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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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Searches for the maximum common atom substructures between a query and a target molecular graph. More...
Inheritance diagram for CDPL.Chem.MaxCommonAtomSubstructureSearch:Public Member Functions | |
| None | __init__ () |
Constructs and initializes the MaxCommonAtomSubstructureSearch instance. | |
| None | __init__ (MolecularGraph query) |
Constructs and initializes the MaxCommonAtomSubstructureSearch instance for the query molecular graph query. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| bool | mappingExists (MolecularGraph target) |
| Searches for a common substructure between the query and the target molecular graph target. More... | |
| bool | findAllMappings (MolecularGraph target) |
| Searches for all atom/bond mappings of query subgraphs to substructures of the target molecular graph target with a maximum atom count. More... | |
| bool | findMaxBondMappings (MolecularGraph target) |
| Searches for all atom/bond mappings of query subgraphs to substructures of the target molecular graph target with a maximum atom and bond count. More... | |
| int | getNumMappings () |
| Returns the number of atom/bond mappings that were recorded in the last search for common substructures. More... | |
| AtomBondMapping | getMapping (int idx) |
| Returns a reference to the stored atom/bond mapping object at index idx. More... | |
| None | uniqueMappingsOnly (bool unique) |
| Allows to specify whether or not to store only unique atom/bond mappings. More... | |
| bool | uniqueMappingsOnly () |
| Tells whether duplicate atom/bond mappings are discarded. More... | |
| int | getMaxNumMappings () |
| Returns the specified limit on the number of stored atom/bond mappings. More... | |
| None | setMaxNumMappings (int max_num_mappings) |
| Allows to specify a limit on the number of stored atom/bond mappings. More... | |
| int | getMinSubstructureSize () |
| Returns the minimum accepted common substructure size. More... | |
| None | setMinSubstructureSize (int min_size) |
| Allows to specify the minimum accepted common substructure size. More... | |
| None | setQuery (MolecularGraph query) |
| Sets query as the new query molecular graph. More... | |
| AtomBondMapping | __getitem__ (int idx) |
| int | __len__ () |
| bool | __nonzero__ (MolecularGraph self) |
| bool | __bool__ (MolecularGraph self) |
Properties | |
| objectID = property(getObjectID) | |
| numMappings = property(getNumMappings) | |
| uniqueMappings = property(uniqueMappingsOnly, uniqueMappingsOnly) | |
| maxNumMappings = property(getMaxNumMappings, setMaxNumMappings) | |
| minSubstructureSize = property(getMinSubstructureSize, setMinSubstructureSize) | |
Searches for the maximum common atom substructures between a query and a target molecular graph.
Successive calls to setQuery() and findAllMappings() or findMaxBondMappings() produce all possible common substructure atom/bond mapping solutions (subject to an atom count lower bound set by setMinSubstructureSize()). The method findAllMappings() enumerates all atom count-maximal common substructures, and findMaxBondMappings() restricts the output to atom and bond count-maximal substructures. If just the information whether or not a common substructure (fulfilling the size lower bound) exists is of interest then the more efficient method mappingExists() can be used. Found common substructures are recorded as Chem.AtomBondMapping objects that can be accessed via index through the method getMapping() or iteration using the iterator pair returned by the methods begin() and end(), respectively. Per-atom, per-bond and per-molecular graph Chem.MatchExpression implementation instances are retrieved as values of the corresponding atom, bond and molecular graph properties (see Chem.AtomProperty.MATCH_EXPRESSION, Chem.BondProperty.MATCH_EXPRESSION and Chem.MolecularGraphProperty.MATCH_EXPRESSION). Result accumulation can be bounded by setMaxNumMappings() and uniqueMappingsOnly().
| None CDPL.Chem.MaxCommonAtomSubstructureSearch.__init__ | ( | MolecularGraph | query | ) |
Constructs and initializes the MaxCommonAtomSubstructureSearch instance for the query molecular graph query.
| query | A molecular graph that represents the query structure. |
| int CDPL.Chem.MaxCommonAtomSubstructureSearch.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MaxCommonAtomSubstructureSearch instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two MaxCommonAtomSubstructureSearch instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().
| bool CDPL.Chem.MaxCommonAtomSubstructureSearch.mappingExists | ( | MolecularGraph | target | ) |
Searches for a common substructure between the query and the target molecular graph target.
The method does not store any atom/bond mappings between query and target molecular graphs — it just tells if a valid common substructure mapping solution involving at least getMinSubstructureSize() atoms could be found. If you need access to the atom/bond mappings, use findAllMappings() or findMaxBondMappings() instead.
| target | The target molecular graph that has to be searched for a substructure in common with the query. |
True if a common substructure of at least the minimum accepted size could be found, and False otherwise.| bool CDPL.Chem.MaxCommonAtomSubstructureSearch.findAllMappings | ( | MolecularGraph | target | ) |
Searches for all atom/bond mappings of query subgraphs to substructures of the target molecular graph target with a maximum atom count.
The method will store all maximum-sized (in number of atoms) common substructure mapping solutions involving at least getMinSubstructureSize() atoms up to the maximum number of recorded mappings specified by setMaxNumMappings(). If only unique mappings have to be stored (see uniqueMappingsOnly(bool unique)), any duplicates of previously found mappings will be discarded.
| target | The target molecular graph that has to be searched for all maximum-sized substructures in common with the query. |
True if common substructures of at least the minimum accepted size were found, and False otherwise.| bool CDPL.Chem.MaxCommonAtomSubstructureSearch.findMaxBondMappings | ( | MolecularGraph | target | ) |
Searches for all atom/bond mappings of query subgraphs to substructures of the target molecular graph target with a maximum atom and bond count.
The method will store all maximum-sized (both in number of atoms and bonds) common substructure mapping solutions involving at least getMinSubstructureSize() atoms up to the maximum number of recorded mappings specified by setMaxNumMappings(). If only unique mappings have to be stored (see uniqueMappingsOnly(bool unique)), any duplicates of previously found mappings will be discarded.
| target | The target molecular graph that has to be searched for all maximum-sized substructures in common with the query. |
True if common substructures of at least the minimum accepted size were found, and False otherwise.| int CDPL.Chem.MaxCommonAtomSubstructureSearch.getNumMappings | ( | ) |
Returns the number of atom/bond mappings that were recorded in the last search for common substructures.
| AtomBondMapping CDPL.Chem.MaxCommonAtomSubstructureSearch.getMapping | ( | int | idx | ) |
Returns a reference to the stored atom/bond mapping object at index idx.
| idx | The zero-based index of the atom/bond mapping object to return. |
| Base.IndexError | if idx is not in the range [0, getNumMappings()). |
| None CDPL.Chem.MaxCommonAtomSubstructureSearch.uniqueMappingsOnly | ( | bool | unique | ) |
Allows to specify whether or not to store only unique atom/bond mappings.
The mapping of a query pattern subgraph to a substructure of the target molecular graph is considered to be unique if it differs from all previously found mappings by at least one atom or bond. If the unique argument is True, and a newly discovered mapping covers the same atoms and bonds of the target (including all permutations) as a mapping that was found earlier in the search process, it is considered as a duplicate and will be discarded.
| unique | If True, only unique mappings will be stored, and all found mappings otherwise. |
| bool CDPL.Chem.MaxCommonAtomSubstructureSearch.uniqueMappingsOnly | ( | ) |
Tells whether duplicate atom/bond mappings are discarded.
True if duplicate mappings are discarded, and False otherwise.| int CDPL.Chem.MaxCommonAtomSubstructureSearch.getMaxNumMappings | ( | ) |
Returns the specified limit on the number of stored atom/bond mappings.
| None CDPL.Chem.MaxCommonAtomSubstructureSearch.setMaxNumMappings | ( | int | max_num_mappings | ) |
Allows to specify a limit on the number of stored atom/bond mappings.
In a call to findAllMappings() or findMaxBondMappings() the common substructure search will terminate as soon as the specified maximum number of stored atom/bond mappings has been reached. A previously set limit on the number of mappings can be disabled by providing zero for the value of max_num_mappings.
| max_num_mappings | The maximum number of atom/bond mappings to store. |
| int CDPL.Chem.MaxCommonAtomSubstructureSearch.getMinSubstructureSize | ( | ) |
Returns the minimum accepted common substructure size.
| None CDPL.Chem.MaxCommonAtomSubstructureSearch.setMinSubstructureSize | ( | int | min_size | ) |
Allows to specify the minimum accepted common substructure size.
Any found common substructures which cover less than min_size atoms are not accepted as a valid solution and will be discarded.
| min_size | The minimum accepted common substructure size in number of atoms. |
| None CDPL.Chem.MaxCommonAtomSubstructureSearch.setQuery | ( | MolecularGraph | query | ) |
Sets query as the new query molecular graph.
| query | A molecular graph that represents the new query. |
1.9.1