Chemical Data Processing Library C++ API - Version 1.1.1
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PharmacophoreAlignment. More...
#include <PharmacophoreAlignment.hpp>
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. |