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 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...

Detailed Description

PharmacophoreAlignment.

Constructor & Destructor Documentation

PharmacophoreAlignment()

CDPL::Pharm::PharmacophoreAlignment::PharmacophoreAlignment

(

bool

query_mode

)

Constructs the PharmacophoreAlignment instance.

Parameters

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.

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

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.

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

• PharmacophoreAlignment.hpp