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Chemical Data Processing Library C++ API - Version 1.1.1
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Chemical Data Processing Library C++ API - Version 1.1.1
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ReactionSubstructureSearch. More...
#include <ReactionSubstructureSearch.hpp>
Public Types | |
| typedef boost::indirect_iterator< ABMappingList::iterator, AtomBondMapping > | MappingIterator |
| A mutable random access iterator used to iterate over the stored atom/bond mapping objects. More... | |
| typedef boost::indirect_iterator< ABMappingList::const_iterator, const AtomBondMapping > | ConstMappingIterator |
| A constant random access iterator used to iterate over the stored atom/bond mapping objects. More... | |
Public Member Functions | |
| ReactionSubstructureSearch () | |
Constructs and initializes a ReactionSubstructureSearch instance. More... | |
| ReactionSubstructureSearch (const Reaction &query) | |
Constructs and initializes a ReactionSubstructureSearch instance for the specified query reaction pattern. More... | |
| ~ReactionSubstructureSearch () | |
| Destructor. More... | |
| void | setQuery (const Reaction &query) |
| Allows to specify a new query reaction pattern. More... | |
| bool | mappingExists (const Reaction &target) |
| Tells whether the query reaction pattern matches the specified target reaction. More... | |
| bool | findMappings (const Reaction &target) |
| Searches for all possible atom/bond between the query reaction pattern and the specified target reaction. More... | |
| std::size_t | getNumMappings () const |
| Returns the number of atom/bond mappings that were recorded in the last call to findMappings(). More... | |
| AtomBondMapping & | getMapping (std::size_t idx) |
Returns a non-const reference to the stored atom/bond mapping object at index idx. More... | |
| const AtomBondMapping & | getMapping (std::size_t idx) const |
Returns a const reference to the stored atom/bond mapping object at index idx. More... | |
| MappingIterator | getMappingsBegin () |
| Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects. More... | |
| ConstMappingIterator | getMappingsBegin () const |
| Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects. More... | |
| MappingIterator | getMappingsEnd () |
| Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects. More... | |
| ConstMappingIterator | getMappingsEnd () const |
| Returns a constant iterator pointing to the end of the stored atom/bond mapping objects. More... | |
| MappingIterator | begin () |
| Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects. More... | |
| ConstMappingIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects. More... | |
| MappingIterator | end () |
| Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects. More... | |
| ConstMappingIterator | end () const |
| Returns a constant iterator pointing to the end of the stored atom/bond mapping objects. More... | |
| void | uniqueMappingsOnly (bool unique) |
| Allows to specify whether or not to store only unique atom/bond mappings. More... | |
| bool | uniqueMappingsOnly () const |
| Tells whether duplicate atom/bond mappings are discarded. More... | |
| void | setMaxNumMappings (std::size_t max_num_mappings) |
| Allows to specify a limit on the number of stored atom/bond mappings. More... | |
| std::size_t | getMaxNumMappings () const |
| Returns the specified limit on the number of stored atom/bond mappings. More... | |
| void | setEnabledReactionRoles (unsigned int roles) |
| Allows the reaction role specific exclusion of query and target components from the search for matching reaction substructures. More... | |
| unsigned int | getEnabledReactionRoles () const |
| Tells which reaction component roles are considered in the search for matching reaction substructures. More... | |
| typedef boost::indirect_iterator<ABMappingList::iterator, AtomBondMapping> CDPL::Chem::ReactionSubstructureSearch::MappingIterator |
A mutable random access iterator used to iterate over the stored atom/bond mapping objects.
| typedef boost::indirect_iterator<ABMappingList::const_iterator, const AtomBondMapping> CDPL::Chem::ReactionSubstructureSearch::ConstMappingIterator |
A constant random access iterator used to iterate over the stored atom/bond mapping objects.
| CDPL::Chem::ReactionSubstructureSearch::ReactionSubstructureSearch | ( | ) |
Constructs and initializes a ReactionSubstructureSearch instance.
| CDPL::Chem::ReactionSubstructureSearch::ReactionSubstructureSearch | ( | const Reaction & | query | ) |
Constructs and initializes a ReactionSubstructureSearch instance for the specified query reaction pattern.
| query | The query reaction. |
| CDPL::Chem::ReactionSubstructureSearch::~ReactionSubstructureSearch | ( | ) |
Destructor.
Destroys the ReactionSubstructureSearch instance and frees all allocated resources.
| void CDPL::Chem::ReactionSubstructureSearch::setQuery | ( | const Reaction & | query | ) |
Allows to specify a new query reaction pattern.
| query | Specifies the reaction pattern to search for. |
Tells whether the query reaction pattern matches the specified target reaction.
The method does not store any atom/bond mappings between the query and target reaction - 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 reaction that has to be searched for a match of the query reaction pattern. |
true if the query pattern matches the target reaction, and false otherwise. Searches for all possible atom/bond between the query reaction pattern and the specified target reaction.
The method will store all found atom/bond 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 reaction that has to be searched for matches of the query reaction pattern. |
true if the query pattern can be mapped to the specified target reaction, and false otherwise. | std::size_t CDPL::Chem::ReactionSubstructureSearch::getNumMappings | ( | ) | const |
Returns the number of atom/bond mappings that were recorded in the last call to findMappings().
| AtomBondMapping& CDPL::Chem::ReactionSubstructureSearch::getMapping | ( | std::size_t | idx | ) |
Returns a non-const reference to the stored atom/bond mapping object at index idx.
| idx | The zero-based index of the atom/bond mapping object to return. |
const reference to the atom/bond mapping object at index idx. | Base::IndexError | if no mappings are available or idx is not in the range [0, getNumMappings() - 1]. |
| const AtomBondMapping& CDPL::Chem::ReactionSubstructureSearch::getMapping | ( | std::size_t | idx | ) | const |
Returns a const reference to the stored atom/bond mapping object at index idx.
| idx | The zero-based index of the atom/bond mapping object to return. |
const reference to the atom/bond mapping object at index idx. | Base::IndexError | if no mappings are available or idx is not in the range [0, getNumMappings() - 1]. |
| MappingIterator CDPL::Chem::ReactionSubstructureSearch::getMappingsBegin | ( | ) |
Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects.
| ConstMappingIterator CDPL::Chem::ReactionSubstructureSearch::getMappingsBegin | ( | ) | const |
Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects.
| MappingIterator CDPL::Chem::ReactionSubstructureSearch::getMappingsEnd | ( | ) |
Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects.
| ConstMappingIterator CDPL::Chem::ReactionSubstructureSearch::getMappingsEnd | ( | ) | const |
Returns a constant iterator pointing to the end of the stored atom/bond mapping objects.
| MappingIterator CDPL::Chem::ReactionSubstructureSearch::begin | ( | ) |
Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects.
| ConstMappingIterator CDPL::Chem::ReactionSubstructureSearch::begin | ( | ) | const |
Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects.
| MappingIterator CDPL::Chem::ReactionSubstructureSearch::end | ( | ) |
Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects.
| ConstMappingIterator CDPL::Chem::ReactionSubstructureSearch::end | ( | ) | const |
Returns a constant iterator pointing to the end of the stored atom/bond mapping objects.
| void CDPL::Chem::ReactionSubstructureSearch::uniqueMappingsOnly | ( | bool | unique | ) |
Allows to specify whether or not to store only unique atom/bond mappings.
A mapping of the query pattern to the target reaction 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::ReactionSubstructureSearch::uniqueMappingsOnly | ( | ) | const |
Tells whether duplicate atom/bond mappings are discarded.
true if duplicate mappings are discarded, and false otherwise. | void CDPL::Chem::ReactionSubstructureSearch::setMaxNumMappings | ( | std::size_t | max_num_mappings | ) |
Allows to specify a limit on the number of stored atom/bond mappings.
In a call to findMappings() the reaction 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. |
| std::size_t CDPL::Chem::ReactionSubstructureSearch::getMaxNumMappings | ( | ) | const |
Returns the specified limit on the number of stored atom/bond mappings.
| void CDPL::Chem::ReactionSubstructureSearch::setEnabledReactionRoles | ( | unsigned int | roles | ) |
Allows the reaction role specific exclusion of query and target components from the search for matching reaction substructures.
The roles argument is a bitwise OR combination of the flags defined in namespace Chem::ReactionRole. When the flag for a particular reaction role is missing in the provided bitmask, then all reaction components with this role assignment (both in the query and target reaction) will be simply ignored during the reaction substructure search. This has the same effect as 'removing' the affected components from the query and target reaction prior to starting the search and adding them again afterwards.
| roles | A bitmask specifying the non-excluded reaction component roles. |
| unsigned int CDPL::Chem::ReactionSubstructureSearch::getEnabledReactionRoles | ( | ) | const |
Tells which reaction component roles are considered in the search for matching reaction substructures.
1.8.20