Chemical Data Processing Library C++ API - Version 1.1.1
Public Member Functions | List of all members
CDPL::Pharm::PharmacophoreAlignment Class Reference

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 Entity3DCoordinatesFunctiongetEntity3DCoordinatesFunction () 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 EntityWeightFunctiongetEntityWeightFunction () 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 TopologicalAlignmentConstraintFunctiongetTopAlignmentConstraintFunction () 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 EntityMatchFunctiongetEntityMatchFunction () 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 EntityPairMatchFunctiongetEntityPairMatchFunction () 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 EntityTypegetEntity (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::Matrix4DgetTransform () const
 Returns the alignment transformation matrix that was calculated in the last successful call to nextAlignment(). More...
 
const Util::STPairArraygetTopologicalMapping () 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...
 

Detailed Description

PharmacophoreAlignment.

Constructor & Destructor Documentation

◆ PharmacophoreAlignment()

CDPL::Pharm::PharmacophoreAlignment::PharmacophoreAlignment ( bool  query_mode)

Constructs the PharmacophoreAlignment instance.

Parameters
query_modeIf 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.

Member Function Documentation

◆ addFeatures()

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.

Parameters
cntnrThe feature container containing features to add.
first_setIf true, the features are added to the first feature set, if false to the second one.

The documentation for this class was generated from the following file: