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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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Contains classes and functions related to chemistry. More...
Classes | |
| class | ANDAtomMatchExpressionList |
| Chem.AtomMatchExpressionList implementation that evaluates the stored expressions as a logical conjunction (AND). More... | |
| class | ANDBondMatchExpressionList |
| Chem.BondMatchExpressionList implementation that evaluates the stored expressions as a logical conjunction (AND). More... | |
| class | ANDMolecularGraphMatchExpressionList |
| Chem.MolecularGraphMatchExpressionList implementation that evaluates the stored expressions as a logical conjunction (AND). More... | |
| class | ANDReactionMatchExpressionList |
| Chem.ReactionMatchExpressionList implementation that evaluates the stored expressions as a logical conjunction (AND). More... | |
| class | AmideImidicAcidTautomerization |
| Implementation of the amide ↔ imidic-acid tautomerization rule. More... | |
| class | AromaticRingSet |
| Implements the perception of aromatic rings in a molecular graph. More... | |
| class | AromaticSSSRSubset |
| Implements the extraction of the aromatic rings in the SSSR of a molecular graph. More... | |
| class | AromaticSubstructure |
| Implements the perception of aromatic atoms and bonds in a molecular graph. More... | |
| class | Atom |
| Abstract base class representing a chemical atom and its bonded neighborhood. More... | |
| class | Atom2DCoordinatesCalculator |
| Generates 2D coordinates for the atoms of a molecular graph. More... | |
| class | Atom3DCoordinatesFunction |
| Generic wrapper class used to store a user-defined Chem.Atom 3D coordinates function. More... | |
| class | Atom3DCoordinatesFunctor |
| Helper-functor for retrieving the 3D coordinates of an atom (via the Chem.Entity3DProperty.COORDINATES_3D property). More... | |
| class | AtomArray3DCoordinatesFunctor |
| Functor for retrieving atom 3D coordinates from a provided coordinates array via index of the atoms in a specified molecular graph. More... | |
| class | AtomBondMapping |
| Data structure for the common storage of related atom to atom and bond to bond mappings. More... | |
| class | AtomConfiguration |
| Provides constants that are used to specify the configuration of stereogenic atoms. More... | |
| class | AtomConfigurationMatchExpression |
| Chem.AtomMatchExpression implementation that constrains target atoms by their stereo configuration relative to a query atom. More... | |
| class | AtomConformer3DCoordinatesFunctor |
| Functor for retrieving atom 3D coordinates from a specific conformer. More... | |
| class | AtomContainer |
| Common interface for data structures that support a random access to stored Chem.Atom instances. More... | |
| class | AtomDictionary |
| A global dictionary for the lookup of data associated with the atom types defined in namespace Chem.AtomType. More... | |
| class | AtomEnvironmentMatchExpression |
| Chem.AtomMatchExpression implementation that constrains target atoms by a specified structural environment. More... | |
| class | AtomMapping |
| Data type for the storage and lookup of arbitrary atom to atom mappings. More... | |
| class | AtomMatchConstraint |
| Provides numerical identifiers for built-in Chem.Atom matching constraints. More... | |
| class | AtomMatchExpression |
| Generic boolean expression interface for the implementation of query/target atom equivalence tests in molecular graph matching algorithms. More... | |
| class | AtomMatchExpressionList |
| Container for the storage and evaluation of logical match expression lists. More... | |
| class | AtomMatchExpressionPtrAtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | AtomPredicate |
| Generic wrapper class used to store a user-defined atom predicate. More... | |
| class | AtomProperty |
| Provides keys for built-in Chem.Atom properties. More... | |
| class | AtomPropertyDefault |
| Provides default values for built-in Chem.Atom properties. More... | |
| class | AtomPropertyFlag |
| Provides flags for the specification of basic Chem.Atom properties. More... | |
| class | AtomType |
| Provides constants for the specification of the chemical element or generic type of an atom. More... | |
| class | AtomTypeMatchExpression |
| MatchExpression that checks the atom type of a target atom against a query atom type. More... | |
| class | AutomorphismGroupSearch |
| Enumerates the atom and bond self-mappings (automorphism group) of a molecular graph. More... | |
| class | BRICSAtomLabel |
| Provides constants for labeling the endpoints of bonds matched by BRICS fragmentation rules. More... | |
| class | BRICSFragmentGenerator |
| Molecular graph fragment generator implementing the BRICS bond-cleavage rule set. More... | |
| class | BRICSRuleID |
| Provides constants for the identification of BRICS fragmentation rules. More... | |
| class | BasicAtom |
| Default implementation of the Chem.Atom interface. More... | |
| class | BasicBond |
| Default implementation of the Chem.Bond interface. More... | |
| class | BasicMolecule |
| Default implementation of the Chem.Molecule interface. More... | |
| class | BasicReaction |
| Default implementation of the Chem.Reaction interface. More... | |
| class | BemisMurckoAnalyzer |
| Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains. More... | |
| class | Bond |
| Abstract base class representing a chemical bond between two atoms (represented by Chem.Atom instances). More... | |
| class | BondConfiguration |
| Provides constants that are used to specify the cis/trans configuration of bonds. More... | |
| class | BondConfigurationMatchExpression |
| Chem.BondMatchExpression implementation that constrains target bonds by their stereo configuration relative to a query bond. More... | |
| class | BondContainer |
| Common interface for data structures that support a random access to stored Chem.Bond instances. More... | |
| class | BondDirection |
| Provides constants for the specification of directional bonds in Daylight SMILES and SMARTS strings. More... | |
| class | BondDirectionMatchExpression |
| Chem.BondMatchExpression implementation that constrains target bonds by their Daylight SMARTS bond direction. More... | |
| class | BondMapping |
| Data type for the storage and lookup of arbitrary bond to bond mappings. More... | |
| class | BondMatchConstraint |
| Provides numerical identifiers for built-in Chem.Bond matching constraints and flags for the specification of bond orders. More... | |
| class | BondMatchExpression |
| Generic boolean expression interface for the implementation of query/target bond equivalence tests in molecular graph matching algorithms. More... | |
| class | BondMatchExpressionList |
| Container for the storage and evaluation of logical match expression lists. More... | |
| class | BondMatchExpressionPtrBondFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BondOrderCalculator |
| Perceives bond orders of a molecular graph from its 3D structure and atom connectivity. More... | |
| class | BondPredicate |
| Generic wrapper class used to store a user-defined bond predicate. More... | |
| class | BondProperty |
| Provides keys for built-in Chem.Bond properties. More... | |
| class | BondPropertyDefault |
| Provides default values for built-in Chem.Bond properties. More... | |
| class | BondPropertyFlag |
| Provides flags for the specification of basic Chem.Bond properties. More... | |
| class | BondReactionCenterStatusMatchExpression |
| Chem.BondMatchExpression implementation that constrains target bonds by their reaction-center status. More... | |
| class | BondStereoFlag |
| Provides constants for the specification of stereo bonds in 2D depictions of chemical structures. More... | |
| class | BondStereoFlagCalculator |
| Calculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph. More... | |
| class | BondSubstituentDirectionMatchExpression |
| Chem.BondMatchExpression implementation that constrains target double bond configuration via the per-substituent bond direction annotations carried by the query. More... | |
| class | BoolAtom2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolAtom4Functor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolAtomMappingFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolBond2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolConstMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolEntity3D2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolEntity3D4Functor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolEntity3DMappingFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolMolecularGraphAtomBondMappingFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | BoolSTPairArrayFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | CDFBZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the native I/O format of the CDPL. More... | |
| class | CDFBZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | CDFBZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More... | |
| class | CDFBZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | CDFBZ2ReactionInputHandler |
| Handler for the input of bzip2-compressed reaction data in the native I/O format of the CDPL. More... | |
| class | CDFBZ2ReactionOutputHandler |
| Handler for the output of bzip2-compressed reaction data in the native I/O format of the CDPL. More... | |
| class | CDFBZ2ReactionReader |
| Reader for reaction data in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | CDFBZ2ReactionWriter |
| Writer for reaction data in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | CDFGZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More... | |
| class | CDFGZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed native I/O format of the CDPL. More... | |
| class | CDFGZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More... | |
| class | CDFGZMoleculeReader |
| Reader for molecule data in the gzip-compressed native I/O format of the CDPL. More... | |
| class | CDFGZReactionInputHandler |
| Handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More... | |
| class | CDFGZReactionOutputHandler |
| Handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More... | |
| class | CDFGZReactionReader |
| Reader for reaction data in the gzip-compressed native I/O format of the CDPL. More... | |
| class | CDFGZReactionWriter |
| Writer for reaction data in the gzip-compressed native I/O format of the CDPL. More... | |
| class | CDFMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the native I/O format of the CDPL. More... | |
| class | CDFMolecularGraphWriter |
| Writer for molecular graph data in the native I/O format of the CDPL. More... | |
| class | CDFMoleculeInputHandler |
| Handler for the input of molecule data in the native I/O format of the CDPL. More... | |
| class | CDFMoleculeReader |
| Reader for molecule data in the native I/O format of the CDPL. More... | |
| class | CDFReactionInputHandler |
| Handler for the input of reaction data in the native I/O format of the CDPL. More... | |
| class | CDFReactionOutputHandler |
| Handler for the output of reaction data in the native I/O format of the CDPL. More... | |
| class | CDFReactionReader |
| Reader for reaction data in the native I/O format of the CDPL. More... | |
| class | CDFReactionWriter |
| Writer for reaction data in the native I/O format of the CDPL. More... | |
| class | CIPConfigurationLabeler |
| Assigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph. More... | |
| class | CIPDescriptor |
| Provides constants for the specification of stereogenic atom/bond configurations determined by the Cahn-Ingold-Prelog (CIP) sequence rules. More... | |
| class | CIPPriorityCalculator |
| Computes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph. More... | |
| class | CMLBZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the Chemical Markup Language [CML] format. More... | |
| class | CMLBZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed Chemical Markup Language [CML] format. More... | |
| class | CMLBZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the Chemical Markup Language [CML] format. More... | |
| class | CMLBZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed Chemical Markup Language [CML] format. More... | |
| class | CMLGZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the Chemical Markup Language [CML] format. More... | |
| class | CMLGZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed Chemical Markup Language [CML] format. More... | |
| class | CMLGZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in the Chemical Markup Language [CML] format. More... | |
| class | CMLGZMoleculeReader |
| Reader for molecule data in the gzip-compressed Chemical Markup Language [CML] format. More... | |
| class | CMLMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the Chemical Markup Language [CML] format. More... | |
| class | CMLMolecularGraphWriter |
| Writer for molecular graph data in the Chemical Markup Language [CML] format. More... | |
| class | CMLMoleculeInputHandler |
| Handler for the input of molecule data in the Chemical Markup Language [CML] format. More... | |
| class | CMLMoleculeReader |
| Reader for molecule data in the Chemical Markup Language [CML] format. More... | |
| class | CanonicalNumberingCalculator |
| Computes canonical atom numberings for molecular graphs using McKay's algorithm. More... | |
| class | ChEMBLStandardizer |
| Implementation of the ChEMBL structure preprocessing pipeline. More... | |
| class | CommonConnectedSubstructureSearch |
| Enumerates all maximal common connected substructures shared between a query and a target molecular graph. More... | |
| class | CompleteRingSet |
| Implements the exhaustive perception of rings in a molecular graph. More... | |
| class | ComponentSet |
| Implements the perception of molecular graph components. More... | |
| class | CompoundMoleculeReader |
| Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream. More... | |
| class | CompoundReactionReader |
| Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream. More... | |
| class | ConjugatedRingBondPatternSwitching |
| Chem.TautomerizationRule implementation that enumerates tautomers obtained by switching the single/double bond pattern of conjugated rings (e.g. the two Kekulé forms of benzene). More... | |
| class | ConnectedSubstructureSet |
| Enumerates the connected substructures of a molecular graph of a specified bond count. More... | |
| class | ControlParameter |
| Provides keys for built-in control-parameters. More... | |
| class | ControlParameterDefault |
| Provides default values for built-in control-parameters. More... | |
| class | CyclicSubstructure |
| Implements the perception of ring atoms and bonds in a molecular graph. More... | |
| class | DataFormat |
| Provides preinitialized Base.DataFormat instances for all supported chemical data formats. More... | |
| class | DefaultMultiConfMoleculeInputProcessor |
| Default Chem.MultiConfMoleculeInputProcessor implementation that detects multi-conformer input by comparing atom and bond properties (and optionally molecule names) between successively read molecules. More... | |
| class | DefaultTautomerGenerator |
| Tautomer generator implementation preconfigured with the default set of tautomerization rules. More... | |
| class | DoubleAtom2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleAtom2UInt2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleAtom2UIntFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleAtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleDVectorFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleEntity3D2Functor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleEntity3DFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | DoubleVector3D2AtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | ElectronSystem |
| Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More... | |
| class | ElectronSystemList |
| Data structure for the storage of Chem.ElectronSystem instances. More... | |
| class | Entity3D |
| Base class for objects that have a position in 3D space (e.g. Chem.Atom and Chem.Feature). More... | |
| class | Entity3DContainer |
| Common interface for data structures that support a random access to stored Chem.Entity3D instances. More... | |
| class | Entity3DMapping |
| Data type for the storage and lookup of arbitrary entity to entity mappings. More... | |
| class | Entity3DProperty |
| Provides keys for built-in Chem.Entity3D properties. More... | |
| class | ExtendedSSSR |
| Implements the perception of the Extended Smallest Set of Smallest Rings (ESSSR) of a molecular graph. More... | |
| class | FileCDFBZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | FileCDFBZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | FileCDFBZ2ReactionReader |
| Reader for reaction data files in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | FileCDFBZ2ReactionWriter |
| Writer for reaction data files in the bzip2-compressed native I/O format of the CDPL. More... | |
| class | FileCDFGZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed native I/O format of the CDPL. More... | |
| class | FileCDFGZMoleculeReader |
| Reader for molecule data files in the gzip-compressed native I/O format of the CDPL. More... | |
| class | FileCDFGZReactionReader |
| Reader for reaction data files in the gzip-compressed native I/O format of the CDPL. More... | |
| class | FileCDFGZReactionWriter |
| Writer for reaction data files in the gzip-compressed native I/O format of the CDPL. More... | |
| class | FileCDFMolecularGraphWriter |
| Writer for molecular graph data files in the native I/O format of the CDPL. More... | |
| class | FileCDFMoleculeReader |
| Reader for molecule data files in the native I/O format of the CDPL. More... | |
| class | FileCDFReactionReader |
| Reader for reaction data files in the native I/O format of the CDPL. More... | |
| class | FileCDFReactionWriter |
| Writer for reaction data files in the native I/O format of the CDPL. More... | |
| class | FileCMLBZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed Chemical Markup Language [CML] format. More... | |
| class | FileCMLBZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed Chemical Markup Language [CML] format. More... | |
| class | FileCMLGZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed Chemical Markup Language [CML] format. More... | |
| class | FileCMLGZMoleculeReader |
| Reader for molecule data files in the gzip-compressed Chemical Markup Language [CML] format. More... | |
| class | FileCMLMolecularGraphWriter |
| Writer for molecular graph data files in the Chemical Markup Language [CML] format. More... | |
| class | FileCMLMoleculeReader |
| Reader for molecule data files in the Chemical Markup Language [CML] format. More... | |
| class | FileINCHIMolecularGraphWriter |
| Writer for molecular graph data files in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | FileINCHIMoleculeReader |
| Reader for molecule data files in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | FileJMEMolecularGraphWriter |
| Writer for molecular graph data files in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | FileJMEMoleculeReader |
| Reader for molecule data files in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | FileJMEReactionReader |
| Reader for reaction data files in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | FileJMEReactionWriter |
| Writer for reaction data files in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | FileMOL2BZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed Sybyl MOL2 format. More... | |
| class | FileMOL2BZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed Sybyl MOL2 format. More... | |
| class | FileMOL2GZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed Sybyl MOL2 format. More... | |
| class | FileMOL2GZMoleculeReader |
| Reader for molecule data files in the gzip-compressed Sybyl MOL2 format. More... | |
| class | FileMOL2MolecularGraphWriter |
| Writer for molecular graph data files in the Sybyl MOL2 format. More... | |
| class | FileMOL2MoleculeReader |
| Reader for molecule data files in the Sybyl MOL2 format. More... | |
| class | FileMOLMolecularGraphWriter |
| Writer for molecular graph data files in the MDL Mol-File [CTFILE] format. More... | |
| class | FileMOLMoleculeReader |
| Reader for molecule data files in the MDL Mol-File [CTFILE] format. More... | |
| class | FileRDFBZ2ReactionReader |
| Reader for reaction data files in the bzip2-compressed MDL RD-File [CTFILE] format. More... | |
| class | FileRDFBZ2ReactionWriter |
| Writer for reaction data files in the bzip2-compressed MDL RD-File [CTFILE] format. More... | |
| class | FileRDFGZReactionReader |
| Reader for reaction data files in the gzip-compressed MDL RD-File [CTFILE] format. More... | |
| class | FileRDFGZReactionWriter |
| Convenience wrapper that adapts a stream-based writer implementation WriterImpl into a file-based Base.DataWriter by opening an file stream and forwarding all write operations to the wrapped writer. More... | |
| class | FileRDFReactionReader |
| Reader for reaction data files in the MDL RD-File [CTFILE] format. More... | |
| class | FileRDFReactionWriter |
| Writer for reaction data files in the MDL RD-File [CTFILE] format. More... | |
| class | FileRXNReactionReader |
| Reader for reaction data files in the MDL Rxn-File [CTFILE] format. More... | |
| class | FileRXNReactionWriter |
| Writer for reaction data files in the MDL Rxn-File [CTFILE] format. More... | |
| class | FileSDFBZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed MDL SD-File [CTFILE] format. More... | |
| class | FileSDFBZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed MDL SD-File [CTFILE] format. More... | |
| class | FileSDFGZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed MDL SD-File [CTFILE] format. More... | |
| class | FileSDFGZMoleculeReader |
| Reader for molecule data files in the gzip-compressed MDL SD-File [CTFILE] format. More... | |
| class | FileSDFMolecularGraphWriter |
| Writer for molecular graph data files in the MDL SD-File [CTFILE] format. More... | |
| class | FileSDFMoleculeReader |
| Reader for molecule data files in the MDL SD-File [CTFILE] format. More... | |
| class | FileSMARTSMolecularGraphWriter |
| Writer for molecular graph data files in the Daylight SMARTS [SMARTS] format. More... | |
| class | FileSMARTSMoleculeReader |
| Reader for molecule data files in the Daylight SMARTS [SMARTS] format. More... | |
| class | FileSMARTSReactionReader |
| Reader for reaction data files in the Daylight SMARTS [SMARTS] format. More... | |
| class | FileSMARTSReactionWriter |
| Writer for reaction data files in the Daylight SMARTS [SMARTS] format. More... | |
| class | FileSMILESBZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESBZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESBZ2ReactionReader |
| Reader for reaction data files in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESBZ2ReactionWriter |
| Writer for reaction data files in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESGZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESGZMoleculeReader |
| Reader for molecule data files in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESGZReactionReader |
| Reader for reaction data files in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESGZReactionWriter |
| Writer for reaction data files in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESMolecularGraphWriter |
| Writer for molecular graph data files in the Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESMoleculeReader |
| Reader for molecule data files in the Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESReactionReader |
| Reader for reaction data files in the Daylight SMILES [SMILES] format. More... | |
| class | FileSMILESReactionWriter |
| Writer for reaction data files in the Daylight SMILES [SMILES] format. More... | |
| class | FileXYZBZ2MolecularGraphWriter |
| Writer for molecular graph data files in the bzip2-compressed XYZ format. More... | |
| class | FileXYZBZ2MoleculeReader |
| Reader for molecule data files in the bzip2-compressed XYZ format. More... | |
| class | FileXYZGZMolecularGraphWriter |
| Writer for molecular graph data files in the gzip-compressed XYZ format. More... | |
| class | FileXYZGZMoleculeReader |
| Reader for molecule data files in the gzip-compressed XYZ format. More... | |
| class | FileXYZMolecularGraphWriter |
| Writer for molecular graph data files in XYZ format to an output stream. More... | |
| class | FileXYZMoleculeReader |
| Reader for molecule data files in XYZ format from an input stream. More... | |
| class | Fragment |
| Concrete implementation of the Chem.MolecularGraph interface that stores references to selectable Chem.Atom and Chem.Bond instances. More... | |
| class | FragmentGenerator |
| Generic rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules. More... | |
| class | FragmentList |
| Data structure for the storage of Chem.Fragment instances. More... | |
| class | GenericHydrogen13ShiftTautomerization |
| Chem.TautomerizationRule implementation for the generation of tautomeric forms that result from proton migration between susceptible atoms separated by two bonds. More... | |
| class | GenericHydrogen15ShiftTautomerization |
| Chem.TautomerizationRule implementation for the generation of tautomeric forms that result from proton migration between susceptible atoms separated by four bonds. More... | |
| class | HashCodeCalculator |
| Computes 64-bit hash codes that are characteristic for the topology of a molecular graph and the properties of its atoms and bonds. More... | |
| class | HybridizationState |
| Provides constants for the specification of atom hybridization states. More... | |
| class | Hydrogen3DCoordinatesCalculator |
| Generates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors. More... | |
| class | INCHIMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | INCHIMolecularGraphWriter |
| Writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | INCHIMoleculeInputHandler |
| Handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | INCHIMoleculeReader |
| Reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More... | |
| class | INCHIReturnCode |
| Provides constants that are used to describe the status of an InChI [INCHI] output or input operation. More... | |
| class | ImineEnamineTautomerization |
| Chem.TautomerizationRule implementation for the generation of imine ⇄ enamine tautomers. More... | |
| class | JMEMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More... | |
| class | JMEMolecularGraphWriter |
| Writer for molecular graph data in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | JMEMoleculeInputHandler |
| Handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More... | |
| class | JMEMoleculeReader |
| Reader for molecule data in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | JMEReactionInputHandler |
| Handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More... | |
| class | JMEReactionOutputHandler |
| Handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More... | |
| class | JMEReactionReader |
| Reader for reaction data in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | JMEReactionWriter |
| Writer for reaction data in the native I/O format of the JME Molecular Editor [JME] Java applet. More... | |
| class | KekuleStructureCalculator |
| Assigns an alternating single/double bond pattern (Kekulé structure) to undefined bonds of a molecular graph. More... | |
| class | KeteneYnolTautomerization |
| Chem.TautomerizationRule implementation for the generation of ketene ⇄ ynol tautomers. More... | |
| class | KetoEnolTautomerization |
| Chem.TautomerizationRule implementation for the generation of keto ⇄ enol tautomers. More... | |
| class | LactamLactimTautomerization |
| Chem.TautomerizationRule implementation for the generation of lactam ⇄ lactim tautomers. More... | |
| class | MDLDataFormatVersion |
| Provides constants that are used to specify the connection table (CTAB) and Rxn-File version for the I/O of molecular graphs and reactions in an MDL CTFile based data format. More... | |
| class | MDLParity |
| Provides constants that are used to specify the MDL stereo parity of atoms. More... | |
| class | MOL2BZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More... | |
| class | MOL2BZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed Sybyl MOL2 format. More... | |
| class | MOL2BZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More... | |
| class | MOL2BZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed Sybyl MOL2 format. More... | |
| class | MOL2ChargeType |
| Provides constants for the specification of the atom charge type in Sybyl MOL2 files. More... | |
| class | MOL2GZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More... | |
| class | MOL2GZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed Sybyl MOL2 format. More... | |
| class | MOL2GZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More... | |
| class | MOL2GZMoleculeReader |
| Reader for molecule data in the gzip-compressed Sybyl MOL2 format. More... | |
| class | MOL2MolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the Sybyl MOL2 format. More... | |
| class | MOL2MolecularGraphWriter |
| Writer for molecular graph data in the Sybyl MOL2 format. More... | |
| class | MOL2MoleculeInputHandler |
| Handler for the input of molecule data in the Sybyl MOL2 format. More... | |
| class | MOL2MoleculeReader |
| Reader for molecule data in the Sybyl MOL2 format. More... | |
| class | MOL2MoleculeType |
| Provides constants for the specification of the molecule type in Sybyl MOL2 files. More... | |
| class | MOLMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More... | |
| class | MOLMolecularGraphWriter |
| Writer for molecular graph data in the MDL Mol-File [CTFILE] format. More... | |
| class | MOLMoleculeInputHandler |
| Handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More... | |
| class | MOLMoleculeReader |
| Reader for molecule data in the MDL Mol-File [CTFILE] format. More... | |
| class | MatchConstraint |
| Describes a single attribute comparison constraint between a query and a target object. More... | |
| class | MatchConstraintList |
| Data structure storing a set of Chem.MatchConstraint objects together with a logical type. More... | |
| class | MaxCommonAtomSubstructureSearch |
| Searches for the maximum common atom substructures between a query and a target molecular graph. More... | |
| class | MaxCommonBondSubstructureSearch |
| Searches for the maximum common bond substructures between a query and a target molecular graph. More... | |
| class | MolGraphMatchExpressionPtrMolGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | MolecularGraph |
| Abstract base class for data structures that represent chemical structures as molecular graphs. More... | |
| class | MolecularGraphComponentGroupingMatchExpression |
| Chem.MatchExpression implementation that constrains the substructure mapping by the query's component-level groupings. More... | |
| class | MolecularGraphIOManager |
| Singleton class that serves as a global registry for Chem.MolecularGraphInputHandler and Chem.MolecularGraphOutputHandler implementation instances. More... | |
| class | MolecularGraphInputHandler |
| class | MolecularGraphMatchConstraint |
| Provides numerical identifiers for built-in Chem.MolecularGraph matching constraints. More... | |
| class | MolecularGraphMatchExpression |
| Generic boolean expression interface for the implementation of query/target equivalence tests in molecular graph matching algorithms. More... | |
| class | MolecularGraphMatchExpressionList |
| Container for the storage and evaluation of logical match expression lists. More... | |
| class | MolecularGraphOutputHandler |
| Factory interface providing methods for the creation of Chem.MolecularGraphWriterBase instances for data output in a particular storage format. More... | |
| class | MolecularGraphProperty |
| Provides keys for built-in Chem.MolecularGraph properties. More... | |
| class | MolecularGraphPropertyDefault |
| Provides default values for built-in Chem.MolecularGraph properties. More... | |
| class | MolecularGraphWriter |
| Writer for molecule data in any supported format. More... | |
| class | MolecularGraphWriterBase |
| Interface for writing data objects of type Chem.MolecularGraph to an arbitrary data sink. More... | |
| class | Molecule |
| Abstract base class representing a mutable molecular graph that owns and manages its atoms and bonds. More... | |
| class | MoleculeIOManager |
| Singleton class that serves as a global registry for Chem.MoleculeInputHandler and Chem.MoleculeOutputHandler implementation instances. More... | |
| class | MoleculeInputHandler |
| Factory interface providing methods for the creation of Chem.MoleculeReaderBase instances for reading data provided in a particular storage format. More... | |
| class | MoleculeOutputHandler |
| class | MoleculeReader |
| Reader for molecule data in any supported format. More... | |
| class | MoleculeReaderBase |
| Interface for reading data objects of type Chem.Molecule from an arbitrary data source. More... | |
| class | MorganNumberingCalculator |
| Computes canonical atom numberings for molecular graphs using Morgan's algorithm. More... | |
| class | MultiConfMoleculeInputProcessor |
| Abstract base for classes that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules. More... | |
| class | MultiSubstructureSearch |
| Evaluates a boolean expression over multiple substructure queries against a target molecular graph. More... | |
| class | NOTAtomMatchExpression |
| Chem.AtomMatchExpression implementation that negates the evaluation results of a wrapped external expression instance. More... | |
| class | NOTBondMatchExpression |
| Chem.BondMatchExpression implementation that negates the evaluation results of a wrapped external expression instance. More... | |
| class | NOTMolecularGraphMatchExpression |
| Chem.MolecularGraphMatchExpression implementation that negates the evaluation results of a wrapped external expression instance. More... | |
| class | NOTReactionMatchExpression |
| Chem.ReactionMatchExpression implementation that negates the evaluation results of a wrapped external expression instance. More... | |
| class | NitroAciTautomerization |
| Implementation of the nitro ↔ aci-nitro tautomerization rule. More... | |
| class | NitrosoOximeTautomerization |
| Chem.TautomerizationRule implementation for the generation of nitroso ⇄ oxime tautomers. More... | |
| class | ORAtomMatchExpressionList |
| Chem.AtomMatchExpressionList implementation that evaluates the stored expressions as a logical disjunction (OR). More... | |
| class | ORBondMatchExpressionList |
| Chem.BondMatchExpressionList implementation that evaluates the stored expressions as a logical disjunction (OR). More... | |
| class | ORMolecularGraphMatchExpressionList |
| Chem.MolecularGraphMatchExpressionList implementation that evaluates the stored expressions as a logical disjunction (OR). More... | |
| class | ORReactionMatchExpressionList |
| Chem.ReactionMatchExpressionList implementation that evaluates the stored expressions as a logical disjunction (OR). More... | |
| class | PatternAtomTyper |
| Assigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns. More... | |
| class | PatternBasedTautomerizationRule |
| Substructure search pattern-based implementation of the Chem.TautomerizationRule interface. More... | |
| class | PhosphinicAcidTautomerization |
| Chem.TautomerizationRule implementation for the generation of phosphinic acid tautomers. More... | |
| class | PiElectronSystemList |
| Implements the perception of all π-electron systems present in a molecule. More... | |
| class | ProtonationStateStandardizer |
| Adjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives. More... | |
| class | RDFBZ2ReactionInputHandler |
| Handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFBZ2ReactionOutputHandler |
| Handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFBZ2ReactionReader |
| Reader for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format. More... | |
| class | RDFBZ2ReactionWriter |
| Writer for reaction data in the bzip2-compressed MDL RD-File [CTFILE] format. More... | |
| class | RDFGZReactionInputHandler |
| Handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFGZReactionOutputHandler |
| Handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFGZReactionReader |
| Reader for reaction data in the gzip-compressed MDL RD-File [CTFILE] format. More... | |
| class | RDFGZReactionWriter |
| Writer for reaction data in the gzip-compressed MDL RD-File [CTFILE] format. More... | |
| class | RDFReactionInputHandler |
| Handler for the input of reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFReactionOutputHandler |
| Handler for the output of reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFReactionReader |
| Reader for reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RDFReactionWriter |
| Writer for reaction data in the MDL RD-File [CTFILE] format. More... | |
| class | RECAPAtomLabel |
| Provides constants for labeling the endpoints of bonds matched by RECAP fragmentation rules. More... | |
| class | RECAPFragmentGenerator |
| Molecular graph fragment generator implementing the RECAP bond-cleavage rule set. More... | |
| class | RECAPRuleID |
| Provides constants for the identification of RECAP fragmentation rules. More... | |
| class | RXNReactionInputHandler |
| Handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More... | |
| class | RXNReactionOutputHandler |
| Handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More... | |
| class | RXNReactionReader |
| Reader for reaction data in the MDL Rxn-File [CTFILE] format. More... | |
| class | RXNReactionWriter |
| Writer for reaction data in the MDL Rxn-File [CTFILE] format. More... | |
| class | RadicalType |
| Provides constants that are used to specify the degeneracy of the electronic state of radical atoms. More... | |
| class | Reaction |
| Abstract base class for chemical reactions composed of role-tagged reaction components of type Chem.Molecule. More... | |
| class | ReactionAtomMappingMatchExpression |
| Chem.AtomMatchExpression that constrains reaction substructure matches by a required reactant-to-product atom mapping. More... | |
| class | ReactionCenterStatus |
| Provides flags that are used to describe state changes of atoms and bonds in a reaction center. More... | |
| class | ReactionComponentGroupingMatchExpression |
| Chem.MatchExpression implementation that constrains reaction substructure matches by the query's component-level groupings. More... | |
| class | ReactionIOManager |
| Singleton class that serves as a global registry for Chem.ReactionInputHandler and Chem.ReactionOutputHandler implementation instances. More... | |
| class | ReactionInputHandler |
| Factory interface providing methods for the creation of Chem.ReactionReaderBase instances for reading data provided in a particular storage format. More... | |
| class | ReactionMatchConstraint |
| Provides numerical identifiers for built-in Chem.Reaction matching constraints. More... | |
| class | ReactionMatchExpression |
| Generic boolean expression interface for the implementation of query/target equivalence tests in reaction matching algorithms. More... | |
| class | ReactionMatchExpressionList |
| Container for the storage and evaluation of logical match expression lists. More... | |
| class | ReactionOutputHandler |
| Factory interface providing methods for the creation of Chem.ReactionWriterBase instances for data output in a particular storage format. More... | |
| class | ReactionProperty |
| Provides keys for built-in Chem.Reaction properties. More... | |
| class | ReactionPropertyDefault |
| Provides default values for built-in Chem.Reaction properties. More... | |
| class | ReactionReader |
| Reader for reaction data in any supported format. More... | |
| class | ReactionReaderBase |
| Interface for reading data objects of type Chem.Reaction from an arbitrary data source. More... | |
| class | ReactionRole |
| Provides constants that are used to specify the role of molecules (components) in a chemical reaction. More... | |
| class | ReactionSubstructureSearch |
| Searches for substructures of the components of a target reaction that match a given query reaction pattern. More... | |
| class | ReactionWriter |
| Writer for reaction data in any supported format. More... | |
| class | ReactionWriterBase |
| Interface for writing data objects of type Chem.Reaction to an arbitrary data sink. More... | |
| class | Reactor |
| Applies a Chem.Reaction template to the reactant components of a target Chem.Reaction to generate the corresponding product molecules. More... | |
| class | ResonanceStructureGenerator |
| Enumerates the resonance structures of a molecular graph by redistributing π-electrons across conjugated bonds. More... | |
| class | SDFBZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFBZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed MDL SD-File [CTFILE] format. More... | |
| class | SDFBZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFBZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed MDL SD-File [CTFILE] format. More... | |
| class | SDFGZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFGZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed MDL SD-File [CTFILE] format. More... | |
| class | SDFGZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFGZMoleculeReader |
| Reader for molecule data in the gzip-compressed MDL SD-File [CTFILE] format. More... | |
| class | SDFMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFMolecularGraphWriter |
| Writer for molecular graph data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFMoleculeInputHandler |
| Handler for the input of molecule data in the MDL SD-File [CTFILE] format. More... | |
| class | SDFMoleculeReader |
| Reader for molecule data in the MDL SD-File [CTFILE] format. More... | |
| class | SMARTSMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSMolecularGraphWriter |
| Writer for molecular graph data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSMoleculeInputHandler |
| Handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSMoleculeReader |
| Reader for molecule data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSReactionInputHandler |
| Handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSReactionOutputHandler |
| Handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSReactionReader |
| Reader for reaction data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMARTSReactionWriter |
| Writer for reaction data in the Daylight SMARTS [SMARTS] format. More... | |
| class | SMILESBZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2ReactionInputHandler |
| Handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2ReactionOutputHandler |
| Handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2ReactionReader |
| Reader for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESBZ2ReactionWriter |
| Writer for reaction data in the bzip2-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZMoleculeReader |
| Reader for molecule data in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZReactionInputHandler |
| Handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZReactionOutputHandler |
| Handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZReactionReader |
| Reader for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESGZReactionWriter |
| Writer for reaction data in the gzip-compressed Daylight SMILES [SMILES] format. More... | |
| class | SMILESMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESMolecularGraphWriter |
| Writer for molecular graph data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESMoleculeInputHandler |
| Handler for the input of molecule data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESMoleculeReader |
| Reader for molecule data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESReactionInputHandler |
| Handler for the input of reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESReactionOutputHandler |
| Handler for the output of reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESReactionReader |
| Reader for reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SMILESReactionWriter |
| Writer for reaction data in the Daylight SMILES [SMILES] format. More... | |
| class | SizeTypeAtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | SizeTypeAtomMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | SmallestSetOfSmallestRings |
| Implements the perception of the Smallest Set of Smallest Rings (SSSR) of a molecular graphs. More... | |
| class | SpatialAtomAlignment |
| class | SpatialEntity3DAlignment |
| class | StereoDescriptor |
| Data structure for the storage and retrieval of stereochemical information about atoms and bonds. More... | |
| class | StereoisomerGenerator |
| Enumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters. More... | |
| class | StringDataBlock |
| Array of Chem.StringDataBlockEntry instances. More... | |
| class | StringDataBlockEntry |
| Represents a data item consisting of a header and a data payload. More... | |
| class | SubstructureEditor |
| Pattern-driven editor that rewrites matched substructures of a molecule according to a given editing template. More... | |
| class | SubstructureHistogramCalculator |
| Counts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container. More... | |
| class | SubstructureSearch |
| Searches for substructures of a target molecular graph that match the topology of a given query molecular graph. More... | |
| class | SulfenicAcidTautomerization |
| Chem.TautomerizationRule implementation for the generation of sulfenic acid tautomers. More... | |
| class | SurfaceAtomExtractor |
| Identifies the accessible surface atoms in a given set of atoms. More... | |
| class | SybylAtomType |
| Provides constants for the specification of the Tripos Sybyl atom type. More... | |
| class | SybylBondType |
| Provides constants for the specification of the Tripos Sybyl bond type. More... | |
| class | SymmetryClassCalculator |
| Perceives the topological symmetry classes of the atoms in a molecular graph. More... | |
| class | TautomerGenerator |
| Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem.TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback. More... | |
| class | TautomerScore |
| Functor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph. More... | |
| class | TautomerizationRule |
| Abstract base class for tautomerization rule implementations employed by the Chem.TautomerGenerator class. More... | |
| class | TautomerizationType |
| Provides constants serving as numeric identifiers for built-in Chem.TautomerizationRule implementations. More... | |
| class | TopologicalAtomAlignment |
| class | TopologicalEntity3DAlignment |
| class | UInt64AtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | UInt64AtomMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | UInt64BondFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | Vector2DAtomFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | Vector3DEntity3DFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | VoidMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | VoidMoleculeMolecularGraphFunctor |
| A wrapper class for various types of callable objects. More... | |
| class | XYZBZ2MolecularGraphOutputHandler |
| Handler for the output of bzip2-compressed molecular graph data in the XYZ format. More... | |
| class | XYZBZ2MolecularGraphWriter |
| Writer for molecular graph data in the bzip2-compressed XYZ format. More... | |
| class | XYZBZ2MoleculeInputHandler |
| Handler for the input of bzip2-compressed molecule data in the XYZ format. More... | |
| class | XYZBZ2MoleculeReader |
| Reader for molecule data in the bzip2-compressed XYZ format. More... | |
| class | XYZGZMolecularGraphOutputHandler |
| Handler for the output of gzip-compressed molecular graph data in the XYZ format. More... | |
| class | XYZGZMolecularGraphWriter |
| Writer for molecular graph data in the gzip-compressed XYZ format. More... | |
| class | XYZGZMoleculeInputHandler |
| Handler for the input of gzip-compressed molecule data in the XYZ format. More... | |
| class | XYZGZMoleculeReader |
| Reader for molecule data in the gzip-compressed XYZ format. More... | |
| class | XYZMolecularGraphOutputHandler |
| Handler for the output of molecular graph data in the XYZ format. More... | |
| class | XYZMolecularGraphWriter |
| Writer for molecular graph data in XYZ format to an output stream. More... | |
| class | XYZMoleculeInputHandler |
| Handler for the input of molecule data in the XYZ format. More... | |
| class | XYZMoleculeReader |
| Reader for molecule data in XYZ format from an input stream. More... | |
Functions | |
| None | set2DCoordinates (Atom atom, Math.Vector2D coords) |
| Sets the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom to coords. More... | |
| bool | has2DCoordinates (Atom atom) |
| Tells whether the Chem.AtomProperty.COORDINATES_2D property of the atom atom is set. More... | |
| Math.Vector2D | get2DCoordinates (Atom atom) |
| Returns the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom. More... | |
| None | clear2DCoordinates (Atom atom) |
| Clears the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom. More... | |
| None | set2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords) |
| Writes the 2D coordinates in coords back to the corresponding atoms of cntnr. More... | |
| None | get2DCoordinates (AtomContainer cntnr, Math.Vector2DArray coords, bool append=False) |
| Extracts the 2D coordinates of all atoms in cntnr into coords. More... | |
| None | set2DStereoFlag (Bond bond, int flag) |
| Sets the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond to flag. More... | |
| bool | has2DStereoFlag (Bond bond) |
| Tells whether the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond is set. More... | |
| int | get2DStereoFlag (Bond bond) |
| Returns the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond. More... | |
| None | clear2DStereoFlag (Bond bond) |
| Clears the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond. More... | |
| None | set3DCoordinatesArray (Atom atom, Math.Vector3DArray coords_array) |
| Sets the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom to coords_array. More... | |
| bool | has3DCoordinatesArray (Atom atom) |
| Tells whether the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom is set. More... | |
| Math.Vector3DArray | get3DCoordinatesArray (Atom atom) |
| Returns the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom. More... | |
| None | clear3DCoordinatesArray (Atom atom) |
| Clears the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom. More... | |
| None | get3DCoordinates (AtomContainer cntnr, Math.Vector3DArray coords, Atom3DCoordinatesFunction coords_func, bool append=False) |
| Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func. More... | |
| None | set3DCoordinates (Entity3D entity, Math.Vector3D coords) |
| Sets the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity to coords. More... | |
| bool | has3DCoordinates (Entity3D entity) |
| Tells whether the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity is set. More... | |
| Math.Vector3D | get3DCoordinates (Entity3D entity) |
| Returns the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity. More... | |
| None | clear3DCoordinates (Entity3D entity) |
| Clears the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity. More... | |
| None | set3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords) |
| Sets the 3D coordinates of the entities of cntnr from coords. More... | |
| None | get3DCoordinates (Entity3DContainer cntnr, Math.Vector3DArray coords, bool append=False) |
| Stores the 3D coordinates of the entities of cntnr in coords. More... | |
| FragmentList | getAromaticRings (MolecularGraph molgraph) |
| Returns the subset of the aromatic rings of the molecular graph molgraph. More... | |
| FragmentList | getAromaticSSSRSubset (MolecularGraph molgraph) |
| Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,. More... | |
| None | setAromaticSubstructure (MolecularGraph molgraph, Fragment substruct) |
| Sets the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More... | |
| bool | hasAromaticSubstructure (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More... | |
| Fragment | getAromaticSubstructure (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More... | |
| None | clearAromaticSubstructure (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph. More... | |
| None | setAromaticityFlag (Atom atom, bool aromatic) |
| Sets the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom to aromatic. More... | |
| bool | hasAromaticityFlag (Atom atom) |
| Tells whether the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom is set. More... | |
| bool | getAromaticityFlag (Atom atom) |
| Returns the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom. More... | |
| None | clearAromaticityFlag (Atom atom) |
| Clears the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom. More... | |
| None | setAromaticityFlag (Bond bond, bool aromatic) |
| Sets the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond to aromatic. More... | |
| bool | hasAromaticityFlag (Bond bond) |
| Tells whether the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond is set. More... | |
| bool | getAromaticityFlag (Bond bond) |
| Returns the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond. More... | |
| None | clearAromaticityFlag (Bond bond) |
| Clears the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond. More... | |
| None | setAromaticityFlags (MolecularGraph molgraph, bool overwrite) |
| Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph. More... | |
| None | setAtomMappingID (Atom atom, int id) |
| Sets the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom to id. More... | |
| bool | hasAtomMappingID (Atom atom) |
| Tells whether the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom is set. More... | |
| int | getAtomMappingID (Atom atom) |
| Returns the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom. More... | |
| None | clearAtomMappingID (Atom atom) |
| Clears the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom. More... | |
| None | setAtomMapping (Reaction rxn, AtomMapping mapping) |
| Sets the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn to mapping. More... | |
| bool | hasAtomMapping (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn is set. More... | |
| AtomMapping | getAtomMapping (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn. More... | |
| None | clearAtomMapping (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn. More... | |
| None | setAtomMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite) |
| Sets the match constraint list constr on every atom of the molecular graph molgraph. More... | |
| None | setAtomMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite) |
| Sets the atom-level match constraint list constr on every atom of every component of the reaction rxn. More... | |
| None | setAtomSymbolsFromTypes (MolecularGraph molgraph, bool overwrite) |
| Sets the atom symbols of the molecular graph molgraph from their atom types. More... | |
| None | setAtomTypesFromSymbols (MolecularGraph molgraph, bool overwrite) |
| Sets the atom types of the molecular graph molgraph from their element symbols. More... | |
| None | setBondMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr, bool overwrite) |
| Sets the match constraint list constr on every bond of the molecular graph molgraph. More... | |
| None | setBondMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite) |
| Sets the bond-level match constraint list constr on every bond of every component of the reaction rxn. More... | |
| None | setCIPConfiguration (Atom atom, int config) |
| Sets the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom to config. More... | |
| bool | hasCIPConfiguration (Atom atom) |
| Tells whether the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom is set. More... | |
| int | getCIPConfiguration (Atom atom) |
| Returns the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom. More... | |
| None | clearCIPConfiguration (Atom atom) |
| Clears the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom. More... | |
| None | setCIPConfiguration (Bond bond, int config) |
| Sets the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond to config. More... | |
| bool | hasCIPConfiguration (Bond bond) |
| Tells whether the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond is set. More... | |
| int | getCIPConfiguration (Bond bond) |
| Returns the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond. More... | |
| None | clearCIPConfiguration (Bond bond) |
| Clears the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond. More... | |
| None | setCIPPriority (Atom atom, int priority) |
| Sets the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom to priority. More... | |
| bool | hasCIPPriority (Atom atom) |
| Tells whether the Chem.AtomProperty.CIP_PRIORITY property of the atom atom is set. More... | |
| int | getCIPPriority (Atom atom) |
| Returns the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom. More... | |
| None | clearCIPPriority (Atom atom) |
| Clears the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom. More... | |
| None | setCanonicalNumber (Atom atom, int num) |
| Sets the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom to num. More... | |
| bool | hasCanonicalNumber (Atom atom) |
| Tells whether the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom is set. More... | |
| int | getCanonicalNumber (Atom atom) |
| Returns the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom. More... | |
| None | clearCanonicalNumber (Atom atom) |
| Clears the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom. More... | |
| None | setComment (MolecularGraph molgraph, str comment) |
| Sets the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph to comment. More... | |
| bool | hasComment (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph is set. More... | |
| str | getComment (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph. More... | |
| None | clearComment (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph. More... | |
| None | setComment (Reaction rxn, str comment) |
| Sets the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn to comment. More... | |
| bool | hasComment (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.COMMENT property of the reaction rxn is set. More... | |
| str | getComment (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn. More... | |
| None | clearComment (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn. More... | |
| int | getCompleteBondCount (MolecularGraph molgraph) |
| Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph. More... | |
| None | setComponentGroupID (Atom atom, int id) |
| Sets the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom to id. More... | |
| bool | hasComponentGroupID (Atom atom) |
| Tells whether the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom is set. More... | |
| int | getComponentGroupID (Atom atom) |
| Returns the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom. More... | |
| None | clearComponentGroupID (Atom atom) |
| Clears the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom. More... | |
| None | setComponentGroups (MolecularGraph molgraph, FragmentList comp_groups) |
| Sets the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph to comp_groups. More... | |
| bool | hasComponentGroups (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph is set. More... | |
| FragmentList | getComponentGroups (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph. More... | |
| None | clearComponentGroups (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph. More... | |
| None | setComponentGroups (Reaction rxn, FragmentList comp_groups) |
| Sets the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn to comp_groups. More... | |
| bool | hasComponentGroups (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn is set. More... | |
| FragmentList | getComponentGroups (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn. More... | |
| None | clearComponentGroups (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn. More... | |
| None | setComponentMatchConstraints (Reaction rxn, MatchConstraintList constr, bool overwrite) |
| Sets the molecular graph-level match constraint list constr on every component of the reaction rxn. More... | |
| None | setComponents (MolecularGraph molgraph, FragmentList comps) |
| Sets the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph to comps. More... | |
| bool | hasComponents (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph is set. More... | |
| FragmentList | getComponents (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph. More... | |
| None | clearComponents (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph. More... | |
| None | getConformation (AtomContainer cntnr, int conf_idx, Math.Vector3DArray coords, bool append=False) |
| Extracts the conformation at index conf_idx into coords. More... | |
| float | getConformationEnergy (MolecularGraph molgraph, int conf_idx) |
| Returns the energy of the conformation at index conf_idx. More... | |
| None | setConformationIndex (MolecularGraph molgraph, int index) |
| Sets the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph to index. More... | |
| bool | hasConformationIndex (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph is set. More... | |
| int | getConformationIndex (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph. More... | |
| None | clearConformationIndex (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph. More... | |
| None | setConformation (MolecularGraph molgraph, int conf_idx, Math.Vector3DArray coords, float energy) |
| Overwrites the conformation at index conf_idx with the supplied coordinates and energy. More... | |
| None | clearConformations (AtomContainer cntnr) |
| Removes all stored conformations from the atoms of cntnr. More... | |
| Math.Vector3D | getConformer3DCoordinates (Atom atom, int conf_idx) |
| Returns the 3D coordinates of the atom atom in the conformer with index conf_idx. More... | |
| None | setConformerEnergies (MolecularGraph molgraph, Util.DArray energies) |
| Sets the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph to energies. More... | |
| bool | hasConformerEnergies (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph is set. More... | |
| Util.DArray | getConformerEnergies (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph. More... | |
| None | clearConformerEnergies (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph. More... | |
| int | getConnectedAtomsAndBonds (Atom atom, MolecularGraph molgraph, list atoms, list bonds, Atom excl_atom) |
| int | getConnectedAtoms (Atom atom, MolecularGraph molgraph, list atoms, Atom excl_atom) |
| None | getContainedFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True) |
| Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list. More... | |
| None | getContainingFragments (Atom atom, FragmentList frag_list, FragmentList cont_frag_list) |
| None | getContainingFragments (Bond bond, FragmentList frag_list, FragmentList cont_frag_list) |
| None | getContainingFragments (MolecularGraph molgraph, FragmentList frag_list, FragmentList cont_frag_list, bool append=False, bool atoms=True, bool bonds=True) |
| Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list. More... | |
| bool | hasCoordinates (AtomContainer cntnr, int dim) |
| Tells whether all atoms of cntnr carry coordinates of the given dimensionality. More... | |
| None | setCyclicSubstructure (MolecularGraph molgraph, Fragment substruct) |
| Sets the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct. More... | |
| bool | hasCyclicSubstructure (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph is set. More... | |
| Fragment | getCyclicSubstructure (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More... | |
| None | clearCyclicSubstructure (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph. More... | |
| None | setDirection (Bond bond, int dir) |
| Sets the value of the Chem.BondProperty.DIRECTION property of the bond bond to dir. More... | |
| bool | hasDirection (Bond bond) |
| Tells whether the Chem.BondProperty.DIRECTION property of the bond bond is set. More... | |
| int | getDirection (Bond bond) |
| Returns the value of the Chem.BondProperty.DIRECTION property of the bond bond. More... | |
| None | clearDirection (Bond bond) |
| Clears the value of the Chem.BondProperty.DIRECTION property of the bond bond. More... | |
| int | getEnvironment (Atom atom, MolecularGraph molgraph, int max_dist, Fragment env, bool append=False) |
| Collects every atom of the molecular graph molgraph that is within max_dist bonds of the atom atom into the fragment env. More... | |
| None | setFormalCharge (Atom atom, int charge) |
| Sets the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom to charge. More... | |
| bool | hasFormalCharge (Atom atom) |
| Tells whether the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom is set. More... | |
| int | getFormalCharge (Atom atom) |
| Returns the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom. More... | |
| None | clearFormalCharge (Atom atom) |
| Clears the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom. More... | |
| int | getGenericType (Atom atom) |
| Returns the generic atom type associated with numeric type property of the atom atom. More... | |
| None | setGeometricalDistanceMatrix (MolecularGraph molgraph, Math.DMatrix mtx) |
| Sets the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More... | |
| bool | hasGeometricalDistanceMatrix (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More... | |
| Math.DMatrix | getGeometricalDistanceMatrix (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More... | |
| None | clearGeometricalDistanceMatrix (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More... | |
| None | setHashCode (MolecularGraph molgraph, int hash_code) |
| Sets the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph to hash_code. More... | |
| bool | hasHashCode (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph is set. More... | |
| int | getHashCode (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph. More... | |
| None | clearHashCode (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph. More... | |
| None | setHybridizationState (Atom atom, int state) |
| Sets the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom to state. More... | |
| bool | hasHybridizationState (Atom atom) |
| Tells whether the Chem.AtomProperty.HYBRIDIZATION property of the atom atom is set. More... | |
| int | getHybridizationState (Atom atom) |
| Returns the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom. More... | |
| None | clearHybridizationState (Atom atom) |
| Clears the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom. More... | |
| None | setImplicitHydrogenCount (Atom atom, int count) |
| Sets the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom to count. More... | |
| bool | hasImplicitHydrogenCount (Atom atom) |
| Tells whether the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom is set. More... | |
| int | getImplicitHydrogenCount (Atom atom) |
| Returns the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom. More... | |
| None | clearImplicitHydrogenCount (Atom atom) |
| Clears the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom. More... | |
| int | getIncidentBonds (Atom atom, MolecularGraph molgraph, list bonds, Atom excl_atom) |
| None | setIsotope (Atom atom, int isotope) |
| Sets the value of the Chem.AtomProperty.ISOTOPE property of the atom atom to isotope. More... | |
| bool | hasIsotope (Atom atom) |
| Tells whether the Chem.AtomProperty.ISOTOPE property of the atom atom is set. More... | |
| int | getIsotope (Atom atom) |
| Returns the value of the Chem.AtomProperty.ISOTOPE property of the atom atom. More... | |
| None | clearIsotope (Atom atom) |
| Clears the value of the Chem.AtomProperty.ISOTOPE property of the atom atom. More... | |
| None | setMDLCTABVersion (MolecularGraph molgraph, int version) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph to version. More... | |
| bool | hasMDLCTABVersion (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph is set. More... | |
| int | getMDLCTABVersion (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph. More... | |
| None | clearMDLCTABVersion (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph. More... | |
| None | setMDLChiralFlag (MolecularGraph molgraph, bool flag) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph to flag. More... | |
| bool | hasMDLChiralFlag (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph is set. More... | |
| bool | getMDLChiralFlag (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph. More... | |
| None | clearMDLChiralFlag (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph. More... | |
| None | setMDLDimensionality (MolecularGraph molgraph, int dim) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph to dim. More... | |
| bool | hasMDLDimensionality (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph is set. More... | |
| int | getMDLDimensionality (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph. More... | |
| None | clearMDLDimensionality (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph. More... | |
| None | setMDLEnergy (MolecularGraph molgraph, float energy) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph to energy. More... | |
| bool | hasMDLEnergy (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph is set. More... | |
| float | getMDLEnergy (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph. More... | |
| None | clearMDLEnergy (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph. More... | |
| None | setMDLExternalRegistryNumber (Reaction rxn, str reg_no) |
| Sets the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More... | |
| bool | hasMDLExternalRegistryNumber (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More... | |
| str | getMDLExternalRegistryNumber (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | clearMDLExternalRegistryNumber (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | setMDLInternalRegistryNumber (Reaction rxn, str reg_no) |
| Sets the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More... | |
| bool | hasMDLInternalRegistryNumber (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set. More... | |
| str | getMDLInternalRegistryNumber (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | clearMDLInternalRegistryNumber (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | setMDLMoleculeRecord (Reaction rxn, Molecule mol_rec) |
| Sets the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec. More... | |
| bool | hasMDLMoleculeRecord (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn is set. More... | |
| Molecule | getMDLMoleculeRecord (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn. More... | |
| None | clearMDLMoleculeRecord (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn. More... | |
| None | setMDLParity (Atom atom, int parity) |
| Sets the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom to parity. More... | |
| bool | hasMDLParity (Atom atom) |
| Tells whether the Chem.AtomProperty.MDL_PARITY property of the atom atom is set. More... | |
| int | getMDLParity (Atom atom) |
| Returns the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom. More... | |
| None | clearMDLParity (Atom atom) |
| Clears the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom. More... | |
| None | setMDLProgramName (MolecularGraph molgraph, str name) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph to name. More... | |
| bool | hasMDLProgramName (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph is set. More... | |
| str | getMDLProgramName (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph. More... | |
| None | clearMDLProgramName (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph. More... | |
| None | setMDLProgramName (Reaction rxn, str name) |
| Sets the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn to name. More... | |
| bool | hasMDLProgramName (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn is set. More... | |
| str | getMDLProgramName (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn. More... | |
| None | clearMDLProgramName (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn. More... | |
| None | setMDLRXNFileVersion (Reaction rxn, int version) |
| Sets the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn to version. More... | |
| bool | hasMDLRXNFileVersion (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn is set. More... | |
| int | getMDLRXNFileVersion (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn. More... | |
| None | clearMDLRXNFileVersion (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn. More... | |
| None | setMDLRegistryNumber (MolecularGraph molgraph, int reg_no) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph to reg_no. More... | |
| bool | hasMDLRegistryNumber (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph is set. More... | |
| int | getMDLRegistryNumber (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More... | |
| None | clearMDLRegistryNumber (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph. More... | |
| None | setMDLRegistryNumber (Reaction rxn, int reg_no) |
| Sets the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no. More... | |
| bool | hasMDLRegistryNumber (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn is set. More... | |
| int | getMDLRegistryNumber (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | clearMDLRegistryNumber (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn. More... | |
| None | setMDLScalingFactor1 (MolecularGraph molgraph, int factor) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph to factor. More... | |
| bool | hasMDLScalingFactor1 (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph is set. More... | |
| int | getMDLScalingFactor1 (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More... | |
| None | clearMDLScalingFactor1 (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph. More... | |
| None | setMDLScalingFactor2 (MolecularGraph molgraph, float factor) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph to factor. More... | |
| bool | hasMDLScalingFactor2 (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph is set. More... | |
| float | getMDLScalingFactor2 (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More... | |
| None | clearMDLScalingFactor2 (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph. More... | |
| None | setMDLStereoCareFlag (Atom atom, bool flag) |
| Sets the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom to flag. More... | |
| bool | hasMDLStereoCareFlag (Atom atom) |
| Tells whether the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom is set. More... | |
| bool | getMDLStereoCareFlag (Atom atom) |
| Returns the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom. More... | |
| None | clearMDLStereoCareFlag (Atom atom) |
| Clears the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom. More... | |
| None | setMDLUserInitials (MolecularGraph molgraph, str initials) |
| Sets the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph to initials. More... | |
| bool | hasMDLUserInitials (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph is set. More... | |
| str | getMDLUserInitials (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph. More... | |
| None | clearMDLUserInitials (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph. More... | |
| None | setMDLUserInitials (Reaction rxn, str initials) |
| Sets the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn to initials. More... | |
| bool | hasMDLUserInitials (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn is set. More... | |
| str | getMDLUserInitials (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn. More... | |
| None | clearMDLUserInitials (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn. More... | |
| None | setMOL2Charge (Atom atom, float charge) |
| Sets the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom to charge. More... | |
| bool | hasMOL2Charge (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_CHARGE property of the atom atom is set. More... | |
| float | getMOL2Charge (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom. More... | |
| None | clearMOL2Charge (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom. More... | |
| None | setMOL2ChargeType (MolecularGraph molgraph, int type) |
| Sets the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph to type. More... | |
| bool | hasMOL2ChargeType (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph is set. More... | |
| int | getMOL2ChargeType (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph. More... | |
| None | clearMOL2ChargeType (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph. More... | |
| None | setMOL2MoleculeType (MolecularGraph molgraph, int type) |
| Sets the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type. More... | |
| bool | hasMOL2MoleculeType (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph is set. More... | |
| int | getMOL2MoleculeType (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph. More... | |
| None | clearMOL2MoleculeType (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph. More... | |
| None | setMOL2Name (Atom atom, str name) |
| Sets the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom to name. More... | |
| bool | hasMOL2Name (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_NAME property of the atom atom is set. More... | |
| str | getMOL2Name (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom. More... | |
| None | clearMOL2Name (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom. More... | |
| None | setMOL2SubstructureChain (Atom atom, str chain) |
| Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom to chain. More... | |
| bool | hasMOL2SubstructureChain (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom is set. More... | |
| str | getMOL2SubstructureChain (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More... | |
| None | clearMOL2SubstructureChain (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom. More... | |
| None | setMOL2SubstructureID (Atom atom, int id) |
| Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom to id. More... | |
| bool | hasMOL2SubstructureID (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom is set. More... | |
| int | getMOL2SubstructureID (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom. More... | |
| None | clearMOL2SubstructureID (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom. More... | |
| None | setMOL2SubstructureName (Atom atom, str name) |
| bool | hasMOL2SubstructureName (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom is set. More... | |
| str | getMOL2SubstructureName (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom. More... | |
| None | clearMOL2SubstructureName (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom. More... | |
| None | setMOL2SubstructureSubtype (Atom atom, str subtype) |
| Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom to subtype. More... | |
| bool | hasMOL2SubstructureSubtype (Atom atom) |
| Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom is set. More... | |
| str | getMOL2SubstructureSubtype (Atom atom) |
| Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More... | |
| None | clearMOL2SubstructureSubtype (Atom atom) |
| Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom. More... | |
| None | setMatchConstraints (Atom atom, MatchConstraintList constr) |
| Sets the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom to constr. More... | |
| bool | hasMatchConstraints (Atom atom) |
| Tells whether the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom is set. More... | |
| MatchConstraintList | getMatchConstraints (Atom atom) |
| Returns the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom. More... | |
| None | clearMatchConstraints (Atom atom) |
| Clears the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom. More... | |
| None | setMatchConstraints (Bond bond, MatchConstraintList constr) |
| Sets the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond to constr. More... | |
| bool | hasMatchConstraints (Bond bond) |
| Tells whether the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond is set. More... | |
| MatchConstraintList | getMatchConstraints (Bond bond) |
| Returns the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond. More... | |
| None | clearMatchConstraints (Bond bond) |
| Clears the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond. More... | |
| None | setMatchConstraints (MolecularGraph molgraph, MatchConstraintList constr) |
| Sets the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph to constr. More... | |
| bool | hasMatchConstraints (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph is set. More... | |
| MatchConstraintList | getMatchConstraints (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph. More... | |
| None | clearMatchConstraints (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph. More... | |
| None | setMatchConstraints (Reaction rxn, MatchConstraintList constr) |
| Sets the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn to constr. More... | |
| bool | hasMatchConstraints (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn is set. More... | |
| MatchConstraintList | getMatchConstraints (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn. More... | |
| None | clearMatchConstraints (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn. More... | |
| None | setMatchExpression (Atom atom, AtomMatchExpression expr) |
| Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom to expr. More... | |
| bool | hasMatchExpression (Atom atom) |
| Tells whether the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom is set. More... | |
| AtomMatchExpression | getMatchExpression (Atom atom) |
| Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom. More... | |
| None | clearMatchExpression (Atom atom) |
| Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom. More... | |
| None | setMatchExpression (Bond bond, BondMatchExpression expr) |
| Sets the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond to expr. More... | |
| bool | hasMatchExpression (Bond bond) |
| Tells whether the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond is set. More... | |
| BondMatchExpression | getMatchExpression (Bond bond) |
| Returns the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond. More... | |
| None | clearMatchExpression (Bond bond) |
| Clears the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond. More... | |
| None | setMatchExpression (MolecularGraph molgraph, MolecularGraphMatchExpression expr) |
| Sets the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph to expr. More... | |
| bool | hasMatchExpression (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph is set. More... | |
| MolecularGraphMatchExpression | getMatchExpression (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph. More... | |
| None | clearMatchExpression (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph. More... | |
| None | setMatchExpression (Reaction rxn, ReactionMatchExpression expr) |
| Sets the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn to expr. More... | |
| bool | hasMatchExpression (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn is set. More... | |
| ReactionMatchExpression | getMatchExpression (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn. More... | |
| None | clearMatchExpression (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn. More... | |
| None | setMatchExpressionString (Atom atom, str expr_str) |
| Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom to expr_str. More... | |
| bool | hasMatchExpressionString (Atom atom) |
| Tells whether the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom is set. More... | |
| str | getMatchExpressionString (Atom atom) |
| Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom. More... | |
| None | clearMatchExpressionString (Atom atom) |
| Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom. More... | |
| None | setMatchExpressionString (Bond bond, str expr_str) |
| Sets the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond to expr_str. More... | |
| bool | hasMatchExpressionString (Bond bond) |
| Tells whether the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond is set. More... | |
| str | getMatchExpressionString (Bond bond) |
| Returns the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond. More... | |
| None | clearMatchExpressionString (Bond bond) |
| Clears the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond. More... | |
| int | getMaxAtomMappingID (AtomContainer cntnr) |
| Returns the largest atom mapping ID assigned to any atom of cntnr. More... | |
| int | getMaxAtomMappingID (Reaction rxn) |
| Returns the largest atom mapping ID found for any of the atoms of the components of the reaction rxn. More... | |
| int | getMaxComponentGroupID (AtomContainer cntnr) |
| Returns the largest component-group ID assigned to any atom of cntnr. More... | |
| int | getMaxComponentGroupID (Reaction rxn) |
| Returns the largest component group ID found for any of the atoms of the components of the reaction rxn. More... | |
| None | setMorganNumber (Atom atom, int num) |
| Sets the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom to num. More... | |
| bool | hasMorganNumber (Atom atom) |
| Tells whether the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom is set. More... | |
| int | getMorganNumber (Atom atom) |
| Returns the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom. More... | |
| None | clearMorganNumber (Atom atom) |
| Clears the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom. More... | |
| None | setName (Atom atom, str name) |
| Sets the value of the Chem.AtomProperty.NAME property of the atom atom to name. More... | |
| bool | hasName (Atom atom) |
| Tells whether the Chem.AtomProperty.NAME property of the atom atom is set. More... | |
| str | getName (Atom atom) |
| Returns the value of the Chem.AtomProperty.NAME property of the atom atom. More... | |
| None | clearName (Atom atom) |
| Clears the value of the Chem.AtomProperty.NAME property of the atom atom. More... | |
| None | setName (MolecularGraph molgraph, str name) |
| Sets the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph to name. More... | |
| bool | hasName (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph is set. More... | |
| str | getName (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph. More... | |
| None | clearName (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph. More... | |
| None | setName (Reaction rxn, str name) |
| Sets the value of the Chem.ReactionProperty.NAME property of the reaction rxn to name. More... | |
| bool | hasName (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.NAME property of the reaction rxn is set. More... | |
| str | getName (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.NAME property of the reaction rxn. More... | |
| None | clearName (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.NAME property of the reaction rxn. More... | |
| int | getNumConformations (AtomContainer cntnr) |
| Returns the number of conformations stored on the atoms of cntnr. More... | |
| int | getNumContainingFragments (Atom atom, FragmentList frag_list) |
| Returns the number of fragments in frag_list that contain the atom atom. More... | |
| int | getNumContainingFragments (Bond bond, FragmentList frag_list) |
| Returns the number of fragments in frag_list that contain the bond bond. More... | |
| None | setOrder (Bond bond, int order) |
| Sets the value of the Chem.BondProperty.ORDER property of the bond bond to order. More... | |
| bool | hasOrder (Bond bond) |
| Tells whether the Chem.BondProperty.ORDER property of the bond bond is set. More... | |
| int | getOrder (Bond bond) |
| Returns the value of the Chem.BondProperty.ORDER property of the bond bond. More... | |
| None | clearOrder (Bond bond) |
| Clears the value of the Chem.BondProperty.ORDER property of the bond bond. More... | |
| None | setPiElectronSystems (MolecularGraph molgraph, ElectronSystemList pi_systems) |
| Sets the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems. More... | |
| bool | hasPiElectronSystems (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set. More... | |
| ElectronSystemList | getPiElectronSystems (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More... | |
| None | clearPiElectronSystems (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph. More... | |
| None | setRadicalType (Atom atom, int type) |
| Sets the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom to type. More... | |
| bool | hasRadicalType (Atom atom) |
| Tells whether the Chem.AtomProperty.RADICAL_TYPE property of the atom atom is set. More... | |
| int | getRadicalType (Atom atom) |
| Returns the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom. More... | |
| None | clearRadicalType (Atom atom) |
| Clears the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom. More... | |
| None | setReactionCenterStatus (Atom atom, int status) |
| Sets the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom to status. More... | |
| bool | hasReactionCenterStatus (Atom atom) |
| Tells whether the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom is set. More... | |
| int | getReactionCenterStatus (Atom atom) |
| Returns the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom. More... | |
| None | clearReactionCenterStatus (Atom atom) |
| Clears the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom. More... | |
| None | setReactionCenterStatus (Bond bond, int status) |
| Sets the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond to status. More... | |
| bool | hasReactionCenterStatus (Bond bond) |
| Tells whether the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond is set. More... | |
| int | getReactionCenterStatus (Bond bond) |
| Returns the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond. More... | |
| None | clearReactionCenterStatus (Bond bond) |
| Clears the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond. More... | |
| None | setReactionData (Reaction rxn, StringDataBlock data) |
| Sets the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn to data. More... | |
| bool | hasReactionData (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn is set. More... | |
| StringDataBlock | getReactionData (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn. More... | |
| None | clearReactionData (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn. More... | |
| None | setRingFlag (Atom atom, bool in_ring) |
| Sets the value of the Chem.AtomProperty.RING_FLAG property of the atom atom to in_ring. More... | |
| bool | hasRingFlag (Atom atom) |
| Tells whether the Chem.AtomProperty.RING_FLAG property of the atom atom is set. More... | |
| bool | getRingFlag (Atom atom) |
| Returns the value of the Chem.AtomProperty.RING_FLAG property of the atom atom. More... | |
| None | clearRingFlag (Atom atom) |
| Clears the value of the Chem.AtomProperty.RING_FLAG property of the atom atom. More... | |
| None | setRingFlag (Bond bond, bool in_ring) |
| Sets the value of the Chem.BondProperty.RING_FLAG property of the bond bond to in_ring. More... | |
| bool | hasRingFlag (Bond bond) |
| Tells whether the Chem.BondProperty.RING_FLAG property of the bond bond is set. More... | |
| bool | getRingFlag (Bond bond) |
| Returns the value of the Chem.BondProperty.RING_FLAG property of the bond bond. More... | |
| None | clearRingFlag (Bond bond) |
| Clears the value of the Chem.BondProperty.RING_FLAG property of the bond bond. More... | |
| None | setRingFlags (MolecularGraph molgraph, bool overwrite) |
| Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph. More... | |
| None | setRings (MolecularGraph molgraph, FragmentList rings) |
| Sets the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph to rings. More... | |
| bool | hasRings (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph is set. More... | |
| FragmentList | getRings (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph. More... | |
| None | clearRings (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph. More... | |
| None | setSSSR (MolecularGraph molgraph, FragmentList sssr) |
| Sets the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph to sssr. More... | |
| bool | hasSSSR (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph is set. More... | |
| FragmentList | getSSSR (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph. More... | |
| None | clearSSSR (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph. More... | |
| int | getSizeOfLargestContainingFragment (Atom atom, FragmentList frag_list) |
| Returns the size (in atoms) of the largest fragment in frag_list that contains the atom atom. More... | |
| int | getSizeOfLargestContainingFragment (Bond bond, FragmentList frag_list) |
| Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond. More... | |
| int | getSizeOfSmallestContainingFragment (Atom atom, FragmentList frag_list) |
| Returns the size (in atoms) of the smallest fragment in frag_list that contains the atom atom. More... | |
| int | getSizeOfSmallestContainingFragment (Bond bond, FragmentList frag_list) |
| Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond. More... | |
| None | setStereoCenterFlag (Atom atom, bool is_center) |
| Sets the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom to is_center. More... | |
| bool | hasStereoCenterFlag (Atom atom) |
| Tells whether the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom is set. More... | |
| bool | getStereoCenterFlag (Atom atom) |
| Returns the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom. More... | |
| None | clearStereoCenterFlag (Atom atom) |
| Clears the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom. More... | |
| None | setStereoCenterFlag (Bond bond, bool is_center) |
| Sets the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond to is_center. More... | |
| bool | hasStereoCenterFlag (Bond bond) |
| Tells whether the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond is set. More... | |
| bool | getStereoCenterFlag (Bond bond) |
| Returns the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond. More... | |
| None | clearStereoCenterFlag (Bond bond) |
| Clears the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond. More... | |
| None | setStereoDescriptor (Atom atom, StereoDescriptor descr) |
| Sets the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom to descr. More... | |
| bool | hasStereoDescriptor (Atom atom) |
| Tells whether the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom is set. More... | |
| StereoDescriptor | getStereoDescriptor (Atom atom) |
| Returns the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom. More... | |
| None | clearStereoDescriptor (Atom atom) |
| Clears the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom. More... | |
| None | setStereoDescriptor (Bond bond, StereoDescriptor descr) |
| Sets the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond to descr. More... | |
| bool | hasStereoDescriptor (Bond bond) |
| Tells whether the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond is set. More... | |
| StereoDescriptor | getStereoDescriptor (Bond bond) |
| Returns the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond. More... | |
| None | clearStereoDescriptor (Bond bond) |
| Clears the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond. More... | |
| None | setStoichiometricNumber (MolecularGraph molgraph, float num) |
| Sets the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph to num. More... | |
| bool | hasStoichiometricNumber (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph is set. More... | |
| float | getStoichiometricNumber (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More... | |
| None | clearStoichiometricNumber (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph. More... | |
| None | setStructureData (MolecularGraph molgraph, StringDataBlock data) |
| Sets the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph to data. More... | |
| bool | hasStructureData (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph is set. More... | |
| StringDataBlock | getStructureData (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph. More... | |
| None | clearStructureData (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph. More... | |
| str | getSybylAtomTypeString (int sybyl_type) |
| Returns the canonical textual representation of the Sybyl atom type sybyl_type. More... | |
| str | getSybylBondTypeString (int sybyl_type) |
| Returns the canonical textual representation of the Sybyl bond type sybyl_type. More... | |
| None | setSybylType (Atom atom, int type) |
| Sets the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom to type. More... | |
| bool | hasSybylType (Atom atom) |
| Tells whether the Chem.AtomProperty.SYBYL_TYPE property of the atom atom is set. More... | |
| int | getSybylType (Atom atom) |
| Returns the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom. More... | |
| None | clearSybylType (Atom atom) |
| Clears the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom. More... | |
| None | setSybylType (Bond bond, int type) |
| Sets the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond to type. More... | |
| bool | hasSybylType (Bond bond) |
| Tells whether the Chem.BondProperty.SYBYL_TYPE property of the bond bond is set. More... | |
| int | getSybylType (Bond bond) |
| Returns the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond. More... | |
| None | clearSybylType (Bond bond) |
| Clears the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond. More... | |
| None | setSymbol (Atom atom, str symbol) |
| Sets the value of the Chem.AtomProperty.SYMBOL property of the atom atom to symbol. More... | |
| bool | hasSymbol (Atom atom) |
| Tells whether the Chem.AtomProperty.SYMBOL property of the atom atom is set. More... | |
| str | getSymbol (Atom atom) |
| Returns the value of the Chem.AtomProperty.SYMBOL property of the atom atom. More... | |
| None | clearSymbol (Atom atom) |
| Clears the value of the Chem.AtomProperty.SYMBOL property of the atom atom. More... | |
| str | getSymbolForType (Atom atom) |
| Returns the symbol that corresponds to the numeric type property of the atom atom. More... | |
| None | setSymmetryClass (Atom atom, int class_id) |
| Sets the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom to class_id. More... | |
| bool | hasSymmetryClass (Atom atom) |
| Tells whether the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom is set. More... | |
| int | getSymmetryClass (Atom atom) |
| Returns the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom. More... | |
| None | clearSymmetryClass (Atom atom) |
| Clears the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom. More... | |
| None | setTimestamp (MolecularGraph molgraph, int time) |
| Sets the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph to time. More... | |
| bool | hasTimestamp (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph is set. More... | |
| int | getTimestamp (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph. More... | |
| None | clearTimestamp (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph. More... | |
| None | setTimestamp (Reaction rxn, int time) |
| Sets the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn to time. More... | |
| bool | hasTimestamp (Reaction rxn) |
| Tells whether the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn is set. More... | |
| int | getTimestamp (Reaction rxn) |
| Returns the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn. More... | |
| None | clearTimestamp (Reaction rxn) |
| Clears the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn. More... | |
| int | getTopologicalDistance (Atom atom1, Atom atom2, MolecularGraph molgraph) |
| Returns the topological distance between the two atoms in the molecular graph molgraph. More... | |
| None | setTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx) |
| Sets the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx. More... | |
| bool | hasTopologicalDistanceMatrix (MolecularGraph molgraph) |
| Tells whether the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set. More... | |
| Math.ULMatrix | getTopologicalDistanceMatrix (MolecularGraph molgraph) |
| Returns the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More... | |
| None | clearTopologicalDistanceMatrix (MolecularGraph molgraph) |
| Clears the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph. More... | |
| None | setType (Atom atom, int type) |
| Sets the value of the Chem.AtomProperty.TYPE property of the atom atom to type. More... | |
| bool | hasType (Atom atom) |
| Tells whether the Chem.AtomProperty.TYPE property of the atom atom is set. More... | |
| int | getType (Atom atom) |
| Returns the value of the Chem.AtomProperty.TYPE property of the atom atom. More... | |
| None | clearType (Atom atom) |
| Clears the value of the Chem.AtomProperty.TYPE property of the atom atom. More... | |
| int | getTypeForSymbol (Atom atom) |
| Returns the numeric atom type that corresponds to the symbol property of the atom atom. More... | |
| None | setUnpairedElectronCount (Atom atom, int count) |
| Sets the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom to count. More... | |
| bool | hasUnpairedElectronCount (Atom atom) |
| Tells whether the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom is set. More... | |
| int | getUnpairedElectronCount (Atom atom) |
| Returns the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom. More... | |
| None | clearUnpairedElectronCount (Atom atom) |
| Clears the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom. More... | |
| None | addConformation (AtomContainer cntnr, Math.Vector3DArray coords) |
| Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr. More... | |
| None | addConformation (MolecularGraph molgraph, Math.Vector3DArray coords, float energy) |
| Appends a new conformation built from the supplied coordinates and energy. More... | |
| bool | align2DCoordinates (MolecularGraph molgraph, AtomContainer atoms, Math.Vector2DArray ref_coords, bool fix_bond_stereo=True) |
| Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of atoms are aligned with the reference coordinates ref_coords. More... | |
| bool | align2DCoordinates (MolecularGraph molgraph, AtomMapping ref_atom_mpg, bool fix_bond_stereo=True) |
| Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of the mapped atoms are aligned. More... | |
| bool | align2DCoordinates (MolecularGraph molgraph, MolecularGraph ref_molgraph, bool use_mcs, bool fix_bond_stereo=True) |
| bool | align2DCoordinates (MolecularGraph molgraph, MolecularGraph ref_molgraph, MolecularGraph substr_ptn, bool fix_bond_stereo=True) |
| Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using substr_ptn as the explicit substructure search pattern. More... | |
| bool | align3DCoordinates (Entity3DContainer cntnr, Entity3DContainer ref_entities, Math.Vector3DArray ref_coords) |
| Transforms the 3D coordinates of the entities of cntnr by the affine matrix that is calculated for the rigid-body alignment of the 3D coordinates of the entities of ref_entities with the given reference coordinates ref_coords. More... | |
| bool | alignConformations (AtomContainer cntnr, Util.BitSet ref_atom_mask, Math.Vector3DArray ref_coords) |
| Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms flagged in ref_atom_mask as alignment anchors. More... | |
| bool | alignConformations (AtomContainer cntnr, AtomContainer ref_atoms, Math.Vector3DArray ref_coords) |
| Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors. More... | |
| bool | alignConformations (AtomContainer cntnr, Util.BitSet ref_atom_mask) |
| Aligns each stored conformation of cntnr to the first conformation using the atoms flagged in ref_atom_mask as alignment anchors. More... | |
| bool | alignConformations (AtomContainer cntnr, AtomContainer ref_atoms) |
| Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors. More... | |
| None | applyConformation (AtomContainer cntnr, int conf_idx) |
| Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates. More... | |
| bool | atomTypesMatch (int qry_type, int tgt_type) |
| Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem.AtomType.HET into account). More... | |
| None | calc2DCoordinates (MolecularGraph molgraph, bool overwrite) |
| Computes 2D atom coordinates for the molecular graph molgraph and stores them as corresponding atom properties. More... | |
| None | calcAtomCIPConfigurations (MolecularGraph molgraph, bool overwrite) |
| Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph. More... | |
| None | calcAtomStereoDescriptorsFromMDLParities (MolecularGraph molgraph, bool overwrite) |
| Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities. More... | |
| None | calcAtomStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True) |
| Computes and stores stereo descriptors for the atoms of the molecular graph molgraph. More... | |
| None | calcBasicProperties (MolecularGraph molgraph, bool overwrite) |
| Computes basic atom/bond/molecular graph properties (aromaticity, SSSR, etc.) of the molecular graph molgraph. More... | |
| None | calcBasicProperties (Reaction rxn, bool overwrite) |
| Computes basic atom/bond/molecular graph properties (aromaticity, ring info, etc.) for every component of the reaction rxn. More... | |
| None | calcBond2DStereoFlags (MolecularGraph molgraph, bool overwrite) |
| Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D coordinates. More... | |
| None | calcBondCIPConfigurations (MolecularGraph molgraph, bool overwrite) |
| Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph. More... | |
| None | calcBondStereoDescriptors (MolecularGraph molgraph, bool overwrite, int dim=1, bool check_stc_flag=True) |
| Computes and stores stereo descriptors for the bonds of the molecular graph molgraph. More... | |
| None | calcBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func, bool reset=True) |
| Computes the axis-aligned bounding box enclosing the atoms of cntnr. More... | |
| None | calcBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max, bool reset=True) |
| Calculates the axis-aligned bounding box of the 3D coordinates of the entities of cntnr. More... | |
| None | calcCIPPriorities (MolecularGraph molgraph, bool overwrite) |
| Computes and stores topological CIP priorities for the atoms of the molecular graph molgraph. More... | |
| None | calcCanonicalNumbering (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648) |
| Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph. More... | |
| bool | calcCenterOfMass (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr) |
| Computes the mass-weighted center of mass of the atoms in cntnr. More... | |
| bool | calcCentroid (AtomContainer cntnr, Atom3DCoordinatesFunction coords_func, Math.Vector3D ctr) |
| Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr. More... | |
| bool | calcCentroid (Entity3DContainer cntnr, Math.Vector3D ctr) |
| Calculates the geometric centroid of the 3D coordinates of the entities of cntnr. More... | |
| int | calcConfiguration (Atom atom, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords) |
| Calculates the atom configuration from the supplied descriptor and reference atom 3D coordinates. More... | |
| int | calcConfiguration (Bond bond, MolecularGraph molgraph, StereoDescriptor descr, Math.Vector3DArray coords) |
| Calculates the bond configuration from the supplied descriptor and reference atom 3D coordinates. More... | |
| int | calcFormalCharge (Atom atom, MolecularGraph molgraph) |
| Computes the formal charge of the atom atom from its connectivity in the molecular graph molgraph. More... | |
| None | calcFormalCharges (MolecularGraph molgraph, bool overwrite) |
| Computes and stores formal charges for the atoms of the molecular graph molgraph. More... | |
| None | calcGeometricalDistanceMatrix (Entity3DContainer cntnr, Math.DMatrix mtx) |
| Calculates the inter-entity geometric distance matrix for the entities of cntnr. More... | |
| Math.DMatrix | calcGeometricalDistanceMatrix (MolecularGraph molgraph, bool overwrite) |
| Computes and stores the geometrical distance matrix of the molecular graph molgraph from its 3D coordinates. More... | |
| int | calcHashCode (MolecularGraph molgraph, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True) |
| Computes a 64-bit hash code for the molecular graph molgraph taking into account the specified atom and bond properties. More... | |
| int | calcHashCode (Reaction rxn, int role_mask=7, int atom_flags=2147483648, int bond_flags=2147483648, bool ord_h_deplete=True) |
| Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties. More... | |
| None | calcHydrogen3DCoordinates (MolecularGraph molgraph, bool undef_only=True) |
| Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the 3D coordinates of their non-hydrogen neighbors. More... | |
| int | calcImplicitHydrogenCount (Atom atom, MolecularGraph molgraph) |
| Computes the implicit hydrogen count of the atom atom from its connectivity in the molecular graph molgraph. More... | |
| None | calcImplicitHydrogenCounts (MolecularGraph molgraph, bool overwrite) |
| Computes and stores implicit hydrogen counts for the atoms of the molecular graph molgraph. More... | |
| None | calcMDLParities (MolecularGraph molgraph, bool overwrite) |
| Computes and stores MDL parities for the atoms of the molecular graph molgraph. More... | |
| int | calcMDLParity (Atom atom, MolecularGraph molgraph) |
| Calculates the MDL parity of the atom atom in the molecular graph molgraph. More... | |
| None | calcMorganNumbering (MolecularGraph molgraph, bool overwrite) |
| Computes and stores Morgan numbers for the atoms of the molecular graph molgraph. More... | |
| StereoDescriptor | calcStereoDescriptor (Atom atom, MolecularGraph molgraph, int dim=1) |
| Computes the stereo descriptor for the atom atom in the molecular graph molgraph. More... | |
| StereoDescriptor | calcStereoDescriptor (Bond bond, MolecularGraph molgraph, int dim=1) |
| Computes the stereo descriptor for the bond bond in the molecular graph molgraph. More... | |
| StereoDescriptor | calcStereoDescriptorFromMDLParity (Atom atom, MolecularGraph molgraph) |
| Calculates the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph. More... | |
| Math.ULMatrix | calcTopologicalDistanceMatrix (MolecularGraph molgraph, bool overwrite) |
| Computes and stores the topological distance matrix of the molecular graph molgraph. More... | |
| None | calcTopologicalDistanceMatrix (MolecularGraph molgraph, Math.ULMatrix mtx) |
| Computes the topological distance matrix of the molecular graph molgraph into the supplied matrix mtx. More... | |
| int | calcUnpairedElectronCount (Atom atom, MolecularGraph molgraph) |
| Computes the unpaired (radical) electron count of the atom atom from its implict hydrogen count property value. More... | |
| None | calcUnpairedElectronCounts (MolecularGraph molgraph, bool overwrite) |
| Computes and stores the unpaired (radical) electron counts for the atoms in the molecular graph molgraph. More... | |
| None | canonicalize (MolecularGraph molgraph, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False) |
| Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical number property value of its atoms. More... | |
| None | canonicalize (MolecularGraph molgraph, BoolAtom2Functor func, bool atoms=True, bool atom_nbrs=True, bool bonds=True, bool bond_atoms=False) |
| Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator. More... | |
| None | connectAtoms (Molecule mol, Atom3DCoordinatesFunction coords_func, float dist_tol=0.3, int atom_idx_offs=0) |
| Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol. More... | |
| None | connectAtoms (Molecule mol, float dist_tol=0.3, int atom_idx_offs=0) |
| Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol. More... | |
| bool | containsFragmentWithBond (FragmentList frag_list, Bond bond) |
| Tells whether any fragment in frag_list contains the bond bond. More... | |
| bool | containsFragmentWithMinSize (FragmentList frag_list, int min_size) |
| Tells whether frag_list contains at least one fragment with at least min_size atoms. More... | |
| bool | containsMolecularGraph (MolecularGraph molgraph, MolecularGraph sub_molgraph, bool atoms=True, bool bonds=True) |
| Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph. More... | |
| None | copyAtomsIf (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False) |
| Copies every atom of cntnr that satisfies pred into the molecule mol. More... | |
| None | copyAtomsIf (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False) |
| Copies every atom of cntnr that satisfies pred into the fragment frag. More... | |
| None | copyAtomsIfNot (AtomContainer cntnr, Molecule mol, AtomPredicate pred, bool append=False) |
| Copies every atom of cntnr that does not satisfy pred into the molecule mol. More... | |
| None | copyAtomsIfNot (AtomContainer cntnr, Fragment frag, AtomPredicate pred, bool append=False) |
| Copies every atom of cntnr that does not satisfy pred into the fragment frag. More... | |
| int | createAtomTypeMask (AtomContainer cntnr, Util.BitSet mask, int type, bool reset=True, bool strict=True) |
| Sets bits in mask corresponding to atoms of cntnr whose atom type matches type. More... | |
| int | editSubstructures (MolecularGraph molgraph, Molecule result_mol, str search_ptns, str result_ptn, str exclude_ptns='') |
| Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn. More... | |
| int | editSubstructures (Molecule mol, str search_ptns, str result_ptn, str exclude_ptns='') |
| Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMILES replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns. More... | |
| None | extendBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords, bool reset=False) |
| Extends the axis-aligned bounding box defined by min and max so that it contains the point coords. More... | |
| None | extractReactionCenter (MolecularGraph molgraph, Fragment rxn_center) |
| Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center. More... | |
| FragmentList | extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph) |
| Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph. More... | |
| FragmentList | extractSSSRSubset (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite) |
| Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph and stores it on the latter. More... | |
| Math.ULMatrix | extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, bool overwrite) |
| Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and stores it on the latter. More... | |
| None | extractTopologicalDistanceSubMatrix (MolecularGraph src_molgraph, MolecularGraph tgt_molgraph, Math.ULMatrix mtx) |
| Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied matrix mtx. More... | |
| None | generateAdjacencyMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx) |
| Builds the adjacency matrix of the molecular graph molgraph. More... | |
| None | generateBondAtomTypeMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx) |
| Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph. More... | |
| None | generateBondElectronMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx) |
| Builds the bond-electron matrix of the molecular graph molgraph. More... | |
| None | generateBondMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx) |
| Builds the bond order matrix of the molecular graph molgraph. More... | |
| object | generateINCHIKey (MolecularGraph molgraph) |
| object | generateINCHI (MolecularGraph molgraph, str options='/WarnOnEmptyStructure/AuxNone/NEWPSOFF', int dim=0) |
| None | generateIncidenceMatrix (MolecularGraph molgraph, Math.SparseULMatrix mtx) |
| Builds the atom/bond incidence matrix of the molecular graph molgraph. More... | |
| AtomMatchExpression | generateMatchExpression (Atom atom, MolecularGraph molgraph) |
| Builds an match expression from the match constraint list attached to the atom atom. More... | |
| BondMatchExpression | generateMatchExpression (Bond bond, MolecularGraph molgraph) |
| Builds a match expression from the match constraint list attached to the bond bond. More... | |
| MolecularGraphMatchExpression | generateMatchExpression (MolecularGraph molgraph) |
| Builds a match expression from the match constraints currently attached to the molecular graph molgraph. More... | |
| MolecularGraphMatchExpression | generateMatchExpression (MolecularGraph molgraph, bool overwrite) |
| Builds and stores the match expression of the molecular graph molgraph. More... | |
| ReactionMatchExpression | generateMatchExpression (Reaction rxn) |
| Builds a match expression from the match constraints currently attached to the reaction rxn. More... | |
| ReactionMatchExpression | generateMatchExpression (Reaction rxn, bool overwrite) |
| Builds and stores the match expression of the reaction rxn. More... | |
| str | generateMatchExpressionString (Atom atom, MolecularGraph molgraph) |
| str | generateMatchExpressionString (Bond bond, MolecularGraph molgraph) |
| None | generateMatchExpressionStrings (MolecularGraph molgraph, bool overwrite) |
| Generates and stores textual representations of the atom/bond match expressions of the molecular graph molgraph. More... | |
| None | generateMatchExpressions (MolecularGraph molgraph, bool overwrite) |
| Generates and stores match expressions for every atom, bond and the molecular graph molgraph itself. More... | |
| None | generateMatchExpressions (Reaction rxn, bool overwrite) |
| Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself. More... | |
| object | generateSMILES (MolecularGraph molgraph, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648) |
| object | generateSMILES (Reaction rxn, bool canonical=False, bool ord_h_deplete=True, int atom_flags=2147483648, int bond_flags=2147483648) |
| None | initSubstructureSearchQuery (MolecularGraph molgraph, bool overwrite) |
| Prepares the molecular graph molgraph for use as a substructure search query. More... | |
| None | initSubstructureSearchQuery (Reaction rxn, bool overwrite) |
| Prepares the reaction rxn for use as a reaction substructure search query. More... | |
| None | initSubstructureSearchTarget (MolecularGraph molgraph, bool overwrite) |
| Prepares the molecular graph molgraph for use as a substructure search target. More... | |
| None | initSubstructureSearchTarget (Reaction rxn, bool overwrite) |
| Prepares the reaction rxn for use as a reaction substructure search target. More... | |
| bool | insideBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func) |
| Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More... | |
| bool | insideBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max) |
| Tells whether all 3D coordinates of the entities of cntnr lie within the axis-aligned bounding box defined by min and max. More... | |
| bool | insideBoundingBox (Math.Vector3D min, Math.Vector3D max, Math.Vector3D coords) |
| Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max. More... | |
| bool | intersectsBoundingBox (AtomContainer cntnr, Math.Vector3D min, Math.Vector3D max, Atom3DCoordinatesFunction coords_func) |
| Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More... | |
| bool | intersectsBoundingBox (Entity3DContainer cntnr, Math.Vector3D min, Math.Vector3D max) |
| Tells whether at least one entity of cntnr lies within the axis-aligned bounding box defined by min and max. More... | |
| bool | isAromatic (Fragment ring, MolecularGraph molgraph, Util.BitSet arom_bond_mask) |
| Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph. More... | |
| bool | isInFragmentOfSize (Atom atom, FragmentList frag_list, int size) |
| Tells whether the atom atom is a member of any fragment in frag_list whose size matches size. More... | |
| bool | isInFragmentOfSize (Bond bond, FragmentList frag_list, int size) |
| Tells whether the bond bond is a member of any fragment in frag_list whose size matches size. More... | |
| bool | isNotAromatic (Fragment ring, MolecularGraph molgraph) |
| Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria). More... | |
| bool | isStereoCenter (Atom atom, MolecularGraph molgraph, bool check_asym=True, bool check_inv_n=True, bool check_quart_n=True, bool check_plan_n=True, bool check_amide_n=True, bool check_res_ctrs=True) |
| Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph. More... | |
| bool | isStereoCenter (Bond bond, MolecularGraph molgraph, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8) |
| Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph. More... | |
| None | kekulizeBonds (MolecularGraph molgraph) |
| Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph. More... | |
| bool | makeHydrogenComplete (Molecule mol, bool corr_impl_h_count=True) |
| Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More... | |
| bool | makeHydrogenDeplete (Fragment frag) |
| Removes all explicit hydrogen atoms from the fragment frag. More... | |
| bool | makeHydrogenDeplete (Molecule mol, bool corr_impl_h_count=True) |
| Removes all explicit hydrogen atoms from the molecule mol. More... | |
| bool | makeOrdinaryHydrogenDeplete (Fragment frag, int flags) |
| Removes all explicit ordinary hydrogen atoms from the fragment frag. More... | |
| bool | makeOrdinaryHydrogenDeplete (Molecule mol, int flags, bool corr_impl_h_count=True) |
| Removes all explicit ordinary hydrogen atoms from the molecule mol. More... | |
| None | markReachableAtoms (Atom atom, MolecularGraph molgraph, Util.BitSet atom_mask, bool reset=True) |
| Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph. More... | |
| Molecule | parseSMARTS (str smarts, bool init_qry=True) |
| Parses the SMARTS string smarts into a freshly allocated query Chem.Molecule. More... | |
| bool | parseSMARTS (str smarts, Molecule mol, bool init_qry=True) |
| Parses the SMARTS string smarts into the supplied molecule mol. More... | |
| Molecule | parseSMILES (str smiles) |
| Parses the SMILES string smiles into a freshly allocated Chem.Molecule. More... | |
| bool | parseSMILES (str smiles, Molecule mol) |
| Parses the SMILES string smiles into the supplied molecule mol. More... | |
| Fragment | perceiveAromaticSubstructure (MolecularGraph molgraph) |
| Perceives the aromatic substructure (union of all aromatic atoms/bonds) of the molecular graph molgraph. More... | |
| Fragment | perceiveAromaticSubstructure (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the aromatic substructure of the molecular graph molgraph. More... | |
| AtomMapping | perceiveAtomMapping (Reaction rxn) |
| Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn. More... | |
| AtomMapping | perceiveAtomMapping (Reaction rxn, bool overwrite) |
| Derives and stores the reactant-to-product atom mapping of the reaction rxn. More... | |
| None | perceiveAtomStereoCenters (MolecularGraph molgraph, bool overwrite, bool check_asym=True, bool check_inv_n=True, bool check_quart_n=True, bool check_plan_n=True, bool check_amide_n=True, bool check_res_ctrs=True) |
| Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More... | |
| None | perceiveBondOrders (MolecularGraph molgraph, bool overwrite) |
| Perceives bond orders for the bonds of the molecular graph molgraph. More... | |
| None | perceiveBondStereoCenters (MolecularGraph molgraph, bool overwrite, bool check_asym=True, bool check_term_n=True, bool check_order=True, int min_ring_size=8) |
| Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria. More... | |
| FragmentList | perceiveComponentGroups (MolecularGraph molgraph) |
| Perceives the component groups of the molecular graph molgraph. More... | |
| FragmentList | perceiveComponentGroups (MolecularGraph molgraph, bool overwrite) |
| Perceives and optionally stores the component groups of the molecular graph molgraph. More... | |
| FragmentList | perceiveComponentGroups (Reaction rxn) |
| Perceives the component groups of the reaction rxn. More... | |
| FragmentList | perceiveComponentGroups (Reaction rxn, bool overwrite) |
| Perceives and stores the component groups of the reaction rxn. More... | |
| FragmentList | perceiveComponents (MolecularGraph molgraph) |
| Perceives the connected components of the molecular graph molgraph. More... | |
| FragmentList | perceiveComponents (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the connected components of the molecular graph molgraph. More... | |
| Fragment | perceiveCyclicSubstructure (MolecularGraph molgraph) |
| Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph. More... | |
| Fragment | perceiveCyclicSubstructure (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the cyclic substructure (union of all rings) of the molecular graph molgraph. More... | |
| int | perceiveHybridizationState (Atom atom, MolecularGraph molgraph) |
| Derives the hybridization state of the atom atom from its connectivity in the molecular graph molgraph. More... | |
| None | perceiveHybridizationStates (MolecularGraph molgraph, bool overwrite) |
| Computes and stores hybridization states for the atoms of the molecular graph molgraph. More... | |
| ElectronSystemList | perceivePiElectronSystems (MolecularGraph molgraph) |
| Perceives the π-electron systems of the molecular graph molgraph. More... | |
| ElectronSystemList | perceivePiElectronSystems (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the π-electron systems of the molecular graph molgraph. More... | |
| FragmentList | perceiveRings (MolecularGraph molgraph) |
| Perceives the full set of rings of the molecular graph molgraph. More... | |
| FragmentList | perceiveRings (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the full set of rings of the molecular graph molgraph. More... | |
| FragmentList | perceiveSSSR (MolecularGraph molgraph) |
| Perceives the SSSR of the molecular graph molgraph. More... | |
| FragmentList | perceiveSSSR (MolecularGraph molgraph, bool overwrite) |
| Perceives and stores the SSSR of the molecular graph molgraph. More... | |
| None | perceiveSybylAtomTypes (MolecularGraph molgraph, bool overwrite) |
| Perceives and assigns Sybyl MOL2 atom types for the atoms of the molecular graph molgraph. More... | |
| int | perceiveSybylType (Atom atom, MolecularGraph molgraph) |
| Derives the Sybyl MOL2 atom type of the atom atom in the molecular graph molgraph. More... | |
| int | perceiveSybylType (Bond bond, MolecularGraph molgraph) |
| Derives the Sybyl MOL2 bond type of the bond bond in the molecular graph molgraph. More... | |
| None | perceiveSymmetryClasses (MolecularGraph molgraph, bool overwrite, int atom_flags=2147483648, int bond_flags=2147483648, bool inc_impl_h=True) |
| Computes and stores topological symmetry classes for the atoms of the molecular graph molgraph. More... | |
| None | removeAtomsIf (Fragment frag, AtomPredicate pred) |
Removes all atoms of the fragment frag for which the predicate pred returns True. More... | |
| None | removeAtomsIf (Molecule mol, AtomPredicate pred) |
Removes all atoms of the molecule mol for which the predicate pred returns True. More... | |
| None | removeAtomsIfNot (Fragment frag, AtomPredicate pred) |
Removes all atoms of the fragment frag for which the predicate pred returns False. More... | |
| None | removeAtomsIfNot (Molecule mol, AtomPredicate pred) |
Removes all atoms of the molecule mol for which the predicate pred returns False. More... | |
| None | splitIntoFragments (MolecularGraph molgraph, FragmentList frag_list, Util.BitSet split_bond_mask, bool append=False) |
| Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask. More... | |
| int | sybylToAtomType (int sybyl_type) |
| Translates a Sybyl atom type identifier to the corresponding generic Chem.AtomType value. More... | |
| None | transform2DCoordinates (AtomContainer cntnr, Math.Matrix3D mtx) |
| Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx. More... | |
| None | transform3DCoordinates (Entity3DContainer cntnr, Math.Matrix4D mtx) |
| Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx. More... | |
| None | transformConformation (AtomContainer cntnr, int conf_idx, Math.Matrix4D mtx) |
| Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx. More... | |
| None | transformConformations (AtomContainer cntnr, Math.Matrix4D mtx) |
| Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx. More... | |
| None | translateFragment (MolecularGraph src_molgraph, Fragment src_frag, MolecularGraph tgt_molgraph, Fragment tgt_frag, bool append=False) |
| Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag. More... | |
| None | translateFragments (MolecularGraph src_molgraph, FragmentList src_frag_list, MolecularGraph tgt_molgraph, FragmentList tgt_frag_list, bool append=False) |
| Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph. More... | |
| None | setBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr, bool fix) |
| Sets the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix. More... | |
| bool | hasBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set. More... | |
| bool | getBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr. More... | |
| None | clearBondMemberSwapStereoFixParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr. More... | |
| None | setCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr, bool single_prec) |
| Sets the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec. More... | |
| bool | hasCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set. More... | |
| bool | getCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr. More... | |
| None | clearCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr. More... | |
| None | setCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable) |
| Sets the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More... | |
| bool | hasCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More... | |
| bool | getCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More... | |
| None | clearCMLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More... | |
| None | setCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr to output. More... | |
| bool | hasCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr is set. More... | |
| bool | getCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter stored in cntnr. More... | |
| None | clearCMLOutputAtomParityParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter from cntnr. More... | |
| None | setCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output. More... | |
| bool | hasCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set. More... | |
| bool | getCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr. More... | |
| None | clearCMLOutputCompactAtomDataParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr. More... | |
| None | setCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output. More... | |
| bool | hasCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set. More... | |
| bool | getCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr. More... | |
| None | clearCMLOutputCompactBondDataParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr. More... | |
| None | setCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output. More... | |
| bool | hasCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set. More... | |
| bool | getCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr. More... | |
| None | clearCMLOutputDoubleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr. More... | |
| None | setCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr, str ns) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns. More... | |
| bool | hasCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set. More... | |
| str | getCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr. More... | |
| None | clearCMLOutputElementPackageParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr. More... | |
| None | setCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr to output. More... | |
| bool | hasCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr is set. More... | |
| bool | getCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter stored in cntnr. More... | |
| None | clearCMLOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter from cntnr. More... | |
| None | setCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output. More... | |
| bool | hasCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set. More... | |
| bool | getCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr. More... | |
| None | clearCMLOutputMoleculeNameParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter from cntnr. More... | |
| None | setCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output. More... | |
| bool | hasCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set. More... | |
| bool | getCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr. More... | |
| None | clearCMLOutputSingleBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr. More... | |
| None | setCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output. More... | |
| bool | hasCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set. More... | |
| bool | getCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr. More... | |
| None | clearCMLOutputSpinMultiplicityParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr. More... | |
| None | setCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output. More... | |
| bool | hasCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set. More... | |
| bool | getCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr. More... | |
| None | clearCMLOutputStructureDataParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter from cntnr. More... | |
| None | setCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr to output. More... | |
| bool | hasCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr is set. More... | |
| bool | getCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter stored in cntnr. More... | |
| None | clearCMLOutputXMLDeclarationParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter from cntnr. More... | |
| None | setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check) |
| Sets the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr to check. More... | |
| bool | hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set. More... | |
| bool | getCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr. More... | |
| None | clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr. More... | |
| None | setConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr, str pattern) |
| Sets the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern. More... | |
| bool | hasConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set. More... | |
| str | getConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr. More... | |
| None | clearConfIndexNameSuffixPatternParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr. More... | |
| None | setCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr, int dim) |
| Sets the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr to dim. More... | |
| bool | hasCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr is set. More... | |
| int | getCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter stored in cntnr. More... | |
| None | clearCoordinatesDimensionParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.COORDINATES_DIMENSION parameter from cntnr. More... | |
| None | setINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr, str opts) |
| Sets the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr to opts. More... | |
| bool | hasINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr is set. More... | |
| str | getINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter stored in cntnr. More... | |
| None | clearINCHIInputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter from cntnr. More... | |
| None | setINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr, str opts) |
| Sets the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr to opts. More... | |
| bool | hasINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr is set. More... | |
| str | getINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter stored in cntnr. More... | |
| None | clearINCHIOutputOptionsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter from cntnr. More... | |
| None | setJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr, bool separate) |
| Sets the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr to separate. More... | |
| bool | hasJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr is set. More... | |
| bool | getJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter stored in cntnr. More... | |
| None | clearJMESeparateComponentsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter from cntnr. More... | |
| None | setMDLCTABVersionParameter (Base.ControlParameterContainer cntnr, int version) |
| Sets the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr to version. More... | |
| bool | hasMDLCTABVersionParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr is set. More... | |
| int | getMDLCTABVersionParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter stored in cntnr. More... | |
| None | clearMDLCTABVersionParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_CTAB_VERSION parameter from cntnr. More... | |
| None | setMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr, str tag) |
| Sets the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag. More... | |
| bool | hasMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set. More... | |
| str | getMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr. More... | |
| None | clearMDLConfEnergySDTagParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter from cntnr. More... | |
| None | setMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable) |
| Sets the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More... | |
| bool | hasMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More... | |
| bool | getMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More... | |
| None | clearMDLEnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More... | |
| None | setMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr, bool ignore) |
| Sets the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr to ignore. More... | |
| bool | hasMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr is set. More... | |
| bool | getMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter stored in cntnr. More... | |
| None | clearMDLIgnoreParityParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_IGNORE_PARITY parameter from cntnr. More... | |
| None | setMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output. More... | |
| bool | hasMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set. More... | |
| bool | getMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr. More... | |
| None | clearMDLOutputConfEnergyAsSDEntryParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr. More... | |
| None | setMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output. More... | |
| bool | hasMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set. More... | |
| bool | getMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr. More... | |
| None | clearMDLOutputConfEnergyToEnergyFieldParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr. More... | |
| None | setMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr, int version) |
| Sets the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr to version. More... | |
| bool | hasMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr is set. More... | |
| int | getMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter stored in cntnr. More... | |
| None | clearMDLRXNFileVersionParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter from cntnr. More... | |
| None | setMDLTrimLinesParameter (Base.ControlParameterContainer cntnr, bool trim) |
| Sets the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr to trim. More... | |
| bool | hasMDLTrimLinesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr is set. More... | |
| bool | getMDLTrimLinesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter stored in cntnr. More... | |
| None | clearMDLTrimLinesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_TRIM_LINES parameter from cntnr. More... | |
| None | setMDLTrimStringsParameter (Base.ControlParameterContainer cntnr, bool trim) |
| Sets the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr to trim. More... | |
| bool | hasMDLTrimStringsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr is set. More... | |
| bool | getMDLTrimStringsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter stored in cntnr. More... | |
| None | clearMDLTrimStringsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_TRIM_STRINGS parameter from cntnr. More... | |
| None | setMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc) |
| Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr to trunc. More... | |
| bool | hasMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr is set. More... | |
| bool | getMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter stored in cntnr. More... | |
| None | clearMDLTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter from cntnr. More... | |
| None | setMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr, bool trunc) |
| Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr to trunc. More... | |
| bool | hasMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr is set. More... | |
| bool | getMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter stored in cntnr. More... | |
| None | clearMDLTruncateStringsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter from cntnr. More... | |
| None | setMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr, bool update) |
| Sets the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr to update. More... | |
| bool | hasMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr is set. More... | |
| bool | getMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter stored in cntnr. More... | |
| None | clearMDLUpdateTimestampParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter from cntnr. More... | |
| None | setMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc) |
| Sets the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc. More... | |
| bool | hasMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set. More... | |
| bool | getMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr. More... | |
| None | clearMOL2CalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter from cntnr. More... | |
| None | setMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr, int type) |
| Sets the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr to type. More... | |
| bool | hasMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr is set. More... | |
| int | getMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter stored in cntnr. More... | |
| None | clearMOL2ChargeTypeParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter from cntnr. More... | |
| None | setMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr, bool enable) |
| Sets the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable. More... | |
| bool | hasMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set. More... | |
| bool | getMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr. More... | |
| None | clearMOL2EnableAromaticBondTypesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr. More... | |
| None | setMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr, bool enable) |
| Sets the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable. More... | |
| bool | hasMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set. More... | |
| bool | getMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr. More... | |
| None | clearMOL2EnableExtendedAtomTypesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr. More... | |
| None | setMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr, int type) |
| Sets the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr to type. More... | |
| bool | hasMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr is set. More... | |
| int | getMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter stored in cntnr. More... | |
| None | clearMOL2MoleculeTypeParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter from cntnr. More... | |
| None | setMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output. More... | |
| bool | hasMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set. More... | |
| bool | getMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr. More... | |
| None | clearMOL2OutputFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr. More... | |
| None | setMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output. More... | |
| bool | hasMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set. More... | |
| bool | getMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr. More... | |
| None | clearMOL2OutputSubstructuresParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr. More... | |
| None | setMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr, bool read) |
| Sets the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read. More... | |
| bool | hasMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set. More... | |
| bool | getMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr. More... | |
| None | clearMOL2ReadPartialAsFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr. More... | |
| None | setMultiConfExportParameter (Base.ControlParameterContainer cntnr, bool multi_conf) |
| Sets the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr to multi_conf. More... | |
| bool | hasMultiConfExportParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr is set. More... | |
| bool | getMultiConfExportParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter stored in cntnr. More... | |
| None | clearMultiConfExportParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MULTI_CONF_EXPORT parameter from cntnr. More... | |
| None | setMultiConfImportParameter (Base.ControlParameterContainer cntnr, bool multi_conf) |
| Sets the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr to multi_conf. More... | |
| bool | hasMultiConfImportParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr is set. More... | |
| bool | getMultiConfImportParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter stored in cntnr. More... | |
| None | clearMultiConfImportParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MULTI_CONF_IMPORT parameter from cntnr. More... | |
| None | setMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr, MultiConfMoleculeInputProcessor proc) |
| Sets the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc. More... | |
| bool | hasMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set. More... | |
| MultiConfMoleculeInputProcessor | getMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr. More... | |
| None | clearMultiConfInputProcessorParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter from cntnr. More... | |
| None | setOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr, bool deplete) |
| Sets the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete. More... | |
| bool | hasOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set. More... | |
| bool | getOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr. More... | |
| None | clearOrdinaryHydrogenDepleteParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter from cntnr. More... | |
| None | setOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output. More... | |
| bool | hasOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set. More... | |
| bool | getOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr. More... | |
| None | clearOutputConfEnergyAsCommentParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr. More... | |
| None | setRecordSeparatorParameter (Base.ControlParameterContainer cntnr, str sep) |
| Sets the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr to sep. More... | |
| bool | hasRecordSeparatorParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr is set. More... | |
| str | getRecordSeparatorParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter stored in cntnr. More... | |
| None | clearRecordSeparatorParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.RECORD_SEPARATOR parameter from cntnr. More... | |
| None | setSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr, int min_size) |
| Sets the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size. More... | |
| bool | hasSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set. More... | |
| int | getSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr. More... | |
| None | clearSMILESMinStereoBondRingSizeParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr. More... | |
| None | setSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More... | |
| bool | hasSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More... | |
| bool | getSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More... | |
| None | clearSMILESMolOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More... | |
| None | setSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr, bool no_subset) |
| Sets the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset. More... | |
| bool | hasSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set. More... | |
| bool | getSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr. More... | |
| None | clearSMILESNoOrganicSubsetParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter from cntnr. More... | |
| None | setSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output. More... | |
| bool | hasSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set. More... | |
| bool | getSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr. More... | |
| None | clearSMILESOutputAromaticBondsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr. More... | |
| None | setSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output. More... | |
| bool | hasSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set. More... | |
| bool | getSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr. More... | |
| None | clearSMILESOutputAtomStereoParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter from cntnr. More... | |
| None | setSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output. More... | |
| bool | hasSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set. More... | |
| bool | getSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr. More... | |
| None | clearSMILESOutputBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter from cntnr. More... | |
| None | setSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output. More... | |
| bool | hasSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set. More... | |
| bool | getSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr. More... | |
| None | clearSMILESOutputCanonicalFormParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr. More... | |
| None | setSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output. More... | |
| bool | hasSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set. More... | |
| bool | getSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr. More... | |
| None | clearSMILESOutputHydrogenCountParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr. More... | |
| None | setSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr to output. More... | |
| bool | hasSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr is set. More... | |
| bool | getSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter stored in cntnr. More... | |
| None | clearSMILESOutputIsotopeParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter from cntnr. More... | |
| None | setSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output. More... | |
| bool | hasSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set. More... | |
| bool | getSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr. More... | |
| None | clearSMILESOutputKekuleFormParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter from cntnr. More... | |
| None | setSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output. More... | |
| bool | hasSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set. More... | |
| bool | getSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr. More... | |
| None | clearSMILESOutputRingBondStereoParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr. More... | |
| None | setSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output. More... | |
| bool | hasSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set. More... | |
| bool | getSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr. More... | |
| None | clearSMILESOutputSingleBondsParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr. More... | |
| None | setSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr, str format) |
| Sets the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr to format. More... | |
| bool | hasSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr is set. More... | |
| str | getSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter stored in cntnr. More... | |
| None | clearSMILESRecordFormatParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter from cntnr. More... | |
| None | setSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr, bool output) |
| Sets the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output. More... | |
| bool | hasSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set. More... | |
| bool | getSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr. More... | |
| None | clearSMILESRxnOutputAtomMappingIDParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr. More... | |
| None | setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict) |
| Sets the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict. More... | |
| bool | hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set. More... | |
| bool | getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr. More... | |
| None | clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr. More... | |
| None | setXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc) |
| Sets the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc. More... | |
| bool | hasXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set. More... | |
| bool | getXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr. More... | |
| None | clearXYZCalcFormalChargesParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter from cntnr. More... | |
| None | setXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr, bool is_name) |
| Sets the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr to is_name. More... | |
| bool | hasXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr is set. More... | |
| bool | getXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter stored in cntnr. More... | |
| None | clearXYZCommentIsNameParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter from cntnr. More... | |
| None | setXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive) |
| Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive. More... | |
| bool | hasXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set. More... | |
| bool | getXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr. More... | |
| None | clearXYZPerceiveBondOrdersParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr. More... | |
| None | setXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr, bool perceive) |
| Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive. More... | |
| bool | hasXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr) |
| Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set. More... | |
| bool | getXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr) |
| Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr. More... | |
| None | clearXYZPerceiveConnectivityParameter (Base.ControlParameterContainer cntnr) |
| Removes the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr. More... | |
Contains classes and functions related to chemistry.
| None CDPL.Chem.set2DCoordinates | ( | Atom | atom, |
| Math.Vector2D | coords | ||
| ) |
Sets the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom to coords.
| atom | The atom for which to set the property value. |
| coords | The new 2D coordinates. |
| bool CDPL.Chem.has2DCoordinates | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.COORDINATES_2D property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | Math.Vector2D CDPL.Chem.get2DCoordinates | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clear2DCoordinates | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.COORDINATES_2D property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.set2DCoordinates | ( | AtomContainer | cntnr, |
| Math.Vector2DArray | coords | ||
| ) |
Writes the 2D coordinates in coords back to the corresponding atoms of cntnr.
| cntnr | The atom container. |
| coords | The 2D coordinates to assign (must contain at least one entry per atom). |
| None CDPL.Chem.get2DCoordinates | ( | AtomContainer | cntnr, |
| Math.Vector2DArray | coords, | ||
| bool | append = False |
||
| ) |
Extracts the 2D coordinates of all atoms in cntnr into coords.
| cntnr | The atom container. |
| coords | The output 2D coordinate array. |
| append | If True, the coordinates are appended to coords. Otherwise, coords is cleared first. |
| None CDPL.Chem.set2DStereoFlag | ( | Bond | bond, |
| int | flag | ||
| ) |
Sets the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond to flag.
| bond | The bond for which to set the property value. |
| flag | The new 2D stereo flag value (see namespace Chem.BondStereoFlag). |
| bool CDPL.Chem.has2DStereoFlag | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.get2DStereoFlag | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clear2DStereoFlag | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.STEREO_2D_FLAG property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.set3DCoordinatesArray | ( | Atom | atom, |
| Math.Vector3DArray | coords_array | ||
| ) |
Sets the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom to coords_array.
| atom | The atom for which to set the property value. |
| coords_array | The new 3D conformer-coordinates array. |
| bool CDPL.Chem.has3DCoordinatesArray | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | Math.Vector3DArray CDPL.Chem.get3DCoordinatesArray | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clear3DCoordinatesArray | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.COORDINATES_3D_ARRAY property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.get3DCoordinates | ( | AtomContainer | cntnr, |
| Math.Vector3DArray | coords, | ||
| Atom3DCoordinatesFunction | coords_func, | ||
| bool | append = False |
||
| ) |
Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func.
| cntnr | The atom container. |
| coords | The output 3D coordinate array. |
| coords_func | The function returning the 3D coordinates of an atom. |
| append | If True, the coordinates are appended to coords. Otherwise, coords is cleared first. |
| None CDPL.Chem.set3DCoordinates | ( | Entity3D | entity, |
| Math.Vector3D | coords | ||
| ) |
Sets the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity to coords.
| entity | The 3D entity for which to set the property value. |
| coords | The new 3D coordinates. |
| bool CDPL.Chem.has3DCoordinates | ( | Entity3D | entity | ) |
Tells whether the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity is set.
| entity | The 3D entity for which to query the property value. |
True if the property is set, and False otherwise. | Math.Vector3D CDPL.Chem.get3DCoordinates | ( | Entity3D | entity | ) |
Returns the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity.
| entity | The 3D entity for which to return the property value. |
| Base.ItemNotFound | if the property has not been set. |
| None CDPL.Chem.clear3DCoordinates | ( | Entity3D | entity | ) |
Clears the value of the Chem.Entity3DProperty.COORDINATES_3D property of the 3D entity entity.
| entity | The 3D entity for which to clear the property value. |
| None CDPL.Chem.set3DCoordinates | ( | Entity3DContainer | cntnr, |
| Math.Vector3DArray | coords | ||
| ) |
Sets the 3D coordinates of the entities of cntnr from coords.
| cntnr | The entity 3D container whose coordinates are to be updated. |
| coords | The input coordinates array (must contain at least one position per entity in cntnr). |
| None CDPL.Chem.get3DCoordinates | ( | Entity3DContainer | cntnr, |
| Math.Vector3DArray | coords, | ||
| bool | append = False |
||
| ) |
Stores the 3D coordinates of the entities of cntnr in coords.
| cntnr | The entity 3D container providing the source coordinates. |
| coords | The output coordinates array. |
| append | If True, the entity coordinates are appended to coords. If False, coords is cleared first. |
| FragmentList CDPL.Chem.getAromaticRings | ( | MolecularGraph | molgraph | ) |
Returns the subset of the aromatic rings of the molecular graph molgraph.
| molgraph | The molecular graph. |
| FragmentList CDPL.Chem.getAromaticSSSRSubset | ( | MolecularGraph | molgraph | ) |
Returns the subset of the SSSR of the molecular graph molgraph that contains only aromatic rings,.
| molgraph | The molecular graph. |
| None CDPL.Chem.setAromaticSubstructure | ( | MolecularGraph | molgraph, |
| Fragment | substruct | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct.
| molgraph | The molecular graph for which to set the property value. |
| substruct | The new aromatic substructure. |
| bool CDPL.Chem.hasAromaticSubstructure | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | Fragment CDPL.Chem.getAromaticSubstructure | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearAromaticSubstructure | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.AROMATIC_SUBSTRUCTURE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setAromaticityFlag | ( | Atom | atom, |
| bool | aromatic | ||
| ) |
Sets the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom to aromatic.
| atom | The atom for which to set the property value. |
| aromatic | True to flag the atom as aromatic, and False to flag it as non-aromatic. |
| bool CDPL.Chem.hasAromaticityFlag | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getAromaticityFlag | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom.
| atom | The atom for which to return the property value. |
True if the atom is flagged as aromatic, and False otherwise. | None CDPL.Chem.clearAromaticityFlag | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.AROMATICITY_FLAG property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setAromaticityFlag | ( | Bond | bond, |
| bool | aromatic | ||
| ) |
Sets the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond to aromatic.
| bond | The bond for which to set the property value. |
| aromatic | True to flag the bond as aromatic, and False to flag it as non-aromatic. |
| bool CDPL.Chem.hasAromaticityFlag | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getAromaticityFlag | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond.
| bond | The bond for which to return the property value. |
True if the bond is flagged as aromatic, and False otherwise. | None CDPL.Chem.clearAromaticityFlag | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.AROMATICITY_FLAG property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setAromaticityFlags | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing aromaticity flag properties should be replaced. |
| None CDPL.Chem.setAtomMappingID | ( | Atom | atom, |
| int | id | ||
| ) |
Sets the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom to id.
| atom | The atom for which to set the property value. |
| id | The new reactant-to-product atom mapping ID. |
| bool CDPL.Chem.hasAtomMappingID | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getAtomMappingID | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearAtomMappingID | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.ATOM_MAPPING_ID property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setAtomMapping | ( | Reaction | rxn, |
| AtomMapping | mapping | ||
| ) |
Sets the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn to mapping.
| rxn | The reaction for which to set the property value. |
| mapping | The new reactant-to-product atom mapping. |
| bool CDPL.Chem.hasAtomMapping | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | AtomMapping CDPL.Chem.getAtomMapping | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearAtomMapping | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.ATOM_MAPPING property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setAtomMatchConstraints | ( | MolecularGraph | molgraph, |
| MatchConstraintList | constr, | ||
| bool | overwrite | ||
| ) |
Sets the match constraint list constr on every atom of the molecular graph molgraph.
| molgraph | The molecular graph. |
| constr | The match constraint list to assign. |
| overwrite | Specifies whether already existing match constraint properties should be replaced. |
| None CDPL.Chem.setAtomMatchConstraints | ( | Reaction | rxn, |
| MatchConstraintList | constr, | ||
| bool | overwrite | ||
| ) |
Sets the atom-level match constraint list constr on every atom of every component of the reaction rxn.
| rxn | The reaction. |
| constr | The match constraint list to assign. |
| overwrite | Specifies whether already existing match constraints properties should be replaced. |
| None CDPL.Chem.setAtomSymbolsFromTypes | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Sets the atom symbols of the molecular graph molgraph from their atom types.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing atom symbol properties should be replaced. |
| None CDPL.Chem.setAtomTypesFromSymbols | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Sets the atom types of the molecular graph molgraph from their element symbols.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing atom type properties should be replaced. |
| None CDPL.Chem.setBondMatchConstraints | ( | MolecularGraph | molgraph, |
| MatchConstraintList | constr, | ||
| bool | overwrite | ||
| ) |
Sets the match constraint list constr on every bond of the molecular graph molgraph.
| molgraph | The molecular graph. |
| constr | The match constraint list to assign. |
| overwrite | Specifies whether already existing match constraint properties should be replaced. |
| None CDPL.Chem.setBondMatchConstraints | ( | Reaction | rxn, |
| MatchConstraintList | constr, | ||
| bool | overwrite | ||
| ) |
Sets the bond-level match constraint list constr on every bond of every component of the reaction rxn.
| rxn | The reaction. |
| constr | The match constraint list to assign. |
| overwrite | Specifies whether already existing match constraint properties should be replaced. |
| None CDPL.Chem.setCIPConfiguration | ( | Atom | atom, |
| int | config | ||
| ) |
Sets the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom to config.
| atom | The atom for which to set the property value. |
| config | The new CIP configuration label (see namespace Chem.CIPDescriptor). |
| bool CDPL.Chem.hasCIPConfiguration | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getCIPConfiguration | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearCIPConfiguration | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.CIP_CONFIGURATION property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setCIPConfiguration | ( | Bond | bond, |
| int | config | ||
| ) |
Sets the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond to config.
| bond | The bond for which to set the property value. |
| config | The new CIP configuration label (see namespace Chem.CIPDescriptor). |
| bool CDPL.Chem.hasCIPConfiguration | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getCIPConfiguration | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearCIPConfiguration | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.CIP_CONFIGURATION property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setCIPPriority | ( | Atom | atom, |
| int | priority | ||
| ) |
Sets the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom to priority.
| atom | The atom for which to set the property value. |
| priority | The new topological CIP priority. |
| bool CDPL.Chem.hasCIPPriority | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.CIP_PRIORITY property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getCIPPriority | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearCIPPriority | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.CIP_PRIORITY property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setCanonicalNumber | ( | Atom | atom, |
| int | num | ||
| ) |
Sets the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom to num.
| atom | The atom for which to set the property value. |
| num | The new canonical number. |
| bool CDPL.Chem.hasCanonicalNumber | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getCanonicalNumber | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearCanonicalNumber | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.CANONICAL_NUMBER property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setComment | ( | MolecularGraph | molgraph, |
| str | comment | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph to comment.
| molgraph | The molecular graph for which to set the property value. |
| comment | The new comment string. |
| bool CDPL.Chem.hasComment | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getComment | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearComment | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.COMMENT property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setComment | ( | Reaction | rxn, |
| str | comment | ||
| ) |
Sets the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn to comment.
| rxn | The reaction for which to set the property value. |
| comment | The new comment string. |
| bool CDPL.Chem.hasComment | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.COMMENT property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getComment | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearComment | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.COMMENT property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| int CDPL.Chem.getCompleteBondCount | ( | MolecularGraph | molgraph | ) |
Returns the number of bonds of the molecular graph molgraph whose connected atoms are likewise contained in molgraph.
| molgraph | The molecular graph. |
| None CDPL.Chem.setComponentGroupID | ( | Atom | atom, |
| int | id | ||
| ) |
Sets the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom to id.
| atom | The atom for which to set the property value. |
| id | The new component-group ID. |
| bool CDPL.Chem.hasComponentGroupID | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getComponentGroupID | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearComponentGroupID | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.COMPONENT_GROUP_ID property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setComponentGroups | ( | MolecularGraph | molgraph, |
| FragmentList | comp_groups | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph to comp_groups.
| molgraph | The molecular graph for which to set the property value. |
| comp_groups | The new component-group fragment list. |
| bool CDPL.Chem.hasComponentGroups | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | FragmentList CDPL.Chem.getComponentGroups | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearComponentGroups | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.COMPONENT_GROUPS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setComponentGroups | ( | Reaction | rxn, |
| FragmentList | comp_groups | ||
| ) |
Sets the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn to comp_groups.
| rxn | The reaction for which to set the property value. |
| comp_groups | The new component-group fragment list. |
| bool CDPL.Chem.hasComponentGroups | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | FragmentList CDPL.Chem.getComponentGroups | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearComponentGroups | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.COMPONENT_GROUPS property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setComponentMatchConstraints | ( | Reaction | rxn, |
| MatchConstraintList | constr, | ||
| bool | overwrite | ||
| ) |
Sets the molecular graph-level match constraint list constr on every component of the reaction rxn.
| rxn | The reaction. |
| constr | The match constraint list to assign. |
| overwrite | Specifies whether already existing match constraint properties should be replaced. |
| None CDPL.Chem.setComponents | ( | MolecularGraph | molgraph, |
| FragmentList | comps | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph to comps.
| molgraph | The molecular graph for which to set the property value. |
| comps | The new connected-component list. |
| bool CDPL.Chem.hasComponents | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | FragmentList CDPL.Chem.getComponents | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearComponents | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.COMPONENTS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.getConformation | ( | AtomContainer | cntnr, |
| int | conf_idx, | ||
| Math.Vector3DArray | coords, | ||
| bool | append = False |
||
| ) |
Extracts the conformation at index conf_idx into coords.
| cntnr | The atom container. |
| conf_idx | The zero-based conformation index. |
| coords | The output 3D coordinate array. |
| append | If True, the coordinates are appended to coords. Otherwise, coords is cleared first. |
| float CDPL.Chem.getConformationEnergy | ( | MolecularGraph | molgraph, |
| int | conf_idx | ||
| ) |
Returns the energy of the conformation at index conf_idx.
| molgraph | The molecular graph to query. |
| conf_idx | The zero-based conformation index. |
| Base.IndexError | if conf_idx is out of the valid range. |
| None CDPL.Chem.setConformationIndex | ( | MolecularGraph | molgraph, |
| int | index | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph to index.
| molgraph | The molecular graph for which to set the property value. |
| index | The new zero-based conformation index. |
| bool CDPL.Chem.hasConformationIndex | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getConformationIndex | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearConformationIndex | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.CONFORMATION_INDEX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setConformation | ( | MolecularGraph | molgraph, |
| int | conf_idx, | ||
| Math.Vector3DArray | coords, | ||
| float | energy | ||
| ) |
Overwrites the conformation at index conf_idx with the supplied coordinates and energy.
| molgraph | The molecular graph. |
| conf_idx | The zero-based conformation index. |
| coords | The 3D coordinates of the conformation. |
| energy | The energy associated with the conformation. |
| Base.IndexError | if conf_idx is out of the valid range. |
| None CDPL.Chem.clearConformations | ( | AtomContainer | cntnr | ) |
Removes all stored conformations from the atoms of cntnr.
| cntnr | The atom container. |
| Math.Vector3D CDPL.Chem.getConformer3DCoordinates | ( | Atom | atom, |
| int | conf_idx | ||
| ) |
Returns the 3D coordinates of the atom atom in the conformer with index conf_idx.
| atom | The atom for which to return the conformer 3D coordinates. |
| conf_idx | The zero-based conformer index. |
| Base.IndexError | if conf_idx is out of the valid range. |
| None CDPL.Chem.setConformerEnergies | ( | MolecularGraph | molgraph, |
| Util.DArray | energies | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph to energies.
| molgraph | The molecular graph for which to set the property value. |
| energies | The new conformer energy array. |
| bool CDPL.Chem.hasConformerEnergies | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | Util.DArray CDPL.Chem.getConformerEnergies | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearConformerEnergies | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.CONFORMER_ENERGIES property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| int CDPL.Chem.getConnectedAtomsAndBonds | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| list | atoms, | ||
| list | bonds, | ||
| Atom | excl_atom | ||
| ) |
| atom | |
| molgraph | |
| atoms | |
| bonds | |
| excl_atom |
| int CDPL.Chem.getConnectedAtoms | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| list | atoms, | ||
| Atom | excl_atom | ||
| ) |
| atom | |
| molgraph | |
| atoms | |
| excl_atom |
| None CDPL.Chem.getContainedFragments | ( | MolecularGraph | molgraph, |
| FragmentList | frag_list, | ||
| FragmentList | cont_frag_list, | ||
| bool | append = False, |
||
| bool | atoms = True, |
||
| bool | bonds = True |
||
| ) |
Collects the fragments in frag_list that are fully contained in the molecular graph molgraph into cont_frag_list.
| molgraph | The host molecular graph. |
| frag_list | The candidate fragment list. |
| cont_frag_list | The output fragment list receiving the matches. |
| append | If True, matches are appended to cont_frag_list. Otherwise, it is cleared first. |
| atoms | If True, atom membership is required for a match. |
| bonds | If True, bond membership is required for a match. |
| None CDPL.Chem.getContainingFragments | ( | Atom | atom, |
| FragmentList | frag_list, | ||
| FragmentList | cont_frag_list | ||
| ) |
| atom | |
| frag_list | |
| cont_frag_list |
| None CDPL.Chem.getContainingFragments | ( | Bond | bond, |
| FragmentList | frag_list, | ||
| FragmentList | cont_frag_list | ||
| ) |
| bond | |
| frag_list | |
| cont_frag_list |
| None CDPL.Chem.getContainingFragments | ( | MolecularGraph | molgraph, |
| FragmentList | frag_list, | ||
| FragmentList | cont_frag_list, | ||
| bool | append = False, |
||
| bool | atoms = True, |
||
| bool | bonds = True |
||
| ) |
Collects the fragments in frag_list that contain the molecular graph molgraph into cont_frag_list.
| molgraph | The query molecular graph. |
| frag_list | The candidate fragment list. |
| cont_frag_list | The output fragment list receiving the matches. |
| append | If True, matches are appended to cont_frag_list. Otherwise, it is cleared first. |
| atoms | If True, atom membership is required for a match. |
| bonds | If True, bond membership is required for a match. |
| bool CDPL.Chem.hasCoordinates | ( | AtomContainer | cntnr, |
| int | dim | ||
| ) |
Tells whether all atoms of cntnr carry coordinates of the given dimensionality.
| cntnr | The atom container. |
| dim | The coordinate dimensionality (2 or 3). |
True if all atoms have the requested coordinates, and False otherwise. | None CDPL.Chem.setCyclicSubstructure | ( | MolecularGraph | molgraph, |
| Fragment | substruct | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph to substruct.
| molgraph | The molecular graph for which to set the property value. |
| substruct | The new cyclic substructure. |
| bool CDPL.Chem.hasCyclicSubstructure | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | Fragment CDPL.Chem.getCyclicSubstructure | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearCyclicSubstructure | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.CYCLIC_SUBSTRUCTURE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setDirection | ( | Bond | bond, |
| int | dir | ||
| ) |
Sets the value of the Chem.BondProperty.DIRECTION property of the bond bond to dir.
| bond | The bond for which to set the property value. |
| dir | The new bond direction descriptor (see namespace Chem.BondDirection). |
| bool CDPL.Chem.hasDirection | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.DIRECTION property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getDirection | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.DIRECTION property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearDirection | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.DIRECTION property of the bond bond.
| bond | The bond for which to clear the property value. |
| int CDPL.Chem.getEnvironment | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| int | max_dist, | ||
| Fragment | env, | ||
| bool | append = False |
||
| ) |
Collects every atom of the molecular graph molgraph that is within max_dist bonds of the atom atom into the fragment env.
| atom | The seed atom. |
| molgraph | The molecular graph providing the structural context. |
| max_dist | The maximum topological distance. |
| env | The output fragment receiving the environment atoms and the bonds between them. |
| append | If False, env gets cleared before adding any atoms and bonds. |
| None CDPL.Chem.setFormalCharge | ( | Atom | atom, |
| int | charge | ||
| ) |
Sets the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom to charge.
| atom | The atom for which to set the property value. |
| charge | The new formal charge. |
| bool CDPL.Chem.hasFormalCharge | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getFormalCharge | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearFormalCharge | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.FORMAL_CHARGE property of the atom atom.
| atom | The atom for which to clear the property value. |
| int CDPL.Chem.getGenericType | ( | Atom | atom | ) |
Returns the generic atom type associated with numeric type property of the atom atom.
| atom | The atom to query. |
| None CDPL.Chem.setGeometricalDistanceMatrix | ( | MolecularGraph | molgraph, |
| Math.DMatrix | mtx | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.
| molgraph | The molecular graph for which to set the property value. |
| mtx | The new geometrical distance matrix. |
| bool CDPL.Chem.hasGeometricalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | Math.DMatrix CDPL.Chem.getGeometricalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearGeometricalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.GEOMETRICAL_DISTANCE_MATRIX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setHashCode | ( | MolecularGraph | molgraph, |
| int | hash_code | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph to hash_code.
| molgraph | The molecular graph for which to set the property value. |
| hash_code | The new 64-bit hash code. |
| bool CDPL.Chem.hasHashCode | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getHashCode | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearHashCode | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.HASH_CODE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setHybridizationState | ( | Atom | atom, |
| int | state | ||
| ) |
Sets the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom to state.
| atom | The atom for which to set the property value. |
| state | The new hybridization state (see namespace Chem.HybridizationState). |
| bool CDPL.Chem.hasHybridizationState | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.HYBRIDIZATION property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getHybridizationState | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearHybridizationState | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.HYBRIDIZATION property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setImplicitHydrogenCount | ( | Atom | atom, |
| int | count | ||
| ) |
Sets the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom to count.
| atom | The atom for which to set the property value. |
| count | The new implicit hydrogen count. |
| bool CDPL.Chem.hasImplicitHydrogenCount | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getImplicitHydrogenCount | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearImplicitHydrogenCount | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.IMPLICIT_HYDROGEN_COUNT property of the atom atom.
| atom | The atom for which to clear the property value. |
| int CDPL.Chem.getIncidentBonds | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| list | bonds, | ||
| Atom | excl_atom | ||
| ) |
| atom | |
| molgraph | |
| bonds | |
| excl_atom |
| None CDPL.Chem.setIsotope | ( | Atom | atom, |
| int | isotope | ||
| ) |
Sets the value of the Chem.AtomProperty.ISOTOPE property of the atom atom to isotope.
| atom | The atom for which to set the property value. |
| isotope | The new mass number (zero for the natural isotope mixture). |
| bool CDPL.Chem.hasIsotope | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.ISOTOPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getIsotope | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.ISOTOPE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearIsotope | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.ISOTOPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMDLCTABVersion | ( | MolecularGraph | molgraph, |
| int | version | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph to version.
| molgraph | The molecular graph for which to set the property value. |
| version | The new CTAB version (see namespace Chem.MDLDataFormatVersion). |
| bool CDPL.Chem.hasMDLCTABVersion | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLCTABVersion | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLCTABVersion | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_CTAB_VERSION property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLChiralFlag | ( | MolecularGraph | molgraph, |
| bool | flag | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph to flag.
| molgraph | The molecular graph for which to set the property value. |
| flag | The new MDL chiral flag. |
| bool CDPL.Chem.hasMDLChiralFlag | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getMDLChiralFlag | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLChiralFlag | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_CHIRAL_FLAG property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLDimensionality | ( | MolecularGraph | molgraph, |
| int | dim | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph to dim.
| molgraph | The molecular graph for which to set the property value. |
| dim | The new MDL coordinate dimensionality. |
| bool CDPL.Chem.hasMDLDimensionality | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLDimensionality | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLDimensionality | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_DIMENSIONALITY property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLEnergy | ( | MolecularGraph | molgraph, |
| float | energy | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph to energy.
| molgraph | The molecular graph for which to set the property value. |
| energy | The new MDL energy. |
| bool CDPL.Chem.hasMDLEnergy | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | float CDPL.Chem.getMDLEnergy | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLEnergy | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_ENERGY property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLExternalRegistryNumber | ( | Reaction | rxn, |
| str | reg_no | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.
| rxn | The reaction for which to set the property value. |
| reg_no | The new MDL external registry number. |
| bool CDPL.Chem.hasMDLExternalRegistryNumber | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLExternalRegistryNumber | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLExternalRegistryNumber | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_EXTERNAL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMDLInternalRegistryNumber | ( | Reaction | rxn, |
| str | reg_no | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn to reg_no.
| rxn | The reaction for which to set the property value. |
| reg_no | The new MDL internal registry number. |
| bool CDPL.Chem.hasMDLInternalRegistryNumber | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLInternalRegistryNumber | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLInternalRegistryNumber | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_INTERNAL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
Sets the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn to mol_rec.
| rxn | The reaction for which to set the property value. |
| mol_rec | The new MDL RD-File molecule record. |
| bool CDPL.Chem.hasMDLMoleculeRecord | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. Returns the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLMoleculeRecord | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_MOLECULE_RECORD property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMDLParity | ( | Atom | atom, |
| int | parity | ||
| ) |
Sets the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom to parity.
| atom | The atom for which to set the property value. |
| parity | The new MDL stereo parity (see namespace Chem.MDLParity). |
| bool CDPL.Chem.hasMDLParity | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MDL_PARITY property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLParity | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMDLParity | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MDL_PARITY property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMDLProgramName | ( | MolecularGraph | molgraph, |
| str | name | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph to name.
| molgraph | The molecular graph for which to set the property value. |
| name | The new MDL program name. |
| bool CDPL.Chem.hasMDLProgramName | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLProgramName | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLProgramName | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_PROGRAM_NAME property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLProgramName | ( | Reaction | rxn, |
| str | name | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn to name.
| rxn | The reaction for which to set the property value. |
| name | The new MDL program name. |
| bool CDPL.Chem.hasMDLProgramName | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLProgramName | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLProgramName | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_PROGRAM_NAME property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMDLRXNFileVersion | ( | Reaction | rxn, |
| int | version | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn to version.
| rxn | The reaction for which to set the property value. |
| version | The new MDL Rxn-File version (see Chem.MDLDataFormatVersion). |
| bool CDPL.Chem.hasMDLRXNFileVersion | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLRXNFileVersion | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLRXNFileVersion | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_RXN_FILE_VERSION property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMDLRegistryNumber | ( | MolecularGraph | molgraph, |
| int | reg_no | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph to reg_no.
| molgraph | The molecular graph for which to set the property value. |
| reg_no | The new MDL registry number. |
| bool CDPL.Chem.hasMDLRegistryNumber | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLRegistryNumber | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLRegistryNumber | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_REGISTRY_NUMBER property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLRegistryNumber | ( | Reaction | rxn, |
| int | reg_no | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn to reg_no.
| rxn | The reaction for which to set the property value. |
| reg_no | The new MDL registry number. |
| bool CDPL.Chem.hasMDLRegistryNumber | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLRegistryNumber | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLRegistryNumber | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_REGISTRY_NUMBER property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMDLScalingFactor1 | ( | MolecularGraph | molgraph, |
| int | factor | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph to factor.
| molgraph | The molecular graph for which to set the property value. |
| factor | The new MDL scaling factor 1. |
| bool CDPL.Chem.hasMDLScalingFactor1 | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMDLScalingFactor1 | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLScalingFactor1 | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR1 property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLScalingFactor2 | ( | MolecularGraph | molgraph, |
| float | factor | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph to factor.
| molgraph | The molecular graph for which to set the property value. |
| factor | The new MDL scaling factor 2. |
| bool CDPL.Chem.hasMDLScalingFactor2 | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | float CDPL.Chem.getMDLScalingFactor2 | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLScalingFactor2 | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_SCALING_FACTOR2 property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLStereoCareFlag | ( | Atom | atom, |
| bool | flag | ||
| ) |
Sets the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom to flag.
| atom | The atom for which to set the property value. |
| flag | The new MDL stereo-care flag. |
| bool CDPL.Chem.hasMDLStereoCareFlag | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getMDLStereoCareFlag | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMDLStereoCareFlag | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MDL_DB_STEREO_CARE_FLAG property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMDLUserInitials | ( | MolecularGraph | molgraph, |
| str | initials | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph to initials.
| molgraph | The molecular graph for which to set the property value. |
| initials | The new MDL user initials. |
| bool CDPL.Chem.hasMDLUserInitials | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLUserInitials | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMDLUserInitials | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MDL_USER_INITIALS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMDLUserInitials | ( | Reaction | rxn, |
| str | initials | ||
| ) |
Sets the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn to initials.
| rxn | The reaction for which to set the property value. |
| initials | The new MDL user initials. |
| bool CDPL.Chem.hasMDLUserInitials | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMDLUserInitials | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMDLUserInitials | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MDL_USER_INITIALS property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMOL2Charge | ( | Atom | atom, |
| float | charge | ||
| ) |
Sets the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom to charge.
| atom | The atom for which to set the property value. |
| charge | The new Sybyl MOL2 partial charge. |
| bool CDPL.Chem.hasMOL2Charge | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_CHARGE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | float CDPL.Chem.getMOL2Charge | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2Charge | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_CHARGE property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMOL2ChargeType | ( | MolecularGraph | molgraph, |
| int | type | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph to type.
| molgraph | The molecular graph for which to set the property value. |
| type | The new Sybyl MOL2 charge type (see namespace Chem.MOL2ChargeType). |
| bool CDPL.Chem.hasMOL2ChargeType | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMOL2ChargeType | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMOL2ChargeType | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MOL2_CHARGE_TYPE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMOL2MoleculeType | ( | MolecularGraph | molgraph, |
| int | type | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph to type.
| molgraph | The molecular graph for which to set the property value. |
| type | The new Sybyl MOL2 molecule type (see namespace Chem.MOL2MoleculeType). |
| bool CDPL.Chem.hasMOL2MoleculeType | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMOL2MoleculeType | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMOL2MoleculeType | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MOL2_MOLECULE_TYPE property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMOL2Name | ( | Atom | atom, |
| str | name | ||
| ) |
Sets the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom to name.
| atom | The atom for which to set the property value. |
| name | The new Sybyl MOL2 atom name. |
| bool CDPL.Chem.hasMOL2Name | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_NAME property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMOL2Name | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2Name | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_NAME property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMOL2SubstructureChain | ( | Atom | atom, |
| str | chain | ||
| ) |
Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom to chain.
| atom | The atom for which to set the property value. |
| chain | The new Sybyl MOL2 substructure chain identifier. |
| bool CDPL.Chem.hasMOL2SubstructureChain | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMOL2SubstructureChain | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2SubstructureChain | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_CHAIN property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMOL2SubstructureID | ( | Atom | atom, |
| int | id | ||
| ) |
Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom to id.
| atom | The atom for which to set the property value. |
| id | The new Sybyl MOL2 substructure ID. |
| bool CDPL.Chem.hasMOL2SubstructureID | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMOL2SubstructureID | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2SubstructureID | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_ID property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMOL2SubstructureName | ( | Atom | atom, |
| str | name | ||
| ) |
| atom | |
| name |
| bool CDPL.Chem.hasMOL2SubstructureName | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMOL2SubstructureName | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2SubstructureName | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_NAME property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMOL2SubstructureSubtype | ( | Atom | atom, |
| str | subtype | ||
| ) |
Sets the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom to subtype.
| atom | The atom for which to set the property value. |
| subtype | The new Sybyl MOL2 substructure subtype string. |
| bool CDPL.Chem.hasMOL2SubstructureSubtype | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMOL2SubstructureSubtype | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMOL2SubstructureSubtype | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MOL2_SUBSTRUCTURE_SUBTYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMatchConstraints | ( | Atom | atom, |
| MatchConstraintList | constr | ||
| ) |
Sets the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom to constr.
| atom | The atom for which to set the property value. |
| constr | The new match constraint list. |
| bool CDPL.Chem.hasMatchConstraints | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | MatchConstraintList CDPL.Chem.getMatchConstraints | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMatchConstraints | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MATCH_CONSTRAINTS property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMatchConstraints | ( | Bond | bond, |
| MatchConstraintList | constr | ||
| ) |
Sets the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond to constr.
| bond | The bond for which to set the property value. |
| constr | The new match constraint list. |
| bool CDPL.Chem.hasMatchConstraints | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | MatchConstraintList CDPL.Chem.getMatchConstraints | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearMatchConstraints | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.MATCH_CONSTRAINTS property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setMatchConstraints | ( | MolecularGraph | molgraph, |
| MatchConstraintList | constr | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph to constr.
| molgraph | The molecular graph for which to set the property value. |
| constr | The new match constraint list. |
| bool CDPL.Chem.hasMatchConstraints | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | MatchConstraintList CDPL.Chem.getMatchConstraints | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMatchConstraints | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MATCH_CONSTRAINTS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMatchConstraints | ( | Reaction | rxn, |
| MatchConstraintList | constr | ||
| ) |
Sets the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn to constr.
| rxn | The reaction for which to set the property value. |
| constr | The new match constraint list to store. |
| bool CDPL.Chem.hasMatchConstraints | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | MatchConstraintList CDPL.Chem.getMatchConstraints | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMatchConstraints | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MATCH_CONSTRAINTS property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMatchExpression | ( | Atom | atom, |
| AtomMatchExpression | expr | ||
| ) |
Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom to expr.
| atom | The atom for which to set the property value. |
| expr | The new atom-level match expression. |
| bool CDPL.Chem.hasMatchExpression | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | AtomMatchExpression CDPL.Chem.getMatchExpression | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMatchExpression | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMatchExpression | ( | Bond | bond, |
| BondMatchExpression | expr | ||
| ) |
Sets the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond to expr.
| bond | The bond for which to set the property value. |
| expr | The new bond-level match expression. |
| bool CDPL.Chem.hasMatchExpression | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | BondMatchExpression CDPL.Chem.getMatchExpression | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearMatchExpression | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.MATCH_EXPRESSION property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setMatchExpression | ( | MolecularGraph | molgraph, |
| MolecularGraphMatchExpression | expr | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph to expr.
| molgraph | The molecular graph for which to set the property value. |
| expr | The new match expression. |
| bool CDPL.Chem.hasMatchExpression | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | MolecularGraphMatchExpression CDPL.Chem.getMatchExpression | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearMatchExpression | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.MATCH_EXPRESSION property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setMatchExpression | ( | Reaction | rxn, |
| ReactionMatchExpression | expr | ||
| ) |
Sets the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn to expr.
| rxn | The reaction for which to set the property value. |
| expr | The new match expression to store. |
| bool CDPL.Chem.hasMatchExpression | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | ReactionMatchExpression CDPL.Chem.getMatchExpression | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearMatchExpression | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.MATCH_EXPRESSION property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setMatchExpressionString | ( | Atom | atom, |
| str | expr_str | ||
| ) |
Sets the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom to expr_str.
| atom | The atom for which to set the property value. |
| expr_str | The new match expression string. |
| bool CDPL.Chem.hasMatchExpressionString | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMatchExpressionString | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMatchExpressionString | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MATCH_EXPRESSION_STRING property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setMatchExpressionString | ( | Bond | bond, |
| str | expr_str | ||
| ) |
Sets the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond to expr_str.
| bond | The bond for which to set the property value. |
| expr_str | The new match expression string. |
| bool CDPL.Chem.hasMatchExpressionString | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getMatchExpressionString | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearMatchExpressionString | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.MATCH_EXPRESSION_STRING property of the bond bond.
| bond | The bond for which to clear the property value. |
| int CDPL.Chem.getMaxAtomMappingID | ( | AtomContainer | cntnr | ) |
Returns the largest atom mapping ID assigned to any atom of cntnr.
| cntnr | The atom container. |
| int CDPL.Chem.getMaxAtomMappingID | ( | Reaction | rxn | ) |
Returns the largest atom mapping ID found for any of the atoms of the components of the reaction rxn.
| rxn | The reaction to scan. |
| int CDPL.Chem.getMaxComponentGroupID | ( | AtomContainer | cntnr | ) |
Returns the largest component-group ID assigned to any atom of cntnr.
| cntnr | The atom container. |
| int CDPL.Chem.getMaxComponentGroupID | ( | Reaction | rxn | ) |
Returns the largest component group ID found for any of the atoms of the components of the reaction rxn.
| rxn | The reaction to scan. |
| None CDPL.Chem.setMorganNumber | ( | Atom | atom, |
| int | num | ||
| ) |
Sets the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom to num.
| atom | The atom for which to set the property value. |
| num | The new Morgan number. |
| bool CDPL.Chem.hasMorganNumber | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getMorganNumber | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearMorganNumber | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.MORGAN_NUMBER property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setName | ( | Atom | atom, |
| str | name | ||
| ) |
Sets the value of the Chem.AtomProperty.NAME property of the atom atom to name.
| atom | The atom for which to set the property value. |
| name | The new atom name. |
| bool CDPL.Chem.hasName | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.NAME property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getName | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.NAME property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearName | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.NAME property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setName | ( | MolecularGraph | molgraph, |
| str | name | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph to name.
| molgraph | The molecular graph for which to set the property value. |
| name | The new name. |
| bool CDPL.Chem.hasName | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getName | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearName | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.NAME property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setName | ( | Reaction | rxn, |
| str | name | ||
| ) |
Sets the value of the Chem.ReactionProperty.NAME property of the reaction rxn to name.
| rxn | The reaction for which to set the property value. |
| name | The new reaction name. |
| bool CDPL.Chem.hasName | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.NAME property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getName | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.NAME property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearName | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.NAME property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| int CDPL.Chem.getNumConformations | ( | AtomContainer | cntnr | ) |
Returns the number of conformations stored on the atoms of cntnr.
| cntnr | The atom container. |
| int CDPL.Chem.getNumContainingFragments | ( | Atom | atom, |
| FragmentList | frag_list | ||
| ) |
Returns the number of fragments in frag_list that contain the atom atom.
| atom | The atom to query. |
| frag_list | The list of fragments to search. |
| int CDPL.Chem.getNumContainingFragments | ( | Bond | bond, |
| FragmentList | frag_list | ||
| ) |
Returns the number of fragments in frag_list that contain the bond bond.
| bond | The bond to query. |
| frag_list | The list of fragments to search. |
| None CDPL.Chem.setOrder | ( | Bond | bond, |
| int | order | ||
| ) |
Sets the value of the Chem.BondProperty.ORDER property of the bond bond to order.
| bond | The bond for which to set the property value. |
| order | The new bond order. |
| bool CDPL.Chem.hasOrder | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.ORDER property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getOrder | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.ORDER property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearOrder | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.ORDER property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setPiElectronSystems | ( | MolecularGraph | molgraph, |
| ElectronSystemList | pi_systems | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph to pi_systems.
| molgraph | The molecular graph for which to set the property value. |
| pi_systems | The new π-electron system list. |
| bool CDPL.Chem.hasPiElectronSystems | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | ElectronSystemList CDPL.Chem.getPiElectronSystems | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearPiElectronSystems | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.PI_ELECTRON_SYSTEMS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setRadicalType | ( | Atom | atom, |
| int | type | ||
| ) |
Sets the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new radical type (see namespace Chem.RadicalType). |
| bool CDPL.Chem.hasRadicalType | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.RADICAL_TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getRadicalType | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearRadicalType | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.RADICAL_TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setReactionCenterStatus | ( | Atom | atom, |
| int | status | ||
| ) |
Sets the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom to status.
| atom | The atom for which to set the property value. |
| status | The new reaction-center status (see namespace Chem.ReactionCenterStatus). |
| bool CDPL.Chem.hasReactionCenterStatus | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getReactionCenterStatus | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearReactionCenterStatus | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.REACTION_CENTER_STATUS property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setReactionCenterStatus | ( | Bond | bond, |
| int | status | ||
| ) |
Sets the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond to status.
| bond | The bond for which to set the property value. |
| status | The new reaction-center status (see namespace Chem.ReactionCenterStatus). |
| bool CDPL.Chem.hasReactionCenterStatus | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getReactionCenterStatus | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearReactionCenterStatus | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.REACTION_CENTER_STATUS property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setReactionData | ( | Reaction | rxn, |
| StringDataBlock | data | ||
| ) |
Sets the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn to data.
| rxn | The reaction for which to set the property value. |
| data | The new reaction data block. |
| bool CDPL.Chem.hasReactionData | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | StringDataBlock CDPL.Chem.getReactionData | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearReactionData | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.REACTION_DATA property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| None CDPL.Chem.setRingFlag | ( | Atom | atom, |
| bool | in_ring | ||
| ) |
Sets the value of the Chem.AtomProperty.RING_FLAG property of the atom atom to in_ring.
| atom | The atom for which to set the property value. |
| in_ring | True to flag the atom as part of a ring, and False to flag it as acyclic. |
| bool CDPL.Chem.hasRingFlag | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.RING_FLAG property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getRingFlag | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.RING_FLAG property of the atom atom.
| atom | The atom for which to return the property value. |
True if the atom is flagged as part of any ring, and False otherwise. | None CDPL.Chem.clearRingFlag | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.RING_FLAG property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setRingFlag | ( | Bond | bond, |
| bool | in_ring | ||
| ) |
Sets the value of the Chem.BondProperty.RING_FLAG property of the bond bond to in_ring.
| bond | The bond for which to set the property value. |
| in_ring | True to flag the bond as part of a ring, and False to flag it as acyclic. |
| bool CDPL.Chem.hasRingFlag | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.RING_FLAG property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getRingFlag | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.RING_FLAG property of the bond bond.
| bond | The bond for which to return the property value. |
True if the bond is flagged as part of any ring, and False otherwise. | None CDPL.Chem.clearRingFlag | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.RING_FLAG property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setRingFlags | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives ring membership and sets the corresponding atom/bond ring flags on the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing ring flag properties should be replaced. |
| None CDPL.Chem.setRings | ( | MolecularGraph | molgraph, |
| FragmentList | rings | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph to rings.
| molgraph | The molecular graph for which to set the property value. |
| rings | The new full ring set. |
| bool CDPL.Chem.hasRings | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | FragmentList CDPL.Chem.getRings | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearRings | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.RINGS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setSSSR | ( | MolecularGraph | molgraph, |
| FragmentList | sssr | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph to sssr.
| molgraph | The molecular graph for which to set the property value. |
| sssr | The new Smallest Set of Smallest Rings. |
| bool CDPL.Chem.hasSSSR | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | FragmentList CDPL.Chem.getSSSR | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearSSSR | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.SSSR property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| int CDPL.Chem.getSizeOfLargestContainingFragment | ( | Atom | atom, |
| FragmentList | frag_list | ||
| ) |
Returns the size (in atoms) of the largest fragment in frag_list that contains the atom atom.
| atom | The atom to query. |
| frag_list | The list of fragments to search. |
| int CDPL.Chem.getSizeOfLargestContainingFragment | ( | Bond | bond, |
| FragmentList | frag_list | ||
| ) |
Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond.
| bond | The bond to query. |
| frag_list | The list of fragments to search. |
| int CDPL.Chem.getSizeOfSmallestContainingFragment | ( | Atom | atom, |
| FragmentList | frag_list | ||
| ) |
Returns the size (in atoms) of the smallest fragment in frag_list that contains the atom atom.
| atom | The atom to query. |
| frag_list | The list of fragments to search. |
| int CDPL.Chem.getSizeOfSmallestContainingFragment | ( | Bond | bond, |
| FragmentList | frag_list | ||
| ) |
Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond.
| bond | The bond to query. |
| frag_list | The list of fragments to search. |
| None CDPL.Chem.setStereoCenterFlag | ( | Atom | atom, |
| bool | is_center | ||
| ) |
Sets the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom to is_center.
| atom | The atom for which to set the property value. |
| is_center | True to flag the atom as a stereo center, and False otherwise. |
| bool CDPL.Chem.hasStereoCenterFlag | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getStereoCenterFlag | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom.
| atom | The atom for which to return the property value. |
True if the atom is flagged as a stereo center, and False otherwise. | None CDPL.Chem.clearStereoCenterFlag | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.STEREO_CENTER_FLAG property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setStereoCenterFlag | ( | Bond | bond, |
| bool | is_center | ||
| ) |
Sets the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond to is_center.
| bond | The bond for which to set the property value. |
| is_center | True to flag the bond as a stereo center, and False otherwise. |
| bool CDPL.Chem.hasStereoCenterFlag | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | bool CDPL.Chem.getStereoCenterFlag | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond.
| bond | The bond for which to return the property value. |
True if the bond is flagged as a stereo center, and False otherwise. | None CDPL.Chem.clearStereoCenterFlag | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.STEREO_CENTER_FLAG property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setStereoDescriptor | ( | Atom | atom, |
| StereoDescriptor | descr | ||
| ) |
Sets the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom to descr.
| atom | The atom for which to set the property value. |
| descr | The new stereo descriptor. |
| bool CDPL.Chem.hasStereoDescriptor | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | StereoDescriptor CDPL.Chem.getStereoDescriptor | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearStereoDescriptor | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.STEREO_DESCRIPTOR property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setStereoDescriptor | ( | Bond | bond, |
| StereoDescriptor | descr | ||
| ) |
Sets the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond to descr.
| bond | The bond for which to set the property value. |
| descr | The new stereo descriptor. |
| bool CDPL.Chem.hasStereoDescriptor | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | StereoDescriptor CDPL.Chem.getStereoDescriptor | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearStereoDescriptor | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.STEREO_DESCRIPTOR property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setStoichiometricNumber | ( | MolecularGraph | molgraph, |
| float | num | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph to num.
| molgraph | The molecular graph for which to set the property value. |
| num | The new stoichiometric number. |
| bool CDPL.Chem.hasStoichiometricNumber | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | float CDPL.Chem.getStoichiometricNumber | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearStoichiometricNumber | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.STOICHIOMETRIC_NUMBER property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setStructureData | ( | MolecularGraph | molgraph, |
| StringDataBlock | data | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph to data.
| molgraph | The molecular graph for which to set the property value. |
| data | The new structure data block. |
| bool CDPL.Chem.hasStructureData | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | StringDataBlock CDPL.Chem.getStructureData | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearStructureData | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.STRUCTURE_DATA property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| str CDPL.Chem.getSybylAtomTypeString | ( | int | sybyl_type | ) |
Returns the canonical textual representation of the Sybyl atom type sybyl_type.
| sybyl_type | The Sybyl atom type identifier (Chem.SybylAtomType value). |
| str CDPL.Chem.getSybylBondTypeString | ( | int | sybyl_type | ) |
Returns the canonical textual representation of the Sybyl bond type sybyl_type.
| sybyl_type | The Sybyl bond-type identifier (Chem.SybylBondType value). |
| None CDPL.Chem.setSybylType | ( | Atom | atom, |
| int | type | ||
| ) |
Sets the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new Sybyl MOL2 atom type (see namespace Chem.SybylAtomType). |
| bool CDPL.Chem.hasSybylType | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.SYBYL_TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getSybylType | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearSybylType | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.SYBYL_TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setSybylType | ( | Bond | bond, |
| int | type | ||
| ) |
Sets the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond to type.
| bond | The bond for which to set the property value. |
| type | The new Sybyl MOL2 bond type (see namespace Chem.SybylBondType). |
| bool CDPL.Chem.hasSybylType | ( | Bond | bond | ) |
Tells whether the Chem.BondProperty.SYBYL_TYPE property of the bond bond is set.
| bond | The bond for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getSybylType | ( | Bond | bond | ) |
Returns the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond.
| bond | The bond for which to return the property value. |
| None CDPL.Chem.clearSybylType | ( | Bond | bond | ) |
Clears the value of the Chem.BondProperty.SYBYL_TYPE property of the bond bond.
| bond | The bond for which to clear the property value. |
| None CDPL.Chem.setSymbol | ( | Atom | atom, |
| str | symbol | ||
| ) |
Sets the value of the Chem.AtomProperty.SYMBOL property of the atom atom to symbol.
| atom | The atom for which to set the property value. |
| symbol | The new element symbol. |
| bool CDPL.Chem.hasSymbol | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.SYMBOL property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | str CDPL.Chem.getSymbol | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.SYMBOL property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearSymbol | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.SYMBOL property of the atom atom.
| atom | The atom for which to clear the property value. |
| str CDPL.Chem.getSymbolForType | ( | Atom | atom | ) |
Returns the symbol that corresponds to the numeric type property of the atom atom.
| atom | The atom to query. |
| None CDPL.Chem.setSymmetryClass | ( | Atom | atom, |
| int | class_id | ||
| ) |
Sets the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom to class_id.
| atom | The atom for which to set the property value. |
| class_id | The new topological-symmetry class ID. |
| bool CDPL.Chem.hasSymmetryClass | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getSymmetryClass | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearSymmetryClass | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.SYMMETRY_CLASS property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.setTimestamp | ( | MolecularGraph | molgraph, |
| int | time | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph to time.
| molgraph | The molecular graph for which to set the property value. |
| time | The new timestamp value. |
| bool CDPL.Chem.hasTimestamp | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getTimestamp | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearTimestamp | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.TIMESTAMP property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setTimestamp | ( | Reaction | rxn, |
| int | time | ||
| ) |
Sets the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn to time.
| rxn | The reaction for which to set the property value. |
| time | The new timestamp value. |
| bool CDPL.Chem.hasTimestamp | ( | Reaction | rxn | ) |
Tells whether the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn is set.
| rxn | The reaction for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getTimestamp | ( | Reaction | rxn | ) |
Returns the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn.
| rxn | The reaction for which to return the property value. |
| None CDPL.Chem.clearTimestamp | ( | Reaction | rxn | ) |
Clears the value of the Chem.ReactionProperty.TIMESTAMP property of the reaction rxn.
| rxn | The reaction for which to clear the property value. |
| int CDPL.Chem.getTopologicalDistance | ( | Atom | atom1, |
| Atom | atom2, | ||
| MolecularGraph | molgraph | ||
| ) |
Returns the topological distance between the two atoms in the molecular graph molgraph.
| atom1 | The first atom. |
| atom2 | The second atom. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.setTopologicalDistanceMatrix | ( | MolecularGraph | molgraph, |
| Math.ULMatrix | mtx | ||
| ) |
Sets the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph to mtx.
| molgraph | The molecular graph for which to set the property value. |
| mtx | The new topological distance matrix. |
| bool CDPL.Chem.hasTopologicalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Tells whether the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
True if the property is set, and False otherwise. | Math.ULMatrix CDPL.Chem.getTopologicalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Returns the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
| None CDPL.Chem.clearTopologicalDistanceMatrix | ( | MolecularGraph | molgraph | ) |
Clears the value of the Chem.MolecularGraphProperty.TOPOLOGICAL_DISTANCE_MATRIX property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| None CDPL.Chem.setType | ( | Atom | atom, |
| int | type | ||
| ) |
Sets the value of the Chem.AtomProperty.TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new atom type (see namespace Chem.AtomType). |
| bool CDPL.Chem.hasType | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getType | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearType | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| int CDPL.Chem.getTypeForSymbol | ( | Atom | atom | ) |
Returns the numeric atom type that corresponds to the symbol property of the atom atom.
| atom | The atom to query. |
| None CDPL.Chem.setUnpairedElectronCount | ( | Atom | atom, |
| int | count | ||
| ) |
Sets the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom to count.
| atom | The atom for which to set the property value. |
| count | The new unpaired electron count. |
| bool CDPL.Chem.hasUnpairedElectronCount | ( | Atom | atom | ) |
Tells whether the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom is set.
| atom | The atom for which to query the property value. |
True if the property is set, and False otherwise. | int CDPL.Chem.getUnpairedElectronCount | ( | Atom | atom | ) |
Returns the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom.
| atom | The atom for which to return the property value. |
| None CDPL.Chem.clearUnpairedElectronCount | ( | Atom | atom | ) |
Clears the value of the Chem.AtomProperty.UNPAIRED_ELECTRON_COUNT property of the atom atom.
| atom | The atom for which to clear the property value. |
| None CDPL.Chem.addConformation | ( | AtomContainer | cntnr, |
| Math.Vector3DArray | coords | ||
| ) |
Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr.
| cntnr | The atom container. |
| coords | The 3D coordinates of the new conformation. |
| None CDPL.Chem.addConformation | ( | MolecularGraph | molgraph, |
| Math.Vector3DArray | coords, | ||
| float | energy | ||
| ) |
Appends a new conformation built from the supplied coordinates and energy.
| molgraph | The molecular graph. |
| coords | The 3D coordinates of the new conformation. |
| energy | The energy associated with the new conformation. |
| bool CDPL.Chem.align2DCoordinates | ( | MolecularGraph | molgraph, |
| AtomContainer | atoms, | ||
| Math.Vector2DArray | ref_coords, | ||
| bool | fix_bond_stereo = True |
||
| ) |
Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of atoms are aligned with the reference coordinates ref_coords.
| molgraph | The molecular graph to align. |
| atoms | The atoms used as alignment anchors. |
| ref_coords | Reference 2D coordinates of the alignment anchor atoms. |
| fix_bond_stereo | If True, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates. |
True if the alignment succeeded, and False otherwise.| bool CDPL.Chem.align2DCoordinates | ( | MolecularGraph | molgraph, |
| AtomMapping | ref_atom_mpg, | ||
| bool | fix_bond_stereo = True |
||
| ) |
Transforms the 2D atom coordinates of molgraph so that the 2D coordinates of the mapped atoms are aligned.
| molgraph | The molecular graph to align. |
| ref_atom_mpg | The atom mapping providing the target atom→atom correspondence. |
| fix_bond_stereo | If True, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates. |
True if the alignment succeeded, and False otherwise.| bool CDPL.Chem.align2DCoordinates | ( | MolecularGraph | molgraph, |
| MolecularGraph | ref_molgraph, | ||
| bool | use_mcs, | ||
| bool | fix_bond_stereo = True |
||
| ) |
| molgraph | |
| ref_molgraph | |
| use_mcs | |
| fix_bond_stereo |
| bool CDPL.Chem.align2DCoordinates | ( | MolecularGraph | molgraph, |
| MolecularGraph | ref_molgraph, | ||
| MolecularGraph | substr_ptn, | ||
| bool | fix_bond_stereo = True |
||
| ) |
Aligns the 2D atom coordinates of molgraph with those of ref_molgraph, using substr_ptn as the explicit substructure search pattern.
| molgraph | The molecular graph to align. |
| ref_molgraph | The reference molecular graph providing the target coordinates. |
| substr_ptn | The substructure search pattern that defines the atoms to align. |
| fix_bond_stereo | If True, postprocess 2D bond stereo flags so that they remain consistent with the aligned coordinates. |
True if the alignment succeeded, and False otherwise.| bool CDPL.Chem.align3DCoordinates | ( | Entity3DContainer | cntnr, |
| Entity3DContainer | ref_entities, | ||
| Math.Vector3DArray | ref_coords | ||
| ) |
Transforms the 3D coordinates of the entities of cntnr by the affine matrix that is calculated for the rigid-body alignment of the 3D coordinates of the entities of ref_entities with the given reference coordinates ref_coords.
| cntnr | The entity 3D container whose coordinates are to be transformed. |
| ref_entities | The reference entity 3D container. |
| ref_coords | The reference coordinates corresponding to the entities of ref_entities. |
True if the alignment succeeded, and False otherwise.| bool CDPL.Chem.alignConformations | ( | AtomContainer | cntnr, |
| Util.BitSet | ref_atom_mask, | ||
| Math.Vector3DArray | ref_coords | ||
| ) |
Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms flagged in ref_atom_mask as alignment anchors.
| cntnr | The atom container holding the conformations to be aligned. |
| ref_atom_mask | Bit mask selecting the atoms of cntnr used as alignment anchors. |
| ref_coords | Reference 3D coordinates of the alignment-anchor atoms. |
True if the alignment succeeded for every conformation, and False otherwise.| bool CDPL.Chem.alignConformations | ( | AtomContainer | cntnr, |
| AtomContainer | ref_atoms, | ||
| Math.Vector3DArray | ref_coords | ||
| ) |
Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors.
| cntnr | The atom container holding the conformations to be aligned. |
| ref_atoms | The atoms used as alignment anchors (must all be members of cntnr). |
| ref_coords | Reference 3D coordinates of the alignment-anchor atoms. |
True if the alignment succeeded for every conformation, and False otherwise.| bool CDPL.Chem.alignConformations | ( | AtomContainer | cntnr, |
| Util.BitSet | ref_atom_mask | ||
| ) |
Aligns each stored conformation of cntnr to the first conformation using the atoms flagged in ref_atom_mask as alignment anchors.
| cntnr | The atom container holding the conformations to be aligned. |
| ref_atom_mask | Bit mask selecting the atoms of cntnr used as alignment anchors. |
True if the alignment succeeded for every conformation, and False otherwise.| bool CDPL.Chem.alignConformations | ( | AtomContainer | cntnr, |
| AtomContainer | ref_atoms | ||
| ) |
Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors.
| cntnr | The atom container holding the conformations to be aligned. |
| ref_atoms | The atoms used as alignment anchors (must all be members of cntnr). |
True if the alignment succeeded for every conformation, and False otherwise.| None CDPL.Chem.applyConformation | ( | AtomContainer | cntnr, |
| int | conf_idx | ||
| ) |
Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates.
| cntnr | The atom container. |
| conf_idx | The zero-based conformation index. |
| bool CDPL.Chem.atomTypesMatch | ( | int | qry_type, |
| int | tgt_type | ||
| ) |
Tells whether the target atom type tgt_type matches the query atom type qry_type (taking generic atom type classes like Chem.AtomType.HET into account).
| qry_type | The query atom type (Chem.AtomType value). |
| tgt_type | The target atom type (Chem.AtomType value). |
True if the target matches the query, and False otherwise. | None CDPL.Chem.calc2DCoordinates | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes 2D atom coordinates for the molecular graph molgraph and stores them as corresponding atom properties.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing 2D coordinates properties should be replaced. |
| None CDPL.Chem.calcAtomCIPConfigurations | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores CIP configuration labels for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing CIP configuration properties should be replaced. |
| None CDPL.Chem.calcAtomStereoDescriptorsFromMDLParities | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Derives atom stereo descriptors of the molecular graph molgraph from previously-assigned MDL parities.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing stereo descriptor properties should be replaced. |
| None CDPL.Chem.calcAtomStereoDescriptors | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| int | dim = 1, |
||
| bool | check_stc_flag = True |
||
| ) |
Computes and stores stereo descriptors for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing stereo descriptor properties should be replaced. |
| dim | The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available). |
| check_stc_flag | If True, descriptors are only computed for atoms whose Chem.AtomProperty.STEREO_CENTER_FLAG property is True. |
| None CDPL.Chem.calcBasicProperties | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes basic atom/bond/molecular graph properties (aromaticity, SSSR, etc.) of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing property values should be replaced. |
| None CDPL.Chem.calcBasicProperties | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Computes basic atom/bond/molecular graph properties (aromaticity, ring info, etc.) for every component of the reaction rxn.
| rxn | The reaction. |
| overwrite | Specifies whether already existing property values should be replaced. |
| None CDPL.Chem.calcBond2DStereoFlags | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Derives 2D wedge/hash bond stereo flags for the bonds of the molecular graph molgraph from the atoms' stereo descriptors and 2D coordinates.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing 2D bond stereo flag properties should be replaced. |
| None CDPL.Chem.calcBondCIPConfigurations | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores CIP configuration labels for the bonds of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing CIP configuration properties should be replaced. |
| None CDPL.Chem.calcBondStereoDescriptors | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| int | dim = 1, |
||
| bool | check_stc_flag = True |
||
| ) |
Computes and stores stereo descriptors for the bonds of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing stereo descriptor properties should be replaced. |
| dim | The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available). |
| check_stc_flag | If True, descriptors are only computed for bonds whose Chem.BondProperty.STEREO_CENTER_FLAG property is True. |
| None CDPL.Chem.calcBoundingBox | ( | AtomContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max, | ||
| Atom3DCoordinatesFunction | coords_func, | ||
| bool | reset = True |
||
| ) |
Computes the axis-aligned bounding box enclosing the atoms of cntnr.
| cntnr | The atom container. |
| min | The output lower-left corner of the bounding box. |
| max | The output upper-right corner of the bounding box. |
| coords_func | The function returning the 3D coordinates of an atom. |
| reset | If True, the bounding box is reset to the first atom. Otherwise, min and max are extended in place. |
| None CDPL.Chem.calcBoundingBox | ( | Entity3DContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max, | ||
| bool | reset = True |
||
| ) |
Calculates the axis-aligned bounding box of the 3D coordinates of the entities of cntnr.
| cntnr | The entity 3D container. |
| min | The output vector receiving the per-axis minimum coordinates. |
| max | The output vector receiving the per-axis maximum coordinates. |
| reset | If True, min and max are reset before the calculation. If False, the given bounding box is extended. |
| None CDPL.Chem.calcCIPPriorities | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores topological CIP priorities for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing CIP priority properties should be replaced. |
| None CDPL.Chem.calcCanonicalNumbering | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648 |
||
| ) |
Computes and stores canonical atom numbers for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing canonical number properties should be replaced. |
| atom_flags | A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties affect the numbering. |
| bond_flags | A bitmask of Chem.BondPropertyFlag flags controlling which bond properties affect the numbering. |
| bool CDPL.Chem.calcCenterOfMass | ( | AtomContainer | cntnr, |
| Atom3DCoordinatesFunction | coords_func, | ||
| Math.Vector3D | ctr | ||
| ) |
Computes the mass-weighted center of mass of the atoms in cntnr.
| cntnr | The atom container. |
| coords_func | The function returning the 3D coordinates of an atom. |
| ctr | The output center-of-mass coordinates. |
True if the center of mass could be computed (at least one atom with non-zero mass), and False otherwise. | bool CDPL.Chem.calcCentroid | ( | AtomContainer | cntnr, |
| Atom3DCoordinatesFunction | coords_func, | ||
| Math.Vector3D | ctr | ||
| ) |
Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr.
| cntnr | The atom container. |
| coords_func | The function returning the 3D coordinates of an atom. |
| ctr | The output centroid coordinates. |
True if the centroid could be computed (cntnr is non-empty), and False otherwise. | bool CDPL.Chem.calcCentroid | ( | Entity3DContainer | cntnr, |
| Math.Vector3D | ctr | ||
| ) |
Calculates the geometric centroid of the 3D coordinates of the entities of cntnr.
| cntnr | The entity 3D container. |
| ctr | The output centroid vector. |
True if the centroid could be calculated (i.e. cntnr is non-empty), and False otherwise. | int CDPL.Chem.calcConfiguration | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| StereoDescriptor | descr, | ||
| Math.Vector3DArray | coords | ||
| ) |
Calculates the atom configuration from the supplied descriptor and reference atom 3D coordinates.
| atom | The atom for which to calculate the configuration. |
| molgraph | The molecular graph providing the structural context. |
| descr | The stereo descriptor providing the reference atoms. |
| coords | The atom 3D coordinates to use for the calculation. |
| int CDPL.Chem.calcConfiguration | ( | Bond | bond, |
| MolecularGraph | molgraph, | ||
| StereoDescriptor | descr, | ||
| Math.Vector3DArray | coords | ||
| ) |
Calculates the bond configuration from the supplied descriptor and reference atom 3D coordinates.
| bond | The bond for which to calculate the configuration. |
| molgraph | The molecular graph providing the structural context. |
| descr | The stereo descriptor providing the reference atoms. |
| coords | The atom 3D coordinates to use for the calculation. |
| int CDPL.Chem.calcFormalCharge | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Computes the formal charge of the atom atom from its connectivity in the molecular graph molgraph.
| atom | The atom for which to calculate the charge. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.calcFormalCharges | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores formal charges for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing formal charge properties should be replaced. |
| None CDPL.Chem.calcGeometricalDistanceMatrix | ( | Entity3DContainer | cntnr, |
| Math.DMatrix | mtx | ||
| ) |
Calculates the inter-entity geometric distance matrix for the entities of cntnr.
| cntnr | The entity 3D container providing the source coordinates. |
| mtx | The output matrix receiving the calculated pairwise distances. |
| Math.DMatrix CDPL.Chem.calcGeometricalDistanceMatrix | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores the geometrical distance matrix of the molecular graph molgraph from its 3D coordinates.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing distance matrix property should be replaced. |
| int CDPL.Chem.calcHashCode | ( | MolecularGraph | molgraph, |
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648, |
||
| bool | ord_h_deplete = True |
||
| ) |
Computes a 64-bit hash code for the molecular graph molgraph taking into account the specified atom and bond properties.
| molgraph | The molecular graph. |
| atom_flags | A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties contribute to the hash. |
| bond_flags | A bitmask of Chem.BondPropertyFlag flags controlling which bond properties contribute to the hash. |
| ord_h_deplete | True to suppress ordinary hydrogens before hashing. |
| int CDPL.Chem.calcHashCode | ( | Reaction | rxn, |
| int | role_mask = 7, |
||
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648, |
||
| bool | ord_h_deplete = True |
||
| ) |
Computes a 64-bit hash code for the reaction rxn taking into account the specified reaction roles and atom/bond properties.
| rxn | The reaction to hash. |
| role_mask | A bitmask of Chem.ReactionRole flags selecting the considered component sets. |
| atom_flags | A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties enter the hash. |
| bond_flags | A bitmask of Chem.BondPropertyFlag flags controlling which bond properties enter the hash. |
| ord_h_deplete | True to suppress ordinary hydrogens before hashing. |
| None CDPL.Chem.calcHydrogen3DCoordinates | ( | MolecularGraph | molgraph, |
| bool | undef_only = True |
||
| ) |
Computes 3D coordinates for the hydrogen atoms of the molecular graph molgraph from the 3D coordinates of their non-hydrogen neighbors.
| molgraph | The molecular graph. |
| undef_only | If True, only hydrogens without prior 3D coordinates are placed. If False, all hydrogen coordinates are recomputed. |
| int CDPL.Chem.calcImplicitHydrogenCount | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Computes the implicit hydrogen count of the atom atom from its connectivity in the molecular graph molgraph.
| atom | The atom for which to calculate the hydrogen count. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.calcImplicitHydrogenCounts | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores implicit hydrogen counts for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing hydrogen count properties should be replaced. |
| None CDPL.Chem.calcMDLParities | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores MDL parities for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing MDL parity properties should be replaced. |
| int CDPL.Chem.calcMDLParity | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Calculates the MDL parity of the atom atom in the molecular graph molgraph.
| atom | The atom for which to calculate the parity. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.calcMorganNumbering | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores Morgan numbers for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing morgan number properties should be replaced. |
| StereoDescriptor CDPL.Chem.calcStereoDescriptor | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| int | dim = 1 |
||
| ) |
Computes the stereo descriptor for the atom atom in the molecular graph molgraph.
| atom | The atom for which to calculate the stereo descriptor. |
| molgraph | The molecular graph providing the structural context. |
| dim | The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available). |
| StereoDescriptor CDPL.Chem.calcStereoDescriptor | ( | Bond | bond, |
| MolecularGraph | molgraph, | ||
| int | dim = 1 |
||
| ) |
Computes the stereo descriptor for the bond bond in the molecular graph molgraph.
| bond | The bond for which to calculate the stereo descriptor. |
| molgraph | The molecular graph providing the structural context. |
| dim | The dimensionality of the atomic coordinates to use (2 = 2D, 3 = 3D, 0 = recalc. existing descriptor, other values = use any information available). |
| StereoDescriptor CDPL.Chem.calcStereoDescriptorFromMDLParity | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Calculates the stereo descriptor of the atom atom from its MDL parity in the molecular graph molgraph.
| atom | The atom for which to calculate the stereo descriptor. |
| molgraph | The molecular graph providing the structural context. |
| Math.ULMatrix CDPL.Chem.calcTopologicalDistanceMatrix | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores the topological distance matrix of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing distance matrix property should be replaced. |
| None CDPL.Chem.calcTopologicalDistanceMatrix | ( | MolecularGraph | molgraph, |
| Math.ULMatrix | mtx | ||
| ) |
Computes the topological distance matrix of the molecular graph molgraph into the supplied matrix mtx.
| molgraph | The molecular graph. |
| mtx | The output topological distance matrix. |
| int CDPL.Chem.calcUnpairedElectronCount | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Computes the unpaired (radical) electron count of the atom atom from its implict hydrogen count property value.
This function calculates the number of valence electrons that are not engaged in a bond and thus reduce the total atom valence to a value lower than the allowed maximum (atom element and formal charge dependent).
| atom | The atom for which to calculate the unpaired electron count. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.calcUnpairedElectronCounts | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores the unpaired (radical) electron counts for the atoms in the molecular graph molgraph.
For each atom of molgraph this function calculates the number of valence electrons that are not engaged in a bond from the value of the property AtomProperty.IMPLICIT_HYDROGEN_COUNT and stores the result as value of the property AtomProperty.UNPAIRED_ELECTRON_COUNT (the treatment of already present property values depends on the flag overwrite). This function can be called after reading molecules from data in formats that do not support explicit atom radical electron count information (e.g. SMILES) in order to generate the missing data (if of relevance for further processing).
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing unpaired electron count properties should be replaced. |
| None CDPL.Chem.canonicalize | ( | MolecularGraph | molgraph, |
| bool | atoms = True, |
||
| bool | atom_nbrs = True, |
||
| bool | bonds = True, |
||
| bool | bond_atoms = False |
||
| ) |
Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to the canonical number property value of its atoms.
| molgraph | The molecular graph. |
| atoms | True to sort atoms. |
| atom_nbrs | True to sort each atom's neighbor list. |
| bonds | True to sort bonds. |
| bond_atoms | True to reorder the start/end atoms of each bond. |
| None CDPL.Chem.canonicalize | ( | MolecularGraph | molgraph, |
| BoolAtom2Functor | func, | ||
| bool | atoms = True, |
||
| bool | atom_nbrs = True, |
||
| bool | bonds = True, |
||
| bool | bond_atoms = False |
||
| ) |
Reorders the atoms (and optionally their neighbors and bonds) of the molecular graph molgraph according to a user-supplied comparator.
| molgraph | The molecular graph. |
| func | The atom comparator that defines the canonical ordering. |
| atoms | True to sort atoms. |
| atom_nbrs | True to sort each atom's neighbor list. |
| bonds | True to sort bonds. |
| bond_atoms | True to reorder the start/end atoms of each bond according to the comparator. |
| None CDPL.Chem.connectAtoms | ( | Molecule | mol, |
| Atom3DCoordinatesFunction | coords_func, | ||
| float | dist_tol = 0.3, |
||
| int | atom_idx_offs = 0 |
||
| ) |
Adds bonds between atoms of the molecule mol whose 3D distance (obtained via coords_func) falls within the covalent-radii sum plus dist_tol.
| mol | The molecule whose atoms are to be connected. |
| coords_func | The function used to retrieve the 3D coordinates of an atom. |
| dist_tol | The tolerance added to the sum of the two atoms' covalent radii. |
| atom_idx_offs | Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs. |
| None CDPL.Chem.connectAtoms | ( | Molecule | mol, |
| float | dist_tol = 0.3, |
||
| int | atom_idx_offs = 0 |
||
| ) |
Adds bonds between atoms of the molecule mol whose 3D distance falls within the covalent-radii sum plus dist_tol.
| mol | The molecule whose atoms shall be connected. |
| dist_tol | The tolerance added to the sum of the two atoms' covalent radii. |
| atom_idx_offs | Bonds are only added when at least one of the two atom indices is greater than or equal to atom_idx_offs. |
| bool CDPL.Chem.containsFragmentWithBond | ( | FragmentList | frag_list, |
| Bond | bond | ||
| ) |
Tells whether any fragment in frag_list contains the bond bond.
| frag_list | The list of fragments to search. |
| bond | The queried bond. |
True if at least one fragment contains bond, and False otherwise. | bool CDPL.Chem.containsFragmentWithMinSize | ( | FragmentList | frag_list, |
| int | min_size | ||
| ) |
Tells whether frag_list contains at least one fragment with at least min_size atoms.
| frag_list | The list of fragments to search. |
| min_size | The minimum required atom count. |
True if such a fragment exists, and False otherwise. | bool CDPL.Chem.containsMolecularGraph | ( | MolecularGraph | molgraph, |
| MolecularGraph | sub_molgraph, | ||
| bool | atoms = True, |
||
| bool | bonds = True |
||
| ) |
Tells whether the molecular graph molgraph contains the atoms and/or bonds of sub_molgraph.
| molgraph | The host molecular graph. |
| sub_molgraph | The candidate sub-graph. |
| atoms | If True, every atom of sub_molgraph must be a member of the molecular graph molgraph. |
| bonds | If True, every bond of sub_molgraph must be a member of the molecular graph molgraph. |
True if the requested containment relations all hold, and False otherwise. | None CDPL.Chem.copyAtomsIf | ( | AtomContainer | cntnr, |
| Molecule | mol, | ||
| AtomPredicate | pred, | ||
| bool | append = False |
||
| ) |
Copies every atom of cntnr that satisfies pred into the molecule mol.
| cntnr | The source atom container. |
| mol | The target molecule. |
| pred | The predicate evaluated for each atom. Only atoms for which it returns True are copied. |
| append | If True, atoms are appended to mol. Otherwise, mol is cleared first. |
| None CDPL.Chem.copyAtomsIf | ( | AtomContainer | cntnr, |
| Fragment | frag, | ||
| AtomPredicate | pred, | ||
| bool | append = False |
||
| ) |
Copies every atom of cntnr that satisfies pred into the fragment frag.
| cntnr | The source atom container. |
| frag | The target fragment. |
| pred | The predicate evaluated for each atom. Only atoms for which it returns True are copied. |
| append | If True, atoms are appended to frag. Otherwise, frag is cleared first. |
| None CDPL.Chem.copyAtomsIfNot | ( | AtomContainer | cntnr, |
| Molecule | mol, | ||
| AtomPredicate | pred, | ||
| bool | append = False |
||
| ) |
Copies every atom of cntnr that does not satisfy pred into the molecule mol.
| cntnr | The source atom container. |
| mol | The target molecule. |
| pred | The predicate evaluated for each atom. Only atoms for which it returns False are copied. |
| append | If True, atoms are appended to mol. Otherwise, mol is cleared first. |
| None CDPL.Chem.copyAtomsIfNot | ( | AtomContainer | cntnr, |
| Fragment | frag, | ||
| AtomPredicate | pred, | ||
| bool | append = False |
||
| ) |
Copies every atom of cntnr that does not satisfy pred into the fragment frag.
| cntnr | The source atom container. |
| frag | The target fragment. |
| pred | The predicate evaluated for each atom. Only atoms for which it returns False are copied. |
| append | If True, atoms are appended to frag. Otherwise, frag is cleared first. |
| int CDPL.Chem.createAtomTypeMask | ( | AtomContainer | cntnr, |
| Util.BitSet | mask, | ||
| int | type, | ||
| bool | reset = True, |
||
| bool | strict = True |
||
| ) |
Sets bits in mask corresponding to atoms of cntnr whose atom type matches type.
| cntnr | The atom container. |
| mask | The output bit mask (bit i is set if atom i of cntnr has the requested type). |
| type | The query atom type (Chem.AtomType value, possibly a generic class such as Chem.AtomType.HET). |
| reset | If True, mask is reset before processing. Otherwise, existing bits are preserved. |
| strict | If True, only exact type matches are accepted. If False, generic-class matches also set the bit. |
| int CDPL.Chem.editSubstructures | ( | MolecularGraph | molgraph, |
| Molecule | result_mol, | ||
| str | search_ptns, | ||
| str | result_ptn, | ||
| str | exclude_ptns = '' |
||
| ) |
Builds the molecule result_mol from the molecular graph molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn.
A molecule editing operation is specified via a string of one or more SMARTS patterns (search_ptns) describing the substructures to edit, optional substructure exclude patterns (exclude_ptns) and a SMILES string (result_ptn) encoding the specific atom and bond modifications to perform. If multiple search and/or exclude patterns are specified then they need to be separated by a whitespace character.
In the substructure search pattern(s), any atoms to be edited and/or atoms connected by bonds to be modified must be labeled by a unique non-zero integer number (by means of a colon followed the integer number at the end of the SMARTS atom specification). These numeric ids are used to establish an unambiguous mapping between the atoms/bonds of the search pattern and the SMILES string encoding the editing instructions. As mentioned above, the atom/bond editing operations are all specified by means of a simple SMILES string. For the purpose of substructure editing, the SMILES format has been extended by additional atom type and bond order symbols that allow to mark atom/bonds for deletion or act as a 'do not change' marker for atom type or bond order.
Editing result SMILES strings have to be composed according to the following rules:
x (only valid in brackets) results in the removal of the mapped molecule atom including any incident bonds~ (only valid in brackets) indicates that the type of the mapped molecule atom shall be left unchangedx results in the removal of the mapped molecule bond~ indicates that the order of the mapped molecule bond shall be left unchanged| molgraph | The source molecular graph. |
| result_mol | The molecule receiving the edited result. |
| search_ptns | A whitespace-separated list of SMARTS patterns specifying the substructures to replace. |
| result_ptn | The SMARTS replacement pattern. |
| exclude_ptns | A whitespace-separated list of SMARTS patterns specifying substructures that shall be retained even if they also match search_ptns. |
| int CDPL.Chem.editSubstructures | ( | Molecule | mol, |
| str | search_ptns, | ||
| str | result_ptn, | ||
| str | exclude_ptns = '' |
||
| ) |
Edits the molecule mol by replacing all substructures matching the SMARTS search patterns in search_ptns with the SMILES replacement pattern result_ptn, optionally skipping matches that also match exclude_ptns.
A molecule editing operation is specified via a string of one or more SMARTS patterns (search_ptns) describing the substructures to edit, optional substructure exclude patterns (exclude_ptns) and a SMILES string (result_ptn) encoding the specific atom and bond modifications to perform. If multiple search and/or exclude patterns are specified then they need to be separated by a whitespace character.
In the substructure search pattern(s), any atoms to be edited and/or atoms connected by bonds to be modified must be labeled by a unique non-zero integer number (by means of a colon followed the integer number at the end of the SMARTS atom specification). These numeric ids are used to establish an unambiguous mapping between the atoms/bonds of the search pattern and the SMILES string encoding the editing instructions. As mentioned above, the atom/bond editing operations are all specified by means of a simple SMILES string. For the purpose of substructure editing, the SMILES format has been extended by additional atom type and bond order symbols that allow to mark atom/bonds for deletion or act as a 'do not change' marker for atom type or bond order.
Editing result SMILES strings have to be composed according to the following rules:
x (only valid in brackets) results in the removal of the mapped molecule atom including any incident bonds~ (only valid in brackets) indicates that the type of the mapped molecule atom shall be left unchangedx results in the removal of the mapped molecule bond~ indicates that the order of the mapped molecule bond shall be left unchanged| mol | The molecule to edit in place. |
| search_ptns | A whitespace-separated list of SMARTS patterns specifying the substructures to replace. |
| result_ptn | The SMARTS replacement pattern. |
| exclude_ptns | A whitespace-separated list of SMARTS patterns specifying substructures that shall be retained even if they match search_ptns. |
| None CDPL.Chem.extendBoundingBox | ( | Math.Vector3D | min, |
| Math.Vector3D | max, | ||
| Math.Vector3D | coords, | ||
| bool | reset = False |
||
| ) |
Extends the axis-aligned bounding box defined by min and max so that it contains the point coords.
| min | The lower-left corner of the bounding box (updated in place). |
| max | The upper-right corner of the bounding box (updated in place). |
| coords | The 3D point to include. |
| reset | If True, the bounding box is first reset to coords (degenerate point box) before extension. |
| None CDPL.Chem.extractReactionCenter | ( | MolecularGraph | molgraph, |
| Fragment | rxn_center | ||
| ) |
Collects every atom and bond of the molecular graph molgraph that carries a reaction-center flag into the fragment rxn_center.
| molgraph | The molecular graph. |
| rxn_center | The output fragment receiving the reaction-center atoms and bonds. |
| FragmentList CDPL.Chem.extractSSSRSubset | ( | MolecularGraph | src_molgraph, |
| MolecularGraph | tgt_molgraph | ||
| ) |
Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph.
| src_molgraph | The source molecular graph whose SSSR is to be projected. |
| tgt_molgraph | The target molecular graph acting as filter. |
| FragmentList CDPL.Chem.extractSSSRSubset | ( | MolecularGraph | src_molgraph, |
| MolecularGraph | tgt_molgraph, | ||
| bool | overwrite | ||
| ) |
Extracts the SSSR subset of the molecular graph src_molgraph whose rings consist of atoms and bonds of tgt_molgraph and stores it on the latter.
| src_molgraph | The source molecular graph whose SSSR is to be projected. |
| tgt_molgraph | The target molecular graph which receives the projected SSSR and acts as filter. |
| overwrite | Specifies whether an already existing tgt_molgraph SSSR property should be replaced. |
| Math.ULMatrix CDPL.Chem.extractTopologicalDistanceSubMatrix | ( | MolecularGraph | src_molgraph, |
| MolecularGraph | tgt_molgraph, | ||
| bool | overwrite | ||
| ) |
Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph and stores it on the latter.
| src_molgraph | The source molecular graph providing the full matrix. |
| tgt_molgraph | The target molecular graph providing the atom subset and (optionally) receiving the sub-matrix. |
| overwrite | Specifies whether an already existing distance matrix property should be replaced. |
| None CDPL.Chem.extractTopologicalDistanceSubMatrix | ( | MolecularGraph | src_molgraph, |
| MolecularGraph | tgt_molgraph, | ||
| Math.ULMatrix | mtx | ||
| ) |
Extracts the topological distance sub-matrix of the molecular graph src_molgraph that covers the atoms of tgt_molgraph into the supplied matrix mtx.
| src_molgraph | The source molecular graph providing the full matrix. |
| tgt_molgraph | The target molecular graph providing the atom subset. |
| mtx | The output topological distance matrix. |
| None CDPL.Chem.generateAdjacencyMatrix | ( | MolecularGraph | molgraph, |
| Math.SparseULMatrix | mtx | ||
| ) |
Builds the adjacency matrix of the molecular graph molgraph.
Entry (i,j) is 1 if atoms i and j are connected by a bond and 0 if there is no bond.
| molgraph | The molecular graph. |
| mtx | The output adjacency matrix. |
| None CDPL.Chem.generateBondAtomTypeMatrix | ( | MolecularGraph | molgraph, |
| Math.SparseULMatrix | mtx | ||
| ) |
Builds a matrix combining bond order and atom type information of the endpoints of every bond in molgraph.
Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond. Diagonal entries (i,i) store the type of each atom i.
| molgraph | The molecular graph. |
| mtx | The output bond and atom type matrix. |
| None CDPL.Chem.generateBondElectronMatrix | ( | MolecularGraph | molgraph, |
| Math.SparseULMatrix | mtx | ||
| ) |
Builds the bond-electron matrix of the molecular graph molgraph.
Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond. Diagonal entries (i,i) store the free valence electron count of each atom i.
| molgraph | The molecular graph. |
| mtx | The output bond-electron matrix. |
| None CDPL.Chem.generateBondMatrix | ( | MolecularGraph | molgraph, |
| Math.SparseULMatrix | mtx | ||
| ) |
Builds the bond order matrix of the molecular graph molgraph.
Entry (i,j) is the order of the bond between atoms i and j and 0 if there is no bond.
| molgraph | The molecular graph. |
| mtx | The output bond matrix. |
| object CDPL.Chem.generateINCHIKey | ( | MolecularGraph | molgraph | ) |
| molgraph |
| object CDPL.Chem.generateINCHI | ( | MolecularGraph | molgraph, |
| str | options = '/WarnOnEmptyStructure /AuxNone /NEWPSOFF', |
||
| int | dim = 0 |
||
| ) |
| molgraph | |
| options | |
| dim |
| None CDPL.Chem.generateIncidenceMatrix | ( | MolecularGraph | molgraph, |
| Math.SparseULMatrix | mtx | ||
| ) |
Builds the atom/bond incidence matrix of the molecular graph molgraph.
Entry (i,j) is 1 if atom i is an endpoint of bond j.
| molgraph | The molecular graph. |
| mtx | The output incidence matrix. |
| AtomMatchExpression CDPL.Chem.generateMatchExpression | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Builds an match expression from the match constraint list attached to the atom atom.
| atom | The atom for which to generate the expression. |
| molgraph | The molecular graph providing the structural context. |
| BondMatchExpression CDPL.Chem.generateMatchExpression | ( | Bond | bond, |
| MolecularGraph | molgraph | ||
| ) |
Builds a match expression from the match constraint list attached to the bond bond.
| bond | The bond for which to generate the expression.. |
| molgraph | The molecular graph providing the structural context. |
| MolecularGraphMatchExpression CDPL.Chem.generateMatchExpression | ( | MolecularGraph | molgraph | ) |
Builds a match expression from the match constraints currently attached to the molecular graph molgraph.
| molgraph | The molecular graph. |
| MolecularGraphMatchExpression CDPL.Chem.generateMatchExpression | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Builds and stores the match expression of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing match expression property should be replaced. |
| ReactionMatchExpression CDPL.Chem.generateMatchExpression | ( | Reaction | rxn | ) |
Builds a match expression from the match constraints currently attached to the reaction rxn.
| rxn | The reaction. |
| ReactionMatchExpression CDPL.Chem.generateMatchExpression | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Builds and stores the match expression of the reaction rxn.
| rxn | The reaction. |
| overwrite | Specifies whether an already existing match expression property should be replaced. |
| str CDPL.Chem.generateMatchExpressionString | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
| atom | |
| molgraph |
| str CDPL.Chem.generateMatchExpressionString | ( | Bond | bond, |
| MolecularGraph | molgraph | ||
| ) |
| bond | |
| molgraph |
| None CDPL.Chem.generateMatchExpressionStrings | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Generates and stores textual representations of the atom/bond match expressions of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing match expression string properties should be replaced. |
| None CDPL.Chem.generateMatchExpressions | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Generates and stores match expressions for every atom, bond and the molecular graph molgraph itself.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing match expression properties should be replaced. |
| None CDPL.Chem.generateMatchExpressions | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Generates and stores match expressions for the atoms, bonds, components, and the reaction rxn itself.
| rxn | The reaction. |
| overwrite | Specifies whether already existing match expression properties should be replaced. |
| object CDPL.Chem.generateSMILES | ( | MolecularGraph | molgraph, |
| bool | canonical = False, |
||
| bool | ord_h_deplete = True, |
||
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648 |
||
| ) |
| molgraph | |
| canonical | |
| ord_h_deplete | |
| atom_flags | |
| bond_flags |
| object CDPL.Chem.generateSMILES | ( | Reaction | rxn, |
| bool | canonical = False, |
||
| bool | ord_h_deplete = True, |
||
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648 |
||
| ) |
| rxn | |
| canonical | |
| ord_h_deplete | |
| atom_flags | |
| bond_flags |
| None CDPL.Chem.initSubstructureSearchQuery | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Prepares the molecular graph molgraph for use as a substructure search query.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing property values should be replaced. |
| None CDPL.Chem.initSubstructureSearchQuery | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Prepares the reaction rxn for use as a reaction substructure search query.
| rxn | The reaction. |
| overwrite | Specifies whether already existing property values should be replaced. |
| None CDPL.Chem.initSubstructureSearchTarget | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Prepares the molecular graph molgraph for use as a substructure search target.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing property values should be replaced. |
| None CDPL.Chem.initSubstructureSearchTarget | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Prepares the reaction rxn for use as a reaction substructure search target.
| rxn | The reaction. |
| overwrite | Specifies whether already existing property values should be replaced. |
| bool CDPL.Chem.insideBoundingBox | ( | AtomContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max, | ||
| Atom3DCoordinatesFunction | coords_func | ||
| ) |
Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max.
| cntnr | The atom container. |
| min | The lower-left corner of the bounding box. |
| max | The upper-right corner of the bounding box. |
| coords_func | The function returning the 3D coordinates of an atom. |
True if all atoms are inside the box, and False otherwise. | bool CDPL.Chem.insideBoundingBox | ( | Entity3DContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max | ||
| ) |
Tells whether all 3D coordinates of the entities of cntnr lie within the axis-aligned bounding box defined by min and max.
| cntnr | The entity 3D container. |
| min | The per-axis minimum coordinates of the box. |
| max | The per-axis maximum coordinates of the box. |
True if every entity coordinate is inside the bounding box, and False otherwise. | bool CDPL.Chem.insideBoundingBox | ( | Math.Vector3D | min, |
| Math.Vector3D | max, | ||
| Math.Vector3D | coords | ||
| ) |
Tells whether the point coords lies inside the axis-aligned bounding box defined by min and max.
| min | The lower-left corner of the bounding box. |
| max | The upper-right corner of the bounding box. |
| coords | The 3D point to test. |
True if the point is inside (componentwise <= max and >= min), and False otherwise. | bool CDPL.Chem.intersectsBoundingBox | ( | AtomContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max, | ||
| Atom3DCoordinatesFunction | coords_func | ||
| ) |
Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max.
| cntnr | The atom container. |
| min | The lower-left corner of the bounding box. |
| max | The upper-right corner of the bounding box. |
| coords_func | The function returning the 3D coordinates of an atom. |
True if at least one atom is inside the box, and False otherwise. | bool CDPL.Chem.intersectsBoundingBox | ( | Entity3DContainer | cntnr, |
| Math.Vector3D | min, | ||
| Math.Vector3D | max | ||
| ) |
Tells whether at least one entity of cntnr lies within the axis-aligned bounding box defined by min and max.
| cntnr | The entity 3D container. |
| min | The per-axis minimum coordinates of the box. |
| max | The per-axis maximum coordinates of the box. |
True if any entity coordinate is inside the bounding box, and False otherwise. | bool CDPL.Chem.isAromatic | ( | Fragment | ring, |
| MolecularGraph | molgraph, | ||
| Util.BitSet | arom_bond_mask | ||
| ) |
Tells whether ring fulfills the Hückel (4n+2)π-electron criterion within molgraph.
| ring | The candidate aromatic ring. |
| molgraph | The parent molecular graph. |
| arom_bond_mask | A bond bit mask flagging bonds already known to be aromatic. |
True if ring satisfies the Hückel rule, and False otherwise. | bool CDPL.Chem.isInFragmentOfSize | ( | Atom | atom, |
| FragmentList | frag_list, | ||
| int | size | ||
| ) |
Tells whether the atom atom is a member of any fragment in frag_list whose size matches size.
| atom | The atom to query. |
| frag_list | The list of fragments to search. |
| size | The required fragment size (in number of atoms). |
True if at least one matching fragment contains the atom atom, and False otherwise. | bool CDPL.Chem.isInFragmentOfSize | ( | Bond | bond, |
| FragmentList | frag_list, | ||
| int | size | ||
| ) |
Tells whether the bond bond is a member of any fragment in frag_list whose size matches size.
| bond | The bond to query. |
| frag_list | The list of fragments to search. |
| size | The required fragment size (in number of atoms). |
True if at least one matching fragment contains the bond bond, and False otherwise. | bool CDPL.Chem.isNotAromatic | ( | Fragment | ring, |
| MolecularGraph | molgraph | ||
| ) |
Tells whether ring is guaranteed not to be aromatic (based on quick geometric/topological criteria).
| ring | The ring to test. |
| molgraph | The parent molecular graph. |
True if ring cannot be aromatic, and False if a more thorough test is required. | bool CDPL.Chem.isStereoCenter | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| bool | check_asym = True, |
||
| bool | check_inv_n = True, |
||
| bool | check_quart_n = True, |
||
| bool | check_plan_n = True, |
||
| bool | check_amide_n = True, |
||
| bool | check_res_ctrs = True |
||
| ) |
Tells whether the atom atom qualifies as a stereo center in the context of the molecular graph molgraph.
| atom | The atom to evaluate. |
| molgraph | The molecular graph providing the structural context. |
| check_asym | True to consider only topologically non-equivalent ligand environments. |
| check_inv_n | True to reject inversion-prone nitrogen centers (umbrella inversion). |
| check_quart_n | True to accept positively charged quaternary nitrogen centers. |
| check_plan_n | True to reject planar nitrogen centers. |
| check_amide_n | True to reject amide nitrogen centers. |
| check_res_ctrs | True to reject centers participating in resonance. |
True if the atom qualifies as a stereo center under the given conditions, and False otherwise. | bool CDPL.Chem.isStereoCenter | ( | Bond | bond, |
| MolecularGraph | molgraph, | ||
| bool | check_asym = True, |
||
| bool | check_term_n = True, |
||
| bool | check_order = True, |
||
| int | min_ring_size = 8 |
||
| ) |
Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph.
| bond | The bond to evaluate. |
| molgraph | The molecular graph providing the structural context. |
| check_asym | True to consider only topologically non-equivalent ligand environments. |
| check_term_n | True to reject bonds to terminal nitrogen atoms. |
| check_order | True to require that the bond order matches a stereogenic pattern. |
| min_ring_size | If the bond bond is a ring bond, the containing ring must have at least this size to qualify. |
True if the bond qualifies as a stereo center under the given conditions, and False otherwise. | None CDPL.Chem.kekulizeBonds | ( | MolecularGraph | molgraph | ) |
Assigns Kekulé bond orders to the aromatic bonds of the molecular graph molgraph.
| molgraph | The molecular graph. |
| bool CDPL.Chem.makeHydrogenComplete | ( | Molecule | mol, |
| bool | corr_impl_h_count = True |
||
| ) |
Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms.
| mol | The molecule that has to be made hydrogen complete. |
| corr_impl_h_count | True if the implicit hydrogen count property of the hydrogen completed shall be set to zero, False if the property shall be left unchanged. |
False if mol was not altered, True otherwise. | bool CDPL.Chem.makeHydrogenDeplete | ( | Fragment | frag | ) |
Removes all explicit hydrogen atoms from the fragment frag.
| frag | The fragment for which to remove all explicit hydrogen atoms. |
False if frag was not altered, True otherwise. | bool CDPL.Chem.makeHydrogenDeplete | ( | Molecule | mol, |
| bool | corr_impl_h_count = True |
||
| ) |
Removes all explicit hydrogen atoms from the molecule mol.
| mol | The molecule for which to remove all explicit hydrogen atoms. |
| corr_impl_h_count | True if the implicit hydrogen count property of the affected remaining atoms shall be corrected, False if the property shall be left unchanged. |
False if mol was not altered, True otherwise. | bool CDPL.Chem.makeOrdinaryHydrogenDeplete | ( | Fragment | frag, |
| int | flags | ||
| ) |
Removes all explicit ordinary hydrogen atoms from the fragment frag.
| frag | The fragment for which to remove all explicit ordinary hydrogen atoms. |
| flags | Specifies the set of atom properties to check (see namespace Chem.AtomPropertyFlag). |
False if frag was not altered, True otherwise.| bool CDPL.Chem.makeOrdinaryHydrogenDeplete | ( | Molecule | mol, |
| int | flags, | ||
| bool | corr_impl_h_count = True |
||
| ) |
Removes all explicit ordinary hydrogen atoms from the molecule mol.
| mol | The molecule for which to remove all explicit ordinary hydrogen atoms. |
| flags | Specifies the set of atom properties to check (see namespace Chem.AtomPropertyFlag). |
| corr_impl_h_count | True if the implicit hydrogen count property of the affected remaining atoms shall be corrected, False if the property shall be left unchanged. |
False if mol was not altered, True otherwise.| None CDPL.Chem.markReachableAtoms | ( | Atom | atom, |
| MolecularGraph | molgraph, | ||
| Util.BitSet | atom_mask, | ||
| bool | reset = True |
||
| ) |
Sets bits in atom_mask for every atom of the molecular graph molgraph that is reachable from the atom atom through the bonds of molgraph.
| atom | The seed atom. |
| molgraph | The molecular graph providing the structural context. |
| atom_mask | The output bit mask. |
| reset | If True, atom_mask is cleared first. Otherwise, existing bits are preserved. |
| Molecule CDPL.Chem.parseSMARTS | ( | str | smarts, |
| bool | init_qry = True |
||
| ) |
Parses the SMARTS string smarts into a freshly allocated query Chem.Molecule.
| smarts | The SMARTS string to parse. |
| init_qry | If True, query-specific perception (e.g. ring-membership, aromaticity) is run on the parsed molecule. |
| bool CDPL.Chem.parseSMARTS | ( | str | smarts, |
| Molecule | mol, | ||
| bool | init_qry = True |
||
| ) |
Parses the SMARTS string smarts into the supplied molecule mol.
| smarts | The SMARTS string to parse. |
| mol | The molecule to populate (cleared before parsing). |
| init_qry | If True, query-specific perception is run on the parsed molecule. |
True if parsing succeeded, and False otherwise. | Molecule CDPL.Chem.parseSMILES | ( | str | smiles | ) |
Parses the SMILES string smiles into a freshly allocated Chem.Molecule.
| smiles | The SMILES string to parse. |
| bool CDPL.Chem.parseSMILES | ( | str | smiles, |
| Molecule | mol | ||
| ) |
Parses the SMILES string smiles into the supplied molecule mol.
| smiles | The SMILES string to parse. |
| mol | The molecule to populate (cleared before parsing). |
True if parsing succeeded, and False otherwise. | Fragment CDPL.Chem.perceiveAromaticSubstructure | ( | MolecularGraph | molgraph | ) |
Perceives the aromatic substructure (union of all aromatic atoms/bonds) of the molecular graph molgraph.
| molgraph | The molecular graph. |
| Fragment CDPL.Chem.perceiveAromaticSubstructure | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the aromatic substructure of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing aromatic substructure property should be replaced. |
| AtomMapping CDPL.Chem.perceiveAtomMapping | ( | Reaction | rxn | ) |
Derives the reactant-to-product atom mapping from the atom mapping IDs of the reaction rxn.
| rxn | The reaction. |
| AtomMapping CDPL.Chem.perceiveAtomMapping | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Derives and stores the reactant-to-product atom mapping of the reaction rxn.
| rxn | The reaction. |
| overwrite | Specifies whether an already existing atom mapping property should be replaced. |
| None CDPL.Chem.perceiveAtomStereoCenters | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| bool | check_asym = True, |
||
| bool | check_inv_n = True, |
||
| bool | check_quart_n = True, |
||
| bool | check_plan_n = True, |
||
| bool | check_amide_n = True, |
||
| bool | check_res_ctrs = True |
||
| ) |
Flags the atoms of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing stereo center flag properties should be replaced. |
| check_asym | True to enforce non-equivalent ligand environments. |
| check_inv_n | True to reject inversion-prone nitrogen centers. |
| check_quart_n | True to accept positively charged quaternary nitrogen centers. |
| check_plan_n | True to reject planar nitrogen centers. |
| check_amide_n | True to reject amide nitrogen centers. |
| check_res_ctrs | True to reject centers participating in resonance. |
| None CDPL.Chem.perceiveBondOrders | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives bond orders for the bonds of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing bond order properties should be replaced. |
| None CDPL.Chem.perceiveBondStereoCenters | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| bool | check_asym = True, |
||
| bool | check_term_n = True, |
||
| bool | check_order = True, |
||
| int | min_ring_size = 8 |
||
| ) |
Flags the bonds of the molecular graph molgraph that qualify as stereo centers under the supplied criteria.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing bond order properties should be replaced. |
| check_asym | True to enforce non-equivalent ligand environments. |
| check_term_n | True to reject bonds to terminal nitrogen atoms. |
| check_order | True to require that the bond order matches a stereogenic pattern. |
| min_ring_size | The minimum ring size required for ring bonds to qualify. |
| FragmentList CDPL.Chem.perceiveComponentGroups | ( | MolecularGraph | molgraph | ) |
Perceives the component groups of the molecular graph molgraph.
Component groups are generated by merging components whose atoms have the same Chem.AtomProperty.COMPONENT_GROUP_ID property value.
| molgraph | The molecular graph. |
| FragmentList CDPL.Chem.perceiveComponentGroups | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and optionally stores the component groups of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing component groups property should be replaced. |
| FragmentList CDPL.Chem.perceiveComponentGroups | ( | Reaction | rxn | ) |
Perceives the component groups of the reaction rxn.
| rxn | The reaction. |
| FragmentList CDPL.Chem.perceiveComponentGroups | ( | Reaction | rxn, |
| bool | overwrite | ||
| ) |
Perceives and stores the component groups of the reaction rxn.
| rxn | The reaction. |
| overwrite | Specifies whether an already existing component groups property should be replaced. |
| FragmentList CDPL.Chem.perceiveComponents | ( | MolecularGraph | molgraph | ) |
Perceives the connected components of the molecular graph molgraph.
| molgraph | The molecular graph. |
| FragmentList CDPL.Chem.perceiveComponents | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the connected components of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing component list property should be replaced. |
| Fragment CDPL.Chem.perceiveCyclicSubstructure | ( | MolecularGraph | molgraph | ) |
Perceives the cyclic substructure (union of all rings) of the molecular graph molgraph.
| molgraph | The molecular graph. |
| Fragment CDPL.Chem.perceiveCyclicSubstructure | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the cyclic substructure (union of all rings) of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing cyclic substructure property should be replaced. |
| int CDPL.Chem.perceiveHybridizationState | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Derives the hybridization state of the atom atom from its connectivity in the molecular graph molgraph.
| atom | The atom for which to perceive the hybridzation state. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.perceiveHybridizationStates | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Computes and stores hybridization states for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing hybridization state properties should be replaced. |
| ElectronSystemList CDPL.Chem.perceivePiElectronSystems | ( | MolecularGraph | molgraph | ) |
Perceives the π-electron systems of the molecular graph molgraph.
| molgraph | The molecular graph. |
| ElectronSystemList CDPL.Chem.perceivePiElectronSystems | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the π-electron systems of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing electron system property should be replaced. |
| FragmentList CDPL.Chem.perceiveRings | ( | MolecularGraph | molgraph | ) |
Perceives the full set of rings of the molecular graph molgraph.
| molgraph | The molecular graph. |
| FragmentList CDPL.Chem.perceiveRings | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the full set of rings of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing ring set property should be replaced. |
| FragmentList CDPL.Chem.perceiveSSSR | ( | MolecularGraph | molgraph | ) |
Perceives the SSSR of the molecular graph molgraph.
| molgraph | The molecular graph. |
| FragmentList CDPL.Chem.perceiveSSSR | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and stores the SSSR of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether an already existing SSSR property should be replaced. |
| None CDPL.Chem.perceiveSybylAtomTypes | ( | MolecularGraph | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and assigns Sybyl MOL2 atom types for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing atom type properties should be replaced. |
| int CDPL.Chem.perceiveSybylType | ( | Atom | atom, |
| MolecularGraph | molgraph | ||
| ) |
Derives the Sybyl MOL2 atom type of the atom atom in the molecular graph molgraph.
| atom | The atom for which to perceive the type. |
| molgraph | The molecular graph providing the structural context. |
| int CDPL.Chem.perceiveSybylType | ( | Bond | bond, |
| MolecularGraph | molgraph | ||
| ) |
Derives the Sybyl MOL2 bond type of the bond bond in the molecular graph molgraph.
| bond | The bond for which to perceive the type.. |
| molgraph | The molecular graph providing the structural context. |
| None CDPL.Chem.perceiveSymmetryClasses | ( | MolecularGraph | molgraph, |
| bool | overwrite, | ||
| int | atom_flags = 2147483648, |
||
| int | bond_flags = 2147483648, |
||
| bool | inc_impl_h = True |
||
| ) |
Computes and stores topological symmetry classes for the atoms of the molecular graph molgraph.
| molgraph | The molecular graph. |
| overwrite | Specifies whether already existing symmetry class ID properties should be replaced. |
| atom_flags | A bitmask of Chem.AtomPropertyFlag flags controlling which atomic properties affect the perception. |
| bond_flags | A bitmask of Chem.BondPropertyFlag flags controlling which bond properties affect the perception. |
| inc_impl_h | If True, implicit hydrogens are treated as if they were explicit. Otherwise, they are ignored. |
| None CDPL.Chem.removeAtomsIf | ( | Fragment | frag, |
| AtomPredicate | pred | ||
| ) |
Removes all atoms of the fragment frag for which the predicate pred returns True.
| frag | The fragment to filter in place. |
| pred | The atom predicate to evaluate. |
| None CDPL.Chem.removeAtomsIf | ( | Molecule | mol, |
| AtomPredicate | pred | ||
| ) |
Removes all atoms of the molecule mol for which the predicate pred returns True.
| mol | The molecule to filter in place. |
| pred | The atom predicate to evaluate. |
| None CDPL.Chem.removeAtomsIfNot | ( | Fragment | frag, |
| AtomPredicate | pred | ||
| ) |
Removes all atoms of the fragment frag for which the predicate pred returns False.
| frag | The fragment to filter in place. |
| pred | The atom predicate to evaluate. |
| None CDPL.Chem.removeAtomsIfNot | ( | Molecule | mol, |
| AtomPredicate | pred | ||
| ) |
Removes all atoms of the molecule mol for which the predicate pred returns False.
| mol | The molecule to filter in place. |
| pred | The atom predicate to evaluate. |
| None CDPL.Chem.splitIntoFragments | ( | MolecularGraph | molgraph, |
| FragmentList | frag_list, | ||
| Util.BitSet | split_bond_mask, | ||
| bool | append = False |
||
| ) |
Splits the molecular graph molgraph into connected fragments by removing the bonds flagged in split_bond_mask.
| molgraph | The molecular graph to split. |
| frag_list | The output fragment list receiving the resulting fragments. |
| split_bond_mask | Bit mask selecting the bonds to be virtually removed before fragmentation (bit i corresponds to the bond at index i in molgraph). |
| append | If True, fragments are appended to frag_list. Otherwise, it is cleared first. |
| int CDPL.Chem.sybylToAtomType | ( | int | sybyl_type | ) |
Translates a Sybyl atom type identifier to the corresponding generic Chem.AtomType value.
| sybyl_type | The Sybyl atom type identifier (Chem.SybylAtomType value). |
| None CDPL.Chem.transform2DCoordinates | ( | AtomContainer | cntnr, |
| Math.Matrix3D | mtx | ||
| ) |
Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx.
| cntnr | The atom container. |
| mtx | The 2D affine transformation matrix. |
| None CDPL.Chem.transform3DCoordinates | ( | Entity3DContainer | cntnr, |
| Math.Matrix4D | mtx | ||
| ) |
Transforms the 3D coordinates of the entities of cntnr by the affine matrix mtx.
| cntnr | The entity 3D container whose coordinates are to be transformed. |
| mtx | The 4×4 affine transformation matrix. |
| None CDPL.Chem.transformConformation | ( | AtomContainer | cntnr, |
| int | conf_idx, | ||
| Math.Matrix4D | mtx | ||
| ) |
Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx.
| cntnr | The atom container. |
| conf_idx | The zero-based conformation index. |
| mtx | The homogeneous 4×4 transformation matrix. |
| None CDPL.Chem.transformConformations | ( | AtomContainer | cntnr, |
| Math.Matrix4D | mtx | ||
| ) |
Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx.
| cntnr | The atom container. |
| mtx | The homogeneous 4×4 transformation matrix. |
| None CDPL.Chem.translateFragment | ( | MolecularGraph | src_molgraph, |
| Fragment | src_frag, | ||
| MolecularGraph | tgt_molgraph, | ||
| Fragment | tgt_frag, | ||
| bool | append = False |
||
| ) |
Translates the atoms/bonds of src_frag to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag.
| src_molgraph | The source molecular graph providing the original atoms/bonds. |
| src_frag | The fragment defining the atom/bond subset to translate (a fragment of the molecular graph src_molgraph). |
| tgt_molgraph | The target molecular graph providing the translated atoms/bonds. |
| tgt_frag | The output fragment receiving the translated atoms/bonds. |
| append | If True, atoms/bonds are appended to tgt_frag. Otherwise, it is cleared first. |
| None CDPL.Chem.translateFragments | ( | MolecularGraph | src_molgraph, |
| FragmentList | src_frag_list, | ||
| MolecularGraph | tgt_molgraph, | ||
| FragmentList | tgt_frag_list, | ||
| bool | append = False |
||
| ) |
Translates every fragment in src_frag_list to the corresponding fragments on tgt_molgraph.
| src_molgraph | The source molecular graph providing the original atoms/bonds. |
| src_frag_list | The fragments to translate (fragments of the molecular graph src_molgraph). |
| tgt_molgraph | The target molecular graph providing the translated atoms/bonds. |
| tgt_frag_list | The output fragment list receiving the translated fragments. |
| append | If True, fragments are appended to tgt_frag_list. Otherwise, it is cleared first. |
| None CDPL.Chem.setBondMemberSwapStereoFixParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | fix | ||
| ) |
Sets the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr to fix.
| cntnr | The control-parameter container. |
| fix | The new parameter value. |
| bool CDPL.Chem.hasBondMemberSwapStereoFixParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getBondMemberSwapStereoFixParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearBondMemberSwapStereoFixParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCDFOutputSinglePrecisionFloatsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | single_prec | ||
| ) |
Sets the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec.
| cntnr | The control-parameter container. |
| single_prec | The new parameter value. |
| bool CDPL.Chem.hasCDFOutputSinglePrecisionFloatsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCDFOutputSinglePrecisionFloatsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCDFOutputSinglePrecisionFloatsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | enable | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.
| cntnr | The control-parameter container. |
| enable | The new parameter value. |
| bool CDPL.Chem.hasCMLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputAtomParityParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputAtomParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputAtomParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputAtomParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_ATOM_PARITY parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputCompactAtomDataParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputCompactAtomDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputCompactAtomDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputCompactAtomDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_ATOM_DATA parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputCompactBondDataParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputCompactBondDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputCompactBondDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputCompactBondDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_COMPACT_BOND_DATA parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputDoubleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputDoubleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputDoubleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputDoubleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_DOUBLE_BOND_STEREO parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputElementPackageParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | ns | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr to ns.
| cntnr | The control-parameter container. |
| ns | The new XML-namespace string. |
| bool CDPL.Chem.hasCMLOutputElementPackageParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| str CDPL.Chem.getCMLOutputElementPackageParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputElementPackageParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_ELEMENT_NAMESPACE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_ISOTOPE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputMoleculeNameParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputMoleculeNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputMoleculeNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputMoleculeNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_MOLECULE_NAME parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputSingleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputSingleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputSingleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputSingleBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_SINGLE_BOND_STEREO parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputSpinMultiplicityParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputSpinMultiplicityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputSpinMultiplicityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputSpinMultiplicityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_SPIN_MULTIPLICITY parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputStructureDataParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputStructureDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputStructureDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputStructureDataParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_STRUCTURE_DATA parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCMLOutputXMLDeclarationParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasCMLOutputXMLDeclarationParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getCMLOutputXMLDeclarationParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCMLOutputXMLDeclarationParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CML_OUTPUT_XML_DECLARATION parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCheckLineLengthParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | check | ||
| ) |
Sets the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr to check.
| cntnr | The control-parameter container. |
| check | The new parameter value. |
| bool CDPL.Chem.hasCheckLineLengthParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getCheckLineLengthParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCheckLineLengthParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setConfIndexNameSuffixPatternParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | pattern | ||
| ) |
Sets the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr to pattern.
| cntnr | The control-parameter container. |
| pattern | The new suffix pattern string. |
| bool CDPL.Chem.hasConfIndexNameSuffixPatternParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getConfIndexNameSuffixPatternParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearConfIndexNameSuffixPatternParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.CONF_INDEX_NAME_SUFFIX_PATTERN parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setCoordinatesDimensionParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | dim | ||
| ) |
Sets the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr to dim.
| cntnr | The control-parameter container. |
| dim | The new coordinates dimensionality. |
| bool CDPL.Chem.hasCoordinatesDimensionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.COORDINATES_DIMENSION parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getCoordinatesDimensionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.COORDINATES_DIMENSION parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearCoordinatesDimensionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.COORDINATES_DIMENSION parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setINCHIInputOptionsParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | opts | ||
| ) |
Sets the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr to opts.
| cntnr | The control-parameter container. |
| opts | The new InChI input-options string. |
| bool CDPL.Chem.hasINCHIInputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getINCHIInputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearINCHIInputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.INCHI_INPUT_OPTIONS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setINCHIOutputOptionsParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | opts | ||
| ) |
Sets the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr to opts.
| cntnr | The control-parameter container. |
| opts | The new InChI output-options string. |
| bool CDPL.Chem.hasINCHIOutputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getINCHIOutputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearINCHIOutputOptionsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.INCHI_OUTPUT_OPTIONS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setJMESeparateComponentsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | separate | ||
| ) |
Sets the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr to separate.
| cntnr | The control-parameter container. |
| separate | The new parameter value. |
| bool CDPL.Chem.hasJMESeparateComponentsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getJMESeparateComponentsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearJMESeparateComponentsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.JME_SEPARATE_COMPONENTS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLCTABVersionParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | version | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr to version.
| cntnr | The control-parameter container. |
| version | The new CTAB version (see namespace Chem.MDLDataFormatVersion). |
| bool CDPL.Chem.hasMDLCTABVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_CTAB_VERSION parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getMDLCTABVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_CTAB_VERSION parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLCTABVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_CTAB_VERSION parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLConfEnergySDTagParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | tag | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr to tag.
| cntnr | The control-parameter container. |
| tag | The new MDL SD-File structure data record header string. |
| bool CDPL.Chem.hasMDLConfEnergySDTagParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getMDLConfEnergySDTagParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLConfEnergySDTagParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_CONF_ENERGY_SD_TAG parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | enable | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.
| cntnr | The control-parameter container. |
| enable | The new parameter value. |
| bool CDPL.Chem.hasMDLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getMDLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLEnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLIgnoreParityParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | ignore | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr to ignore.
| cntnr | The control-parameter container. |
| ignore | The new parameter value. |
| bool CDPL.Chem.hasMDLIgnoreParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_IGNORE_PARITY parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLIgnoreParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_IGNORE_PARITY parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLIgnoreParityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_IGNORE_PARITY parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLOutputConfEnergyAsSDEntryParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasMDLOutputConfEnergyAsSDEntryParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLOutputConfEnergyAsSDEntryParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLOutputConfEnergyAsSDEntryParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLOutputConfEnergyToEnergyFieldParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasMDLOutputConfEnergyToEnergyFieldParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLOutputConfEnergyToEnergyFieldParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLOutputConfEnergyToEnergyFieldParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLRXNFileVersionParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | version | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr to version.
| cntnr | The control-parameter container. |
| version | The new MDL Rxn-File version (see namespace Chem.MDLDataFormatVersion). |
| bool CDPL.Chem.hasMDLRXNFileVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getMDLRXNFileVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLRXNFileVersionParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_RXN_FILE_VERSION parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLTrimLinesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | trim | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr to trim.
| cntnr | The control-parameter container. |
| trim | The new parameter value. |
| bool CDPL.Chem.hasMDLTrimLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_TRIM_LINES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLTrimLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_TRIM_LINES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLTrimLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_TRIM_LINES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLTrimStringsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | trim | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr to trim.
| cntnr | The control-parameter container. |
| trim | The new parameter value. |
| bool CDPL.Chem.hasMDLTrimStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_TRIM_STRINGS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLTrimStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_TRIM_STRINGS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLTrimStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_TRIM_STRINGS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLTruncateLinesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | trunc | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr to trunc.
| cntnr | The control-parameter container. |
| trunc | The new parameter value. |
| bool CDPL.Chem.hasMDLTruncateLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLTruncateLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLTruncateLinesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_TRUNCATE_LINES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLTruncateStringsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | trunc | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr to trunc.
| cntnr | The control-parameter container. |
| trunc | The new parameter value. |
| bool CDPL.Chem.hasMDLTruncateStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLTruncateStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLTruncateStringsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_TRUNCATE_STRINGS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMDLUpdateTimestampParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | update | ||
| ) |
Sets the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr to update.
| cntnr | The control-parameter container. |
| update | The new parameter value. |
| bool CDPL.Chem.hasMDLUpdateTimestampParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMDLUpdateTimestampParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMDLUpdateTimestampParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MDL_UPDATE_TIMESTAMP parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2CalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | calc | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr to calc.
| cntnr | The control-parameter container. |
| calc | The new parameter value. |
| bool CDPL.Chem.hasMOL2CalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMOL2CalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2CalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_CALC_FORMAL_CHARGES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2ChargeTypeParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | type | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr to type.
| cntnr | The control-parameter container. |
| type | The new Sybyl MOL2 charge type (see namespace Chem.MOL2ChargeType). |
| bool CDPL.Chem.hasMOL2ChargeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getMOL2ChargeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2ChargeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_CHARGE_TYPE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2EnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | enable | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr to enable.
| cntnr | The control-parameter container. |
| enable | The new parameter value. |
| bool CDPL.Chem.hasMOL2EnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMOL2EnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2EnableAromaticBondTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_ENABLE_AROMATIC_BOND_TYPES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2EnableExtendedAtomTypesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | enable | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr to enable.
| cntnr | The control-parameter container. |
| enable | The new parameter value. |
| bool CDPL.Chem.hasMOL2EnableExtendedAtomTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMOL2EnableExtendedAtomTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2EnableExtendedAtomTypesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_ENABLE_EXTENDED_ATOM_TYPES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2MoleculeTypeParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | type | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr to type.
| cntnr | The control-parameter container. |
| type | The new Sybyl MOL2 molecule type (see namespace Chem.MOL2MoleculeType). |
| bool CDPL.Chem.hasMOL2MoleculeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getMOL2MoleculeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2MoleculeTypeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_MOLECULE_TYPE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2OutputFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasMOL2OutputFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getMOL2OutputFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2OutputFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_OUTPUT_FORMAL_CHARGES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2OutputSubstructuresParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasMOL2OutputSubstructuresParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMOL2OutputSubstructuresParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2OutputSubstructuresParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_OUTPUT_SUBSTRUCTURES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMOL2ReadPartialAsFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | read | ||
| ) |
Sets the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr to read.
| cntnr | The control-parameter container. |
| read | The new parameter value. |
| bool CDPL.Chem.hasMOL2ReadPartialAsFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getMOL2ReadPartialAsFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMOL2ReadPartialAsFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MOL2_READ_PARTIAL_AS_FORMAL_CHARGES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMultiConfExportParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | multi_conf | ||
| ) |
Sets the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr to multi_conf.
| cntnr | The control-parameter container. |
| multi_conf | The new parameter value. |
| bool CDPL.Chem.hasMultiConfExportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MULTI_CONF_EXPORT parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMultiConfExportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MULTI_CONF_EXPORT parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMultiConfExportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MULTI_CONF_EXPORT parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMultiConfImportParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | multi_conf | ||
| ) |
Sets the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr to multi_conf.
| cntnr | The control-parameter container. |
| multi_conf | The new parameter value. |
| bool CDPL.Chem.hasMultiConfImportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MULTI_CONF_IMPORT parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getMultiConfImportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MULTI_CONF_IMPORT parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMultiConfImportParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MULTI_CONF_IMPORT parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setMultiConfInputProcessorParameter | ( | Base.ControlParameterContainer | cntnr, |
| MultiConfMoleculeInputProcessor | proc | ||
| ) |
Sets the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr to proc.
| cntnr | The control-parameter container. |
| proc | The new Chem.MultiConfMoleculeInputProcessor implementation reference. |
| bool CDPL.Chem.hasMultiConfInputProcessorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | MultiConfMoleculeInputProcessor CDPL.Chem.getMultiConfInputProcessorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearMultiConfInputProcessorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setOrdinaryHydrogenDepleteParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | deplete | ||
| ) |
Sets the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr to deplete.
| cntnr | The control-parameter container. |
| deplete | The new parameter value. |
| bool CDPL.Chem.hasOrdinaryHydrogenDepleteParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getOrdinaryHydrogenDepleteParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearOrdinaryHydrogenDepleteParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setOutputConfEnergyAsCommentParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasOutputConfEnergyAsCommentParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getOutputConfEnergyAsCommentParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearOutputConfEnergyAsCommentParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.OUTPUT_CONF_ENERGY_AS_COMMENT parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setRecordSeparatorParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | sep | ||
| ) |
Sets the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr to sep.
| cntnr | The control-parameter container. |
| sep | The new record separator string. |
| bool CDPL.Chem.hasRecordSeparatorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.RECORD_SEPARATOR parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getRecordSeparatorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.RECORD_SEPARATOR parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearRecordSeparatorParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.RECORD_SEPARATOR parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESMinStereoBondRingSizeParameter | ( | Base.ControlParameterContainer | cntnr, |
| int | min_size | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr to min_size.
| cntnr | The control-parameter container. |
| min_size | The new minimum ring size. |
| bool CDPL.Chem.hasSMILESMinStereoBondRingSizeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | int CDPL.Chem.getSMILESMinStereoBondRingSizeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESMinStereoBondRingSizeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESMolOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESMolOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESMolOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESMolOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_MOL_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESNoOrganicSubsetParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | no_subset | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr to no_subset.
| cntnr | The control-parameter container. |
| no_subset | The new parameter value. |
| bool CDPL.Chem.hasSMILESNoOrganicSubsetParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getSMILESNoOrganicSubsetParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESNoOrganicSubsetParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputAromaticBondsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputAromaticBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputAromaticBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputAromaticBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_AROMATIC_BONDS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputAtomStereoParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputAtomStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputAtomStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputAtomStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_ATOM_STEREO parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputBondStereoParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_BOND_STEREO parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputCanonicalFormParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputCanonicalFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputCanonicalFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputCanonicalFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_CANONICAL_FORM parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputHydrogenCountParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputHydrogenCountParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputHydrogenCountParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputHydrogenCountParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_HYDROGEN_COUNT parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputIsotopeParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_ISOTOPE parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputKekuleFormParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputKekuleFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputKekuleFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputKekuleFormParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_KEKULE_FORM parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputRingBondStereoParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputRingBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputRingBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputRingBondStereoParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_RING_BOND_STEREO parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESOutputSingleBondsParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESOutputSingleBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESOutputSingleBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESOutputSingleBondsParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_OUTPUT_SINGLE_BONDS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESRecordFormatParameter | ( | Base.ControlParameterContainer | cntnr, |
| str | format | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr to format.
| cntnr | The control-parameter container. |
| format | The new record-format string. |
| bool CDPL.Chem.hasSMILESRecordFormatParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | str CDPL.Chem.getSMILESRecordFormatParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESRecordFormatParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_RECORD_FORMAT parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setSMILESRxnOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | output | ||
| ) |
Sets the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr to output.
| cntnr | The control-parameter container. |
| output | The new parameter value. |
| bool CDPL.Chem.hasSMILESRxnOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getSMILESRxnOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearSMILESRxnOutputAtomMappingIDParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.SMILES_RXN_OUTPUT_ATOM_MAPPING_ID parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setStrictErrorCheckingParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | strict | ||
| ) |
Sets the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict.
| cntnr | The control-parameter container. |
| strict | The new parameter value. |
| bool CDPL.Chem.hasStrictErrorCheckingParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise. | bool CDPL.Chem.getStrictErrorCheckingParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearStrictErrorCheckingParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setXYZCalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | calc | ||
| ) |
Sets the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr to calc.
| cntnr | The control-parameter container. |
| calc | The new parameter value. |
| bool CDPL.Chem.hasXYZCalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getXYZCalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearXYZCalcFormalChargesParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.XYZ_CALC_FORMAL_CHARGES parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setXYZCommentIsNameParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | is_name | ||
| ) |
Sets the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr to is_name.
| cntnr | The control-parameter container. |
| is_name | The new parameter value. |
| bool CDPL.Chem.hasXYZCommentIsNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getXYZCommentIsNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearXYZCommentIsNameParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.XYZ_COMMENT_IS_NAME parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setXYZPerceiveBondOrdersParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | perceive | ||
| ) |
Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr to perceive.
| cntnr | The control-parameter container. |
| perceive | The new parameter value. |
| bool CDPL.Chem.hasXYZPerceiveBondOrdersParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getXYZPerceiveBondOrdersParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearXYZPerceiveBondOrdersParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.XYZ_PERCEIVE_BOND_ORDERS parameter from cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.setXYZPerceiveConnectivityParameter | ( | Base.ControlParameterContainer | cntnr, |
| bool | perceive | ||
| ) |
Sets the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr to perceive.
| cntnr | The control-parameter container. |
| perceive | The new parameter value. |
| bool CDPL.Chem.hasXYZPerceiveConnectivityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Tells whether the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter of cntnr is set.
| cntnr | The control-parameter container. |
True if the parameter is set, and False otherwise.| bool CDPL.Chem.getXYZPerceiveConnectivityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Returns the value of the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter stored in cntnr.
| cntnr | The control-parameter container. |
| None CDPL.Chem.clearXYZPerceiveConnectivityParameter | ( | Base.ControlParameterContainer | cntnr | ) |
Removes the Chem.ControlParameter.XYZ_PERCEIVE_CONNECTIVITY parameter from cntnr.
| cntnr | The control-parameter container. |
1.9.1