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Chemical Data Processing Library Python API - Version 1.2.0
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Chemical Data Processing Library Python API - Version 1.2.0
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Inheritance diagram for CDPL.Chem.SubstructureSearch:Public Member Functions | |
| None | __init__ () |
Constructs and initializes a SubstructureSearch instance. | |
| None | __init__ (MolecularGraph query) |
Constructs and initializes a SubstructureSearch instance for the specified query structure. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setAtomMatchExpressionFunction (AtomMatchExpressionPtrAtomFunctor func) |
| None | setBondMatchExpressionFunction (BondMatchExpressionPtrBondFunctor func) |
| None | setMolecularGraphMatchExpressionFunction (MolGraphMatchExpressionPtrMolGraphFunctor func) |
| bool | mappingExists (MolecularGraph target) |
| Tells whether the query structure matches a substructure of the specified target molecular graph. More... | |
| bool | findMappings (MolecularGraph target) |
| Searches for all possible atom/bond mappings of the query structure to substructures of the specified target molecular graph. More... | |
| None | stopSearch () |
| int | getNumMappings () |
| Returns the number of atom/bond mappings that were recorded in the last call to findMappings(). 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... | |
| None | clearAtomMappingConstraints () |
| Clears all previously defined query to target atom mapping constraints. More... | |
| None | addAtomMappingConstraint (int query_atom_idx, int target_atom_idx) |
| Adds a constraint on the allowed mappings between query and target structure atoms. More... | |
| None | clearBondMappingConstraints () |
| Clears all previously defined query to target bond mapping constraints. More... | |
| None | addBondMappingConstraint (int query_bond_idx, int target_bond_idx) |
| Adds a constraint on the allowed mappings between query and target structure bonds. More... | |
| None | setQuery (MolecularGraph query) |
| Allows to specify a new query structure. 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) | |
| None CDPL.Chem.SubstructureSearch.__init__ | ( | MolecularGraph | query | ) |
Constructs and initializes a SubstructureSearch instance for the specified query structure.
| query | A molecular graph that represents the query structure. |
| int CDPL.Chem.SubstructureSearch.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python SubstructureSearch 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 SubstructureSearch 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().
| None CDPL.Chem.SubstructureSearch.setAtomMatchExpressionFunction | ( | AtomMatchExpressionPtrAtomFunctor | func | ) |
| func |
| None CDPL.Chem.SubstructureSearch.setBondMatchExpressionFunction | ( | BondMatchExpressionPtrBondFunctor | func | ) |
| func |
| None CDPL.Chem.SubstructureSearch.setMolecularGraphMatchExpressionFunction | ( | MolGraphMatchExpressionPtrMolGraphFunctor | func | ) |
| func |
| bool CDPL.Chem.SubstructureSearch.mappingExists | ( | MolecularGraph | target | ) |
Tells whether the query structure matches a substructure of the specified target molecular graph.
The method does not store any atom/bond mappings between the query and target structure - it just tells if a complete mapping of the query is possible. If you need access to the atom/bond mappings, use findMappings() instead.
| target | The molecular graph that has to be searched for a match of the query structure. |
True if the query matches a substructure of the target molecular graph, and False otherwise.| bool CDPL.Chem.SubstructureSearch.findMappings | ( | MolecularGraph | target | ) |
Searches for all possible atom/bond mappings of the query structure to substructures of the specified target molecular graph.
The method will store all found subgraph mapping solutions 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 molecular graph that has to be searched for matches of the query structure. |
True if the query matches at least one substructure of the specified target molecular graph, and False otherwise.| int CDPL.Chem.SubstructureSearch.getNumMappings | ( | ) |
Returns the number of atom/bond mappings that were recorded in the last call to findMappings().
| AtomBondMapping CDPL.Chem.SubstructureSearch.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 no mappings are available or idx is not in the range [0, getNumMappings() - 1]. |
| None CDPL.Chem.SubstructureSearch.uniqueMappingsOnly | ( | bool | unique | ) |
Allows to specify whether or not to store only unique atom/bond mappings.
A mapping of the query pattern 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.SubstructureSearch.uniqueMappingsOnly | ( | ) |
Tells whether duplicate atom/bond mappings are discarded.
True if duplicate mappings are discarded, and False otherwise.| int CDPL.Chem.SubstructureSearch.getMaxNumMappings | ( | ) |
Returns the specified limit on the number of stored atom/bond mappings.
| None CDPL.Chem.SubstructureSearch.setMaxNumMappings | ( | int | max_num_mappings | ) |
Allows to specify a limit on the number of stored atom/bond mappings.
In a call to findMappings() the 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. |
| None CDPL.Chem.SubstructureSearch.clearAtomMappingConstraints | ( | ) |
Clears all previously defined query to target atom mapping constraints.
| None CDPL.Chem.SubstructureSearch.addAtomMappingConstraint | ( | int | query_atom_idx, |
| int | target_atom_idx | ||
| ) |
Adds a constraint on the allowed mappings between query and target structure atoms.
By default, an atom of the query structure is free to match any suitable target structure atom. When this method gets called for a particular query/target atom pair (specified by query_atom_idx and target_atom_idx), future substructure searches will find only those subgraph mapping solutions (if any) where the given query atom maps to the specified target structure atom. Multiple calls to addAtomMappingConstraint() for the same query atom have an additive effect and allow to restrict the valid query atom mappings not only to a single but also a larger set of target structure atoms.
| query_atom_idx | The index of the query structure atom. |
| target_atom_idx | The index of the target structure atom that has to be matched by the query atom. |
| None CDPL.Chem.SubstructureSearch.clearBondMappingConstraints | ( | ) |
Clears all previously defined query to target bond mapping constraints.
| None CDPL.Chem.SubstructureSearch.addBondMappingConstraint | ( | int | query_bond_idx, |
| int | target_bond_idx | ||
| ) |
Adds a constraint on the allowed mappings between query and target structure bonds.
By default, a bond of the query structure is free to match any suitable target structure bond. When this method gets called for a particular query/target bond pair (specified by query_bond_idx and target_bond_idx), future substructure searches will find only those subgraph mapping solutions (if any) where the given query bond maps to the specified target structure bond. Multiple calls to addBondMappingConstraint() for the same query bond have an additive effect and allow to restrict the valid query bond mappings not only to a single but also a larger set of target structure bonds.
| query_bond_idx | The index of the query structure bond. |
| target_bond_idx | The index of the target structure bond that has to be matched by the query bond. |
| None CDPL.Chem.SubstructureSearch.setQuery | ( | MolecularGraph | query | ) |
Allows to specify a new query structure.
| query | A molecular graph that represents the query structure. |
| AtomBondMapping CDPL.Chem.SubstructureSearch.__getitem__ | ( | int | idx | ) |
| idx |
| int CDPL.Chem.SubstructureSearch.__len__ | ( | ) |
| bool CDPL.Chem.SubstructureSearch.__nonzero__ | ( | MolecularGraph | self | ) |
| arg1 |
| bool CDPL.Chem.SubstructureSearch.__bool__ | ( | MolecularGraph | self | ) |
| arg1 |
1.9.1