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Chemical Data Processing Library C++ API - Version 1.2.0
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Chemical Data Processing Library C++ API - Version 1.2.0
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PharmacophoreAlignment. More...
#include <PharmacophoreAlignment.hpp>
Inheritance diagram for CDPL::Pharm::PharmacophoreAlignment:Public Member Functions | |
| PharmacophoreAlignment (bool query_mode) | |
Constructs the PharmacophoreAlignment instance. More... | |
| void | addFeatures (const FeatureContainer &cntnr, bool first_set) |
| Adds the features of the feature container cntnr to the specified alignment feature set. More... | |
| Public Member Functions inherited from CDPL::Chem::SpatialEntityAlignment< Feature > | |
| SpatialEntityAlignment () | |
Constructs the SpatialEntityAlignment instance. More... | |
| virtual | ~SpatialEntityAlignment () |
| Virtual destructor. More... | |
| void | setMinTopologicalMappingSize (std::size_t min_size) |
| Specifies the minimum number of topologically mapped entities that is required to enable a subsequent spatial alignment. More... | |
| std::size_t | getMinTopologicalMappingSize () |
| Returns the minimum number of topologically mapped entities that is required to enable a subsequent spatial alignment. More... | |
| void | setEntity3DCoordinatesFunction (const Entity3DCoordinatesFunction &func) |
| Specifies a function for the retrieval of entity 3D-coordinates. More... | |
| const Entity3DCoordinatesFunction & | getEntity3DCoordinatesFunction () const |
| Returns the function that was registered for the retrieval of entity 3D-coordinates. More... | |
| void | setEntityWeightFunction (const EntityWeightFunction &func) |
| Specifies a function for the retrieval of entity weights for spatial alignment. More... | |
| const EntityWeightFunction & | getEntityWeightFunction () const |
| Returns the function that was registered for the retrieval of entity weights for spatial alignment. More... | |
| void | setTopAlignmentConstraintFunction (const TopologicalAlignmentConstraintFunction &func) |
| Specifies a function for restricting allowed topological entity alignments. More... | |
| const TopologicalAlignmentConstraintFunction & | getTopAlignmentConstraintFunction () const |
| Returns the function that was registered for restricting allowed topological entity alignments. More... | |
| void | setEntityMatchFunction (const EntityMatchFunction &func) |
| Specifies a function for restricting allowed topological entity mappings in the search for alignment solutions. More... | |
| const EntityMatchFunction & | getEntityMatchFunction () const |
| Returns the function that was registered for restricting allowed topological entity mappings. More... | |
| void | setEntityPairMatchFunction (const EntityPairMatchFunction &func) |
| Specifies a function for checking the compatibility of entity-pairs in the search for alignment solutions. More... | |
| const EntityPairMatchFunction & | getEntityPairMatchFunction () const |
| Returns the function that was registered for checking the compatibility of entity-pairs. More... | |
| void | performExhaustiveSearch (bool exhaustive) |
| bool | exhaustiveSearchPerformed () const |
| void | addEntity (const EntityType &entity, bool first_set) |
| Adds an entity to the specified alignment entity set. More... | |
| void | clearEntities (bool first_set) |
| Removes all entities in the specified alignment entity set. More... | |
| std::size_t | getNumEntities (bool first_set) const |
| Returns the number of entities in the specified alignment entity set. More... | |
| ConstEntityIterator | getEntitiesBegin (bool first_set) const |
| Returns a constant iterator pointing to the beginning of the entities stored in the specified set. More... | |
| ConstEntityIterator | getEntitiesEnd (bool first_set) const |
| Returns a constant iterator pointing to the end of the entities stored in the specified set. More... | |
| const EntityType & | getEntity (std::size_t idx, bool first_set) const |
Returns a non-const reference to the stored entity at index idx in the specified set. More... | |
| bool | nextAlignment () |
| Searches for the next alignment solution. More... | |
| void | reset () |
| const Math::Matrix4D & | getTransform () const |
| Returns the alignment transformation matrix that was calculated in the last successful call to nextAlignment(). More... | |
| const Util::STPairArray & | getTopologicalMapping () const |
| Returns the topological entity mapping resulting from the last successful call to nextAlignment(). More... | |
Additional Inherited Members | |
| Public Types inherited from CDPL::Chem::SpatialEntityAlignment< Feature > | |
| typedef Feature | EntityType |
| The actual entity type. More... | |
| typedef TopologicalAlignment::ConstEntityIterator | ConstEntityIterator |
| A constant iterator over the stored entities. More... | |
| typedef std::function< bool(const Util::STPairArray &)> | TopologicalAlignmentConstraintFunction |
| A generic wrapper class used to store a user-defined predicate to restrict allowed topological entity alignments. More... | |
| typedef std::function< const Math::Vector3D &(const EntityType &)> | Entity3DCoordinatesFunction |
| A generic wrapper class used to store a user-defined entity 3D-coordinates function. More... | |
| typedef std::function< double(const EntityType &)> | EntityWeightFunction |
| A generic wrapper class used to store a user-defined entity alignment weight function. More... | |
| typedef TopologicalAlignment::EntityMatchFunction | EntityMatchFunction |
| A generic wrapper class used to store a user-defined topological entity match constraint function. More... | |
| typedef TopologicalAlignment::EntityPairMatchFunction | EntityPairMatchFunction |
| A generic wrapper class used to store a user-defined entity-pair match constraint function. More... | |
| CDPL::Pharm::PharmacophoreAlignment::PharmacophoreAlignment | ( | bool | query_mode | ) |
Constructs the PharmacophoreAlignment instance.
| query_mode | If true, the features of the first set are interpreted as a query pharmacophore and the features of the second have to match this query after alignment. If false, there is no distinction between the features of the first and second set in various performed intermediate checks. |
| void CDPL::Pharm::PharmacophoreAlignment::addFeatures | ( | const FeatureContainer & | cntnr, |
| bool | first_set | ||
| ) |
Adds the features of the feature container cntnr to the specified alignment feature set.
| cntnr | The feature container containing features to add. |
| first_set | If true, the features are added to the first feature set, if false to the second one. |
1.9.1