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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 substructures of a target molecular graph that match the topology of a given query molecular graph. More...
Inheritance diagram for CDPL.Chem.SubstructureSearch:Public Member Functions | |
| None | __init__ () |
Constructs and initializes the SubstructureSearch instance. | |
| None | __init__ (MolecularGraph query) |
Constructs and initializes the SubstructureSearch instance for the query molecular graph query. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setAtomMatchExpressionFunction (AtomMatchExpressionPtrAtomFunctor func) |
| Installs a function that resolves the Chem.MatchExpression implementation instance for a query atom. More... | |
| None | setBondMatchExpressionFunction (BondMatchExpressionPtrBondFunctor func) |
| Installs a function that resolves the Chem.MatchExpression implementation instance for a query bond. More... | |
| None | setMolecularGraphMatchExpressionFunction (MolGraphMatchExpressionPtrMolGraphFunctor func) |
| Installs a function that resolves the Chem.MatchExpression implementation instance for the query molecular graph. More... | |
| bool | mappingExists (MolecularGraph target) |
| Tells whether the query molecular graph matches a substructure of the target molecular graph target. More... | |
| bool | findMappings (MolecularGraph target) |
| Searches for all possible atom/bond mappings of the query molecular graph to substructures of the target molecular graph target. More... | |
| None | stopSearch () |
| Aborts the currently running substructure search process. More... | |
| 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 molecular graph 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 molecular graph atoms. More... | |
| None | clearBondMappingConstraints () |
| Clears all previously defined query to target molecular graph 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 molecular graph bonds. 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) | |
Searches for substructures of a target molecular graph that match the topology of a given query molecular graph.
Successive calls to setQuery() and findMappings() produce all possible atom/bond mapping solutions. If just the information whether or not a mapping exists is of interest then the more efficient method mappingExists() can be used. Found mappings 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. User-defined per-atom, per-bond and per-molecular graph Chem.MatchExpression implementation instance accessor functions can be installed to extend equivalence tests beyond pure topology. The default functions retrieve the expressions saved as corresponding atom, bond and molecular graph property values (see Chem.AtomProperty.MATCH_EXPRESSION, Chem.BondProperty.MATCH_EXPRESSION and Chem.MolecularGraphProperty.MATCH_EXPRESSION). Result accumulation can be bounded by setMaxNumMappings() and uniqueMappingsOnly(). stopSearch() allows an immediate abort of the search process. Furthermore, query ↔ target atom and bond mappings can be restricted to user-defined subsets by the methods addAtomMappingConstraint() and addBondMappingConstraint(), respectively.
| None CDPL.Chem.SubstructureSearch.__init__ | ( | MolecularGraph | query | ) |
Constructs and initializes the SubstructureSearch instance for the query molecular graph query.
| 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 | ) |
Installs a function that resolves the Chem.MatchExpression implementation instance for a query atom.
| func | The accessor function to use. |
| None CDPL.Chem.SubstructureSearch.setBondMatchExpressionFunction | ( | BondMatchExpressionPtrBondFunctor | func | ) |
Installs a function that resolves the Chem.MatchExpression implementation instance for a query bond.
| func | The accessor function to use. |
| None CDPL.Chem.SubstructureSearch.setMolecularGraphMatchExpressionFunction | ( | MolGraphMatchExpressionPtrMolGraphFunctor | func | ) |
Installs a function that resolves the Chem.MatchExpression implementation instance for the query molecular graph.
| func | The accessor function to use. |
| bool CDPL.Chem.SubstructureSearch.mappingExists | ( | MolecularGraph | target | ) |
Tells whether the query molecular graph matches a substructure of the target molecular graph target.
The method does not store any atom/bond mappings between the query and target molecular graph — 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 target molecular graph that has to be searched for a match of the query. |
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 molecular graph to substructures of the target molecular graph target.
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 target molecular graph that has to be searched for matches of the query. |
True if the query matches at least one substructure of the specified target molecular graph, and False otherwise.| None CDPL.Chem.SubstructureSearch.stopSearch | ( | ) |
Aborts the currently running substructure search process.
Intended to be invoked from a callback (typically a match expression evaluator) running on the same thread as findMappings(). Once flagged, findMappings() returns at the next loop boundary.
| 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 idx is not in the range [0, getNumMappings()). |
| 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 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 molecular graph 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 molecular graph atoms.
By default, an atom of the query molecular graph is free to match any suitable target 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 molecular graph 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 molecular graph atoms.
| query_atom_idx | The index of the query molecular graph atom. |
| target_atom_idx | The index of the target molecular graph atom that has to be matched by the query atom. |
| None CDPL.Chem.SubstructureSearch.clearBondMappingConstraints | ( | ) |
Clears all previously defined query to target molecular graph 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 molecular graph bonds.
By default, a bond of the query molecular graph is free to match any suitable target 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 molecular graph 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 molecular graph bonds.
| query_bond_idx | The index of the query molecular graph bond. |
| target_bond_idx | The index of the target molecular graph bond that has to be matched by the query bond. |
| None CDPL.Chem.SubstructureSearch.setQuery | ( | MolecularGraph | query | ) |
Sets query as the new query molecular graph.
| query | A molecular graph that represents the new query. |
1.9.1