all elements have the value zero of type unsigned long |
| CULZeroVector | Memory-efficient immutable vector where all elements have the value zero of type unsigned long |
| CUnitLower | Tag selecting the unit-lower-triangular view (zero above the diagonal, one on the diagonal) for Math.TriangularAdapter |
| CUnitUpper | Tag selecting the unit-upper-triangular view (zero below the diagonal, one on the diagonal) for Math.TriangularAdapter |
| CUpper | Tag selecting the upper-triangular view (entries strictly below the diagonal read as zero) for Math.TriangularAdapter |
| CVector2D | Bounded 2 element vector holding floating-point values of type double |
| CVector2DArray | Array storing vectors of type Math.Vector2D |
| CVector2DArrayAlignmentCalculator | |
| ►CVector2DArrayBFGSMinimizer | |
| CStatus | |
| CVector2F | Bounded 2 element vector holding floating-point values of type float |
| CVector2FArray | Array storing vectors of type Math.Vector2F |
| CVector2FArrayAlignmentCalculator | |
| ►CVector2FArrayBFGSMinimizer | |
| CStatus | |
| CVector2L | Bounded 2 element vector holding signed integers of type long |
| CVector2LArray | Array storing vectors of type Math.Vector2L |
| CVector2UL | Bounded 2 element vector holding unsigned integers of type unsigned long |
| CVector2ULArray | Array storing vectors of type Math.Vector2UL |
| CVector3D | Bounded 3 element vector holding floating-point values of type double |
| CVector3DArray | Array storing vectors of type Math.Vector3D |
| CVector3DArrayAlignmentCalculator | |
| ►CVector3DArrayBFGSMinimizer | |
| CStatus | |
| CVector3F | Bounded 3 element vector holding floating-point values of type float |
| CVector3FArray | Array storing vectors of type Math.Vector3F |
| CVector3FArrayAlignmentCalculator | |
| ►CVector3FArrayBFGSMinimizer | |
| CStatus | |
| CVector3L | Bounded 3 element vector holding signed integers of type long |
| CVector3LArray | Array storing vectors of type Math.Vector3L |
| CVector3UL | Bounded 3 element vector holding unsigned integers of type unsigned long |
| CVector3ULArray | Array storing vectors of type Math.Vector3UL |
| CVector4D | Bounded 4 element vector holding floating-point values of type double |
| CVector4F | Bounded 4 element vector holding floating-point values of type float |
| CVector4L | Bounded 4 element vector holding signed integers of type long |
| CVector4UL | Bounded 4 element vector holding unsigned integers of type unsigned long |
| CVector7D | Bounded 7 element vector holding floating-point values of type double |
| ►NMolProp | Contains classes and functions related to the calculation/preciction of physicochemical molecular properties |
| CAtomHydrophobicityCalculator | Implementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities |
| CAtomProperty | Provides keys for built-in Chem.Atom properties |
| CAtomPropertyDefault | Provides default values for MolProp-specific Chem.Atom properties |
| CBondProperty | Provides keys for built-in Chem.Bond properties |
| CCoordinationGeometry | Provides constants used to specify the spatial geometry of atom arrangements around a common central atom |
| CElementHistogram | Data type for the storage of element histograms of chemical compounds |
| CFunctionalGroupList | Implementation of Ertl's algorithm [FGPE] for the identification of functional groups in organic molecules |
| CHBondAcceptorAtomType | Provides constants used to specify the structural class of H-bond acceptor atoms |
| CHBondAcceptorAtomTyper | Implements the perception of H-bond acceptor atom types (see namespace MolProp.HBondAcceptorAtomType) |
| CHBondDonorAtomType | Provides constants used to specify the structural class of H-bond donor atoms |
| CHBondDonorAtomTyper | Implements the perception of H-bond donor atom types (see namespace MolProp.HBondDonorAtomType) |
| CLogSCalculator | Calculation of the aqueous solubility ( \( \log S \)) of molecular graphs using the atom-contribution method of Hou, Xia, Zhang and Xu |
| CMHMOPiChargeCalculator | 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 |
| CMassComposition | Data type for the storage of mass percent compositions of chemical compounds |
| CMolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CPEOESigmaChargeCalculator | 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 |
| CTPSACalculator | Calculation of the topological polar surface area (TPSA) of molecular graphs based on fragment contributions |
| CXLogPCalculator | Calculation of the octanol/water partition coefficient ( \( \log P \)) of molecular graphs using the atom-additive method of Wang, Gao and Lai |
| ►NPharm | Contains classes and functions related to pharmacophore perception and pharmacophore applications |
| CAromaticFeatureGenerator | Pharm.FeatureGenerator implementation that perceives aromatic ring features by enumerating the aromatic SSSR subset of the input molecular graph |
| CBasicFeature | Pharm.Feature implementation owned by a Pharm.BasicPharmacophore parent |
| CBasicPharmacophore | Concrete Pharm.Pharmacophore implementation that owns its features as Pharm.BasicFeature instances managed through an internal object pool |
| CBoolDoubleFunctor | |
| CBoolFeature2Functor | |
| CBoolFeature2Matrix4DFunctor | |
| CBoolFeature4Functor | |
| CBoolFeatureFunctor | |
| CBoolSearchHitDoubleFunctor | |
| CBoolSizeType2Functor | |
| CCDFBZ2FeatureContainerOutputHandler | Handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL |
| CCDFBZ2FeatureContainerWriter | Writer for bzip2-compressed feature container data in the native I/O format of the CDPL |
| CCDFBZ2PharmacophoreInputHandler | Handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDFBZ2PharmacophoreReader | Reader for bzip2-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDFFeatureContainerOutputHandler | Handler for the output of feature container data in the native I/O format of the CDPL |
| CCDFFeatureContainerWriter | Writer for feature container data in the native I/O format of the CDPL |
| CCDFGZFeatureContainerOutputHandler | Handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL |
| CCDFGZFeatureContainerWriter | Writer for gzip-compressed feature container data in the native I/O format of the CDPL |
| CCDFGZPharmacophoreInputHandler | Handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDFGZPharmacophoreReader | Reader for gzip-compressed pharmacophore data in the native I/O format of the CDPL |
| CCDFPharmacophoreInputHandler | Handler for the input of pharmacophore data in the native I/O format of the CDPL |
| CCDFPharmacophoreReader | Reader for pharmacophore data in the native I/O format of the CDPL |
| CCationPiInteractionConstraint | 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) |
| CCationPiInteractionScore | 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 |
| CCompoundPharmacophoreReader | Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported data formats |
| CDefaultInteractionAnalyzer | Interaction analyzer pre-configured with the built-in default set of interaction constraints (hydrogen-bonding, ionic, aromatic-aromatic, cation-π, hydrophobic, halogen-bonding) |
| ►CDefaultPharmacophoreGenerator | Pharmacophore generator pre-configured with the built-in default set of feature generators |
| CConfiguration | Flags controlling feature generation |
| CDoubleDouble2Functor | |
| CDoubleDoubleFunctor | |
| CDoubleFeature2Functor | |
| CDoubleFeature2Matrix4DFunctor | |
| CDoubleFeature2UIntFunctor | |
| CDoubleFeatureFunctor | |
| CDoubleSearchHitFunctor | |
| CFeature | Abstract base class representing a single pharmacophore feature within a parent Pharm.Pharmacophore |
| CFeature3DCoordinatesFunction | Generic wrapper class used to store a user-defined Pharm.Feature 3D-coordinates function |
| CFeatureContainer | Abstract base class for containers holding a sequence of Pharm.Feature objects with associated properties (e.g |
| ►CFeatureContainerIOManager | Singleton class that serves as a global registry for Pharm.FeatureContainerInputHandler and Pharm.FeatureContainerOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CFeatureContainerOutputHandler | Factory interface providing methods for the creation of Pharm.FeatureContainerWriterBase instances for data output in a particular storage format |
| CFeatureContainerProperty | Provides keys for built-in Pharm.FeatureContainer properties |
| CFeatureContainerPropertyDefault | Provides default values for built-in Pharm.FeatureContainer properties |
| CFeatureContainerWriter | Writer for pharmacophore data in any supported format |
| CFeatureContainerWriterBase | Interface for writing data objects of type Pharm.FeatureContainer to an arbitrary data sink |
| CFeatureDistanceConstraint | Constraint functor that accepts a pair of features whose 3D-position distance lies within a configured [min, max] interval |
| CFeatureDistanceScore | Pharm.FeatureInteractionScore implementation that scores a feature pair based on whether their 3D-position distance falls within a configured [min, max] interval |
| CFeatureGenerator | Abstract base class for generators that perceive one type of pharmacophore feature (e.g |
| CFeatureGeometry | Provides constants for the specification of the generic geometry of a pharmacophore feature |
| CFeatureGeometryMatchFunctor | 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 |
| CFeatureInteractionScore | Abstract base class for scoring functors that quantify the strength of a directional pharmacophore-feature interaction (e.g |
| CFeatureInteractionScoreCombiner | Composite Pharm.FeatureInteractionScore that combines two underlying interaction scores via a user-supplied binary combination function (default: maximum) |
| CFeatureMapping | Data type for the storage and lookup of arbitrary feature to feature mappings |
| CFeaturePairDistanceMatchFunctor | 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) |
| CFeaturePositionMatchFunctor | 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 |
| CFeatureProperty | Provides keys for built-in Pharm.Feature properties |
| CFeaturePropertyDefault | Provides default values for built-in Pharm.Feature properties |
| CFeatureSet | Concrete Pharm.FeatureContainer implementation that stores references to existing Pharm.Feature instances |
| CFeatureType | Provides constants for the specification of the generic type of a pharmacophore feature |
| CFeatureTypeHistogram | Data type for the storage of feature type histograms of pharmacophores |
| CFeatureTypeMatchFunctor | Match functor that accepts a feature pair when both features share the same Pharm.FeatureType identifier |
| CFileCDFBZ2FeatureContainerWriter | |
| CFileCDFBZ2PharmacophoreReader | |
| CFileCDFFeatureContainerWriter | |
| CFileCDFGZFeatureContainerWriter | |
| CFileCDFGZPharmacophoreReader | |
| CFileCDFPharmacophoreReader | |
| CFilePMLFeatureContainerWriter | |
| CFilePMLPharmacophoreReader | |
| CFileScreeningHitCollector | 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 |
| CHBondAcceptorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives H-bond acceptor features by matching a built-in set of SMARTS patterns |
| CHBondDonorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives H-bond donor features by matching a built-in set of SMARTS patterns |
| CHBondingInteractionConstraint | 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) |
| CHBondingInteractionScore | 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 |
| CHydrophobicAtomFeatureGenerator | Pharm.FeatureGenerator implementation that emits one hydrophobic feature per atom whose individual hydrophobicity exceeds a configurable threshold |
| CHydrophobicFeatureGenerator | 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 |
| CHydrophobicInteractionConstraint | Pharm.FeatureDistanceConstraint specialization that accepts a hydrophobic feature pair when its center distance lies within the typical hydrophobic interaction range |
| CHydrophobicInteractionScore | Pharm.FeatureDistanceScore specialization that scores a hydrophobic feature pair based on its center distance in the typical hydrophobic interaction range |
| CInteractionAnalyzer | Analyzer that detects pairwise interactions between features of two Pharm.FeatureContainer instances based on user-registered per-feature-type-pair interaction constraint functions |
| CInteractionConstraintConnector | Composite feature-interaction constraint that combines two underlying constraint functions via a logical conjunction or disjunction |
| CInteractionPharmacophoreGenerator | 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) |
| CIonicInteractionConstraint | Pharm.FeatureDistanceConstraint specialization that accepts an oppositely-charged ionic feature pair when its center distance lies within the typical salt-bridge range |
| CIonicInteractionScore | Pharm.FeatureDistanceScore specialization that scores an oppositely-charged ionic feature pair based on its center distance in the typical salt-bridge range |
| CNegIonizableFeatureGenerator | Pharm.FeatureGenerator implementation that perceives negative ionizable group features by matching a built-in set of SMARTS patterns |
| COrthogonalPiPiInteractionConstraint | 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) |
| COrthogonalPiPiInteractionScore | 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 |
| CPMLFeatureContainerOutputHandler | Handler for the output of pharmacophore data in the native I/O format of LigandScout |
| CPMLFeatureContainerWriter | Writer for feature container data in the native I/O format of LigandScout |
| CPMLPharmacophoreInputHandler | Handler for the input of pharmacophore data in the native I/O format of LigandScout |
| CPMLPharmacophoreReader | Reader for pharmacophore data in the native I/O format of LigandScout |
| CPSDMolecularGraphOutputHandler | Handler for the output of molecular graph data in the CDPL PSD-format |
| CPSDMolecularGraphWriter | Writer for molecular graph data in the CDPL PSD-format |
| CPSDMoleculeInputHandler | Handler for the input of molecule data in the CDPL PSD-format |
| CPSDMoleculeReader | Reader for molecule data in the CDPL PSD-format |
| CPSDPharmacophoreInputHandler | Handler for the input of pharmacophore data in the CDPL PSD-format |
| CPSDPharmacophoreReader | Reader for pharmacophore data in the CDPL PSD-format |
| CPSDScreeningDBAccessor | Pharm.ScreeningDBAccessor implementation that reads pharmacophore screening databases stored in the built-in optimized PSD format |
| CPSDScreeningDBCreator | Pharm.ScreeningDBCreator implementation that builds optimized pharmacophore screening databases in the built-in PSD format |
| CParallelPiPiInteractionConstraint | 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) |
| CParallelPiPiInteractionScore | 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 |
| ►CPatternBasedFeatureGenerator | Pharm.FeatureGenerator implementation that perceives pharmacophore features by substructure pattern matching, with separate include and exclude pattern lists |
| CPatternAtomLabelFlag | Role-flags assigned (via the atom-mapping-ID property) to atoms of feature substructure patterns added through addIncludePattern() |
| CPharmacophore | Abstract base class for mutable containers of Pharm.Feature instances representing a pharmacophore model |
| CPharmacophoreAlignment | Pharmacophore alignment driver — a Chem.SpatialEntityAlignment specialization for Pharm.Feature objects that aligns two feature sets according to their type, geometry and 3D positions |
| CPharmacophoreFitScore | 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 |
| CPharmacophoreFitScreeningScore | Pharm.PharmacophoreFitScore specialization that scores a Pharm.ScreeningProcessor.SearchHit by applying the underlying pharmacophore-fit score to its query and hit features |
| CPharmacophoreGenerator | 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 |
| ►CPharmacophoreIOManager | Singleton class that serves as a global registry for Pharm.PharmacophoreInputHandler and Pharm.PharmacophoreOutputHandler implementation instances |
| CInputHandlerSequence | |
| COutputHandlerSequence | |
| CPharmacophoreInputHandler | Factory interface providing methods for the creation of Pharm.PharmacophoreReaderBase instances for reading data provided in a particular storage format |
| CPharmacophoreReader | Reader for pharmacophore data in any supported format |
| CPharmacophoreReaderBase | Interface for reading data objects of type Pharm.Pharmacophore from an arbitrary data source |
| CPosIonizableFeatureGenerator | Pharm.FeatureGenerator implementation that perceives positive ionizable group features by matching a built-in set of SMARTS patterns |
| CScreeningDBAccessor | Abstract base class for accessors that read the data stored in pharmacophore screening databases |
| ►CScreeningDBCreator | Abstract base class for creators that build optimized pharmacophore screening databases |
| CMode | Specifies how an existing database file is treated by open() |
| ►CScreeningProcessor | 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 |
| CHitReportMode | Specifies which conformer-level hits are reported per molecule |
| CSearchHit | 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 |
| CSpatialFeatureAlignment | |
| CSpatialFeatureMapping | 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 |
| CTopologicalFeatureAlignment | |
| CXBondAcceptorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives halogen-bond acceptor features by matching a built-in set of SMARTS patterns |
| CXBondDonorFeatureGenerator | Pharm.FeatureGenerator implementation that perceives halogen-bond donor features by matching a built-in set of SMARTS patterns |
| CXBondingInteractionConstraint | 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) |
| CXBondingInteractionScore | 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 |
| ►NShape | Contains classes and functions related to molecular shape representation and processing |
| CAlignedColorTverskyScore | Functor wrapping Shape.calcAlignedColorTverskyScore() |
| CAlignedShapeTverskyScore | Functor wrapping Shape.calcAlignedShapeTverskyScore() |
| CAlignedTotalOverlapTverskyScore | Functor wrapping Shape.calcAlignedTotalOverlapTverskyScore() |
| CAlignedTverskyComboScore | Functor wrapping Shape.calcAlignedTverskyComboScore() |
| CAlignmentResult | Result of a Gaussian-shape alignment between a reference and an aligned shape |
| CAlignmentResultSelectionMode | Provides constants for selecting which alignment results are kept by alignment routines |
| CBoolAlignmentResult2Functor | |
| CBoolSizeType2Functor | |
| CBoolSizeTypeFunctor | |
| CColorTanimotoScore | Functor wrapping Shape.calcColorTanimotoScore() |
| CColorTverskyScore | Functor wrapping Shape.calcColorTverskyScore() |
| CDoubleAlignmentResultFunctor | |
| CExactGaussianShapeOverlapFunction | Shape.GaussianShapeOverlapFunction implementation that evaluates the overlap analytically using the full Gaussian-product expansion (no approximations) |
| CFastGaussianShapeAlignment | High-level driver for the fast alignment of Gaussian shapes against a set of reference shapes |
| CFastGaussianShapeOverlapFunction | Shape.GaussianShapeOverlapFunction implementation that uses two approximation techniques to trade some accuracy for a substantial speedup compared to Shape.ExactGaussianShapeOverlapFunction |
| ►CGaussianShape | Data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions |
| CElement | Data structure representing a single sphere of the Gaussian shape, characterized by a position, radius, hardness and color |
| CGaussianShapeAlignment | High-level driver for the alignment of Gaussian shapes against a set of reference shapes |
| CGaussianShapeAlignmentStartGenerator | Abstract base class for generators of starting transformations used to seed Gaussian-shape overlap optimization |
| CGaussianShapeFunction | Function representation of a Gaussian shape, used to evaluate the shape's density, volume, surface area and related quantities at arbitrary 3D positions |
| ►CGaussianShapeFunctionAlignment | Driver for the alignment of one Shape.GaussianShapeFunction (the aligned shape) against a fixed reference Shape.GaussianShapeFunction |
| CResult | A single alignment result: rigid-body transformation plus shape and color overlap values |
| CGaussianShapeGenerator | Generates Shape.GaussianShape instances from molecular graphs |
| CGaussianShapeOverlapFunction | Abstract base class for functions evaluating the overlap between two Gaussian shape functions |
| CGaussianShapeSet | Data structure storing a set of (shared) Gaussian shapes |
| CPrincipalAxesAlignmentStartGenerator | Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape |
| CReferenceColorTverskyScore | Functor wrapping Shape.calcReferenceColorTverskyScore() |
| CReferenceShapeTverskyScore | Functor wrapping Shape.calcReferenceShapeTverskyScore() |
| CReferenceTotalOverlapTverskyScore | Functor wrapping Shape.calcReferenceTotalOverlapTverskyScore() |
| CReferenceTverskyComboScore | Functor wrapping Shape.calcReferenceTverskyComboScore() |
| CScreeningProcessor | High-level driver for shape-based virtual screening of molecular databases |
| ►CScreeningSettings | Bundle of configuration parameters for Shape.ScreeningProcessor |
| CAlignmentMode | Bitmask flags specifying the strategies used to seed alignment starting transformations |
| CColorFeatureType | Specifies which kind of color (pharmacophore) features are used during shape alignment |
| CScreeningMode | Specifies which alignment hits are reported by the screening processor |
| CShapeTanimotoScore | Functor wrapping Shape.calcShapeTanimotoScore() |
| CShapeTverskyScore | Functor wrapping Shape.calcShapeTverskyScore() |
| CSymmetryClass | Provides constants for the rotational symmetry class of a Gaussian shape |
| CTanimotoComboScore | Functor wrapping Shape.calcTanimotoComboScore() |
| CTotalOverlapTanimotoScore | Functor wrapping Shape.calcTotalOverlapTanimotoScore() |
| CTotalOverlapTverskyScore | Functor wrapping Shape.calcTotalOverlapTverskyScore() |
| CTverskyComboScore | Functor wrapping Shape.calcTverskyComboScore() |
| CVector7D | |
| CVoidMolecularGraph2AlignmentResultFunctor | |
| ►NUtil | Contains general purpose algorithms, containers, functors and other classes |
| CBZip2IOStream | Bidirectional stream that transparently (de)compresses bzip2 data |
| CBZip2IStream | Input stream that transparently decompresses bzip2-compressed data |
| CBZip2OStream | Output stream that transparently writes bzip2-compressed data |
| CBitSet | Dynamic bitset class |
| CBitSetArray | Array storing Util.BitSet objects |
| CBronKerboschAlgorithm | Implementation of the Bron-Kerbosch clique-detection algorithm [BKA] |
| CDArray | Array storing floating-point values of type double |
| ►CDG2DCoordinatesGenerator | |
| CDistanceConstraint | |
| CDistanceConstraintList | |
| ►CDG3DCoordinatesGenerator | Convenience alias for the 3D coordinates generator with double-precision values |
| CDistanceConstraint | |
| CDistanceConstraintList | |
| CVolumeConstraint | |
| CVolumeConstraintList | |
| CGZipIOStream | Bidirectional stream that transparently (de)compresses gzip data |
| CGZipIStream | Input stream that transparently decompresses gzip-compressed data |
| CGZipOStream | Output stream that transparently writes gzip-compressed data |
| CLArray | Array storing integers of type long |
| CPropertyValue | Unary functor that retrieves the value of a given property from the Base.PropertyContainer instance provided as argument |
| CPropertyValueProduct | Binary functor that calculates the product of two property values retrieved from a pair of Base.PropertyContainer instances passed as argument |
| CSArray | Array storing std::string objects |
| CSTArray | Array storing unsigned integers of type std::size_t |
| CSTPair | Pair of unsigned integers of type std::size_t |
| CSTPairArray | Array storing pairs of unsigned integers of type std::size_t |
| CUIArray | Array storing unsigned integers of type unsigned int |
| ►NVis | Contains classes and functions related to data visualization |
| ►NCairoBackend | Contains classes related to the implementation of CDPL.Vis interfaces on top of the Cairo 2D Graphics Library [CAIRO] |
| CCairoFontMetrics | Implements the FontMetrics interface for the Cairo rendering backend |
| CCairoRenderer2D | Implements the Renderer2D interface on top of the Cairo 2D Graphics Library |
| ►NQtBackend | Contains classes related to the implementation of CDPL.Vis interfaces on top of the Qt Toolkit [QTDOC] |
| CQtFontMetrics | Implements the FontMetrics interface for the Qt rendering backend |
| CQtObjectFactory | Provides methods for the creation of QFont, QColor, QPen and QBrush objects from Font, Color, Pen and Brush instances |
| CQtRenderer2D | Implements the Renderer2D interface on top of the Qt Toolkit |
| CAlignment | Provides flags that are used to specify the 2D alignment of graphical objects within a bounded rectangular area |
| CArrowStyle | Provides constants for the specification of reaction arrow styles in 2D depictions of chemical reactions |
| CAtomProperty | Provides keys for built-in Chem.Atom properties |
| CAtomPropertyDefault | Provides default values for built-in Chem.Atom properties |
| CBondProperty | Provides keys for built-in Chem.Bond properties |
| CBondPropertyDefault | Provides default values for built-in Chem.Bond properties |
| ►CBrush | Specifies the fill pattern and fill color of shapes |
| CStyle | Defines constants for supported fill pattern styles |
| CClipPathPrimitive2D | 2D graphics primitive representing a clipping region in 2D space |
| CColor | Specifies a color in terms of its red, green and blue components and an alpha-channel for transparency |
| CColorTable | Container for the storage and lookup of Vis.Color objects that are associated with a numeric identifier |
| CCompoundObject3DReader | |
| CControlParameter | Provides keys for built-in control-parameters |
| CControlParameterDefault | Provides default values for built-in control-parameters |
| CDataFormat | Provides preinitialized Base.DataFormat objects for all supported image output formats |
| CDefaultAtomColorTable | Provides default colors for the element dependent coloring of atom labels in 2D depictions of chemical structures |
| CDefaultFeatureColorTable | Provides default colors for the type dependent coloring of chemical features in 3D visualizations of pharmacophores |
| CEllipsePrimitive2D | 2D graphics primitive representing an ellipse |
| CFeatureContainerObject3DFactory | Class implementing the creation of Vis.Object3D instances providing a 3D representation of Pharm.FeatureContainer data objects for visualization purposes |
| CFeatureContainerObject3DFactoryBase | |
| CFilePDFMolecularGraphWriter | |
| CFilePDFReactionWriter | |
| CFilePLYFeatureContainerWriter | |
| CFilePLYObject3DWriter | |
| CFilePNGMolecularGraphWriter | |
| CFilePNGReactionWriter | |
| CFilePSMolecularGraphWriter | |
| CFilePSReactionWriter | |
| CFileR3DFeatureContainerWriter | |
| CFileR3DObject3DWriter | |
| CFileSTLFeatureContainerWriter | |
| CFileSTLObject3DWriter | |
| CFileSVGMolecularGraphWriter | |
| CFileSVGReactionWriter | |
| CFileVRMLFeatureContainerWriter | |
| CFileVRMLObject3DWriter | |
| CFont | Specifies a font for drawing text |
| CFontMetrics | Interface providing methods for querying information about the metrics of a font |
| CGraphicsPrimitive2D | The abstract base class of all 2D graphics primitives |
| CIcosahedronMesh3D | A pre-defined triangle mesh providing the vertices and faces of a regular icosahedron |
| CLayoutDirection | Provides constants that are used to specify the main direction of object layouts |
| CLayoutStyle | Provides constants that are used to specify the layout of a set of graphical objects |
| CLine2D | Specifies a line segment in 2D space |
| CLinePrimitive2D | 2D graphics primitive representing a single line |
| CLineSegmentListPrimitive2D | 2D graphics primitive representing a list of disjoint line segments |
| CMaterial | Defines material properties of Vis.Object3D instances |
| CMolecularGraphProperty | Provides keys for built-in Chem.MolecularGraph properties |
| CMolecularGraphPropertyDefault | Provides default values for built-in Chem.MolecularGraph properties |
| CObject3D | Hierarchical 3D scene object that owns a list of nested sub-objects and inherits its property bag from Base.PropertyContainer |
| CObject3DInputHandler | |
| CObject3DOutputHandler | |
| CObject3DProperty | Provides keys for built-in Vis.Object3D properties |
| CObject3DPropertyDefault | Provides default values for built-in Vis.Object3D properties |
| CObject3DReader | Reader for Vis.Object3D data in any supported format |
| CObject3DReaderBase | |
| CObject3DWriter | Writer for Vis.Object3D data in any supported format |
| CObject3DWriterBase | |
| CPDFMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Portable Document Format (PDF) [WPDF] |
| CPDFMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Portable Document Format (PDF) [WPDF] |
| CPDFReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF] |
| CPDFReactionWriter | Creates 2D depictions of chemical reactions in the Portable Document Format (PDF) [WPDF] |
| CPLYFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the Polygon File Format [PLYFMT] |
| CPLYFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the Polygon File Format [PLYFMT] |
| CPLYObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the Polygon File Format [PLYFMT] |
| CPLYObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the Polygon File Format [PLYFMT] |
| CPNGMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Portable Network Graphics (PNG) [WPNG] format |
| CPNGMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Portable Network Graphics (PNG) [WPNG] format |
| CPNGReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG] format |
| CPNGReactionWriter | Creates 2D depictions of chemical reactions in the Portable Network Graphics (PNG) [WPNG] format |
| CPSMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the PostScript (PS) [WPS] format |
| CPSMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the PostScript (PS) [WPS] format |
| CPSReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the PostScript (PS) [WPS] format |
| CPSReactionWriter | Creates 2D depictions of chemical reactions in the PostScript (PS) [WPS] format |
| ►CPath2D | Provides a container for painting operations, enabling arbitrary graphical shapes to be constructed and reused |
| CFillRule | Specifies which method to use for filling closed shapes described by the Path2D object |
| CPath2DConverter | Provides an interface for classes that implement the conversion of Vis.Path2D objects into rendering backend specific path descriptions or drawing operations |
| CPathPrimitive2D | 2D graphics primitive representing an arbitrary path in 2D space |
| ►CPen | Specifies how to draw lines and outlines of shapes |
| CCapStyle | Defines constants for supported line cap styles |
| CJoinStyle | Defines constants for supported line join styles |
| CLineStyle | Defines constants for supported line styles |
| CPointArray2D | Stores a set of points in 2D space |
| CPointListPrimitive2D | 2D graphics primitive representing a list of points |
| CPolygonPrimitive2D | 2D graphics primitive representing a polygon |
| CPolylinePrimitive2D | 2D graphics primitive representing a set of connected line segments |
| CR3DFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the Raster3D [R3DFMT] format |
| CR3DFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the Raster3D [R3DFMT] format |
| CR3DObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the Raster3D [R3DFMT] format |
| CR3DObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the Raster3D [R3DFMT] format |
| CReactionProperty | Provides keys for built-in Chem.Reaction properties |
| CReactionPropertyDefault | Provides default values for built-in Chem.Reaction properties |
| CReactionView2D | Implements the 2D visualization of chemical reactions |
| CRectangle2D | Specifies an axis aligned rectangular area in 2D space |
| CRenderer2D | Interface providing methods for low level 2D drawing operations |
| CRightFrustumMesh3D | A pre-defined triangle mesh providing the vertices and faces of a right frustum specified by the contructor arguments |
| CSTLFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the STL [STLFMT] format |
| CSTLFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the STL [STLFMT] format |
| CSTLObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the STL [STLFMT] format |
| CSTLObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the STL [STLFMT] format |
| CSVGMolecularGraphOutputHandler | Handler for the output of 2D depictions of chemical structures in the Scalable Vector Graphics (SVG) [WSVG] format |
| CSVGMolecularGraphWriter | Creates 2D structure diagrams of molecular graphs in the Scalable Vector Graphics (SVG) [WSVG] format |
| CSVGReactionOutputHandler | Handler for the output of 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG] format |
| CSVGReactionWriter | Creates 2D depictions of chemical reactions in the Scalable Vector Graphics (SVG) [WSVG] format |
| CShape3D | The abstract base of all classes describing the geometric shape of 3D objects |
| CShape3DVisitor | The base of all Vis.Shape3D visitor implementations [VPTN] |
| CSizeAdjustment | Provides constants that are used to specify the size adjustment policy for graphical objects within a bounded rectangular area |
| CSizeSpecification | Specifies the value and type of a size attribute and defines how the value may change during processing steps |
| ►CStructureGridView2D | Implements the 2D visualization of multiple chemical structures arranged in a grid |
| CCell | Data structure storing the contents of a grid cell |
| CStructureView2D | Implements the 2D visualization of chemical structures |
| CTextBlockPrimitive2D | 2D graphics primitive representing a block of styled text |
| CTextLabelPrimitive2D | 2D graphics primitive representing a text label |
| CTorusMesh3D | Pre-defined triangle mesh providing the vertices and faces of a torus specified by the contructor arguments |
| CTriangleMesh3D | Data structure for describing the geometric shape of 3D objects by means of a triangle mesh |
| CVRMLFeatureContainerOutputHandler | Handler for the output of Pharm.FeatureContainer instances in the VRML [VRML97] format |
| CVRMLFeatureContainerWriter | Outputs 3D visualization data of Pharm.FeatureContainer instances in the VRML [VRML97] format |
| CVRMLObject3DOutputHandler | Handler for the output of Vis.Object3D instances in the VRML [VRML97] format |
| CVRMLObject3DWriter | Outputs 3D visualization data represented by Vis.Object3D instances in the VRML [VRML97] format |
| CView2D | The abstract base of classes implementing the 2D visualization of data objects |
1.9.1