Pharm::FeatureGenerator implementation that perceives pharmacophore features by SMARTS-like substructure pattern matching, with separate include and exclude pattern lists. More...

#include <PatternBasedFeatureGenerator.hpp>

Inheritance diagram for CDPL::Pharm::PatternBasedFeatureGenerator:

Public Types
enum	PatternAtomLabelFlag { FEATURE_ATOM_FLAG = 0x01 , POS_REF_ATOM_FLAG = 0x02 , GEOM_REF_ATOM1_FLAG = 0x04 , GEOM_REF_ATOM2_FLAG = 0x08 }
	Role-flags assigned (via the atom-mapping-ID property) to atoms of feature substructure patterns added through addIncludePattern(). The flags are bit-OR-combinable so that a single pattern atom can act in several roles simultaneously. More...

typedef std::shared_ptr< PatternBasedFeatureGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `PatternBasedFeatureGenerator` instances. More...

Public Types inherited from CDPL::Pharm::FeatureGenerator
typedef std::shared_ptr< FeatureGenerator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `FeatureGenerator` instances. More...

Public Member Functions
	PatternBasedFeatureGenerator ()
	Constructs the `PatternBasedFeatureGenerator` instance. More...

	PatternBasedFeatureGenerator (const PatternBasedFeatureGenerator &gen)
	Constructs a copy of the `PatternBasedFeatureGenerator` instance gen. More...

virtual	~PatternBasedFeatureGenerator ()
	Virtual destructor. More...

void	addIncludePattern (const Chem::MolecularGraph::SharedPointer &molgraph, unsigned int type, double tol, unsigned int geom, double length=1.0)
	Appends a new feature substructure include pattern to the current set of patterns. More...

void	addExcludePattern (const Chem::MolecularGraph::SharedPointer &molgraph)
	Appends a new feature substructure exclude pattern to the current set of patterns. More...

void	clearIncludePatterns ()
	Clears the current set of include patterns. More...

void	clearExcludePatterns ()
	Clears the current set of exclude patterns. More...

void	generate (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)
	Perceives pharmacophore features according to the specified include/exclude patterns and adds them to the pharmacophore pharm. More...

PatternBasedFeatureGenerator &	operator= (const PatternBasedFeatureGenerator &gen)
	Replaces the current set include/exclude patterns by the patterns in the `PatternBasedFeatureGenerator` instance gen. More...

FeatureGenerator::SharedPointer	clone () const
	Creates a deep copy of the `PatternBasedFeatureGenerator` instance. More...

Public Member Functions inherited from CDPL::Pharm::FeatureGenerator
	FeatureGenerator ()
	Constructs the `FeatureGenerator` instance. More...

virtual	~FeatureGenerator ()
	Virtual destructor. More...

virtual void	setAtom3DCoordinatesFunction (const Chem::Atom3DCoordinatesFunction &func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...

const Chem::Atom3DCoordinatesFunction &	getAtom3DCoordinatesFunction () const
	Returns the function that was registered for the retrieval of atom 3D-coordinates. More...

Protected Types
typedef std::vector< const Chem::Atom * >	AtomList

Protected Member Functions
double	calcVecFeatureOrientation (const AtomList &, const AtomList &, Math::Vector3D &) const

bool	calcPlaneFeatureOrientation (const AtomList &, Math::Vector3D &, Math::Vector3D &)

bool	calcCentroid (const AtomList &, Math::Vector3D &) const

virtual void	addNonPatternFeatures (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)

bool	isContainedInIncMatchList (const Util::BitSet &) const

bool	isContainedInExMatchList (const Util::BitSet &) const

Protected Member Functions inherited from CDPL::Pharm::FeatureGenerator
	FeatureGenerator (const FeatureGenerator &gen)
	Constructs a copy of the `FeatureGenerator` instance gen. More...

FeatureGenerator &	operator= (const FeatureGenerator &gen)
	Copy assignment operator. More...

Detailed Description

Pharm::FeatureGenerator implementation that perceives pharmacophore features by SMARTS-like substructure pattern matching, with separate include and exclude pattern lists.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<PatternBasedFeatureGenerator> CDPL::Pharm::PatternBasedFeatureGenerator::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated PatternBasedFeatureGenerator instances.

◆ AtomList

typedef std::vector<const Chem::Atom*> CDPL::Pharm::PatternBasedFeatureGenerator::AtomList

protected

Member Enumeration Documentation

◆ PatternAtomLabelFlag

enum CDPL::Pharm::PatternBasedFeatureGenerator::PatternAtomLabelFlag

Role-flags assigned (via the atom-mapping-ID property) to atoms of feature substructure patterns added through addIncludePattern(). The flags are bit-OR-combinable so that a single pattern atom can act in several roles simultaneously.

Enumerator
FEATURE_ATOM_FLAG	The atom is part of the generated feature's substructure.
POS_REF_ATOM_FLAG	The atom contributes (via centroid averaging) to the feature's 3D position.
GEOM_REF_ATOM1_FLAG	The atom defines the first orientation reference (used by both vector- and plane-type features).
GEOM_REF_ATOM2_FLAG	The atom defines the second orientation reference (used by plane-type features).

Constructor & Destructor Documentation

◆ PatternBasedFeatureGenerator() [1/2]

CDPL::Pharm::PatternBasedFeatureGenerator::PatternBasedFeatureGenerator ( )

Constructs the PatternBasedFeatureGenerator instance.

◆ PatternBasedFeatureGenerator() [2/2]

CDPL::Pharm::PatternBasedFeatureGenerator::PatternBasedFeatureGenerator ( const PatternBasedFeatureGenerator & gen )

Constructs a copy of the PatternBasedFeatureGenerator instance gen.

Parameters

gen	The `PatternBasedFeatureGenerator` instance to copy.

◆ ~PatternBasedFeatureGenerator()

virtual CDPL::Pharm::PatternBasedFeatureGenerator::~PatternBasedFeatureGenerator ( )

virtual

Virtual destructor.

Member Function Documentation

◆ addIncludePattern()

void CDPL::Pharm::PatternBasedFeatureGenerator::addIncludePattern	(	const Chem::MolecularGraph::SharedPointer &	molgraph,
		unsigned int	type,
		double	tol,
		unsigned int	geom,
		double	length = `1.0`
	)

Appends a new feature substructure include pattern to the current set of patterns.

Parameters

molgraph	The molecular graph of the feature substructure search pattern.
type	The value of the type property of the feature.
tol	The value of the tolerance property of the feature.
geom	The value of the geometry property of the feature.
length	The value of the length property of vector features.

◆ addExcludePattern()

void CDPL::Pharm::PatternBasedFeatureGenerator::addExcludePattern ( const Chem::MolecularGraph::SharedPointer & molgraph )

Appends a new feature substructure exclude pattern to the current set of patterns.

Parameters

molgraph The molecular graph of the feature substructure exclude pattern.

◆ clearIncludePatterns()

void CDPL::Pharm::PatternBasedFeatureGenerator::clearIncludePatterns ( )

Clears the current set of include patterns.

◆ clearExcludePatterns()

void CDPL::Pharm::PatternBasedFeatureGenerator::clearExcludePatterns ( )

Clears the current set of exclude patterns.

◆ generate()

void CDPL::Pharm::PatternBasedFeatureGenerator::generate	(	const Chem::MolecularGraph &	molgraph,
		Pharmacophore &	pharm
	)

virtual

Perceives pharmacophore features according to the specified include/exclude patterns and adds them to the pharmacophore pharm.

Parameters

molgraph	The molecular graph for which to perceive the features.
pharm	The output pharmacophore where to add the generated features.

Implements CDPL::Pharm::FeatureGenerator.

◆ operator=()

PatternBasedFeatureGenerator& CDPL::Pharm::PatternBasedFeatureGenerator::operator= ( const PatternBasedFeatureGenerator & gen )

Replaces the current set include/exclude patterns by the patterns in the PatternBasedFeatureGenerator instance gen.

Parameters

gen	The `PatternBasedFeatureGenerator` instance providing the new patterns to use.

Returns: A reference to itself.

◆ clone()

FeatureGenerator::SharedPointer CDPL::Pharm::PatternBasedFeatureGenerator::clone ( ) const

virtual

Creates a deep copy of the PatternBasedFeatureGenerator instance.

Returns: A smart pointer to the cloned feature generator.

Implements CDPL::Pharm::FeatureGenerator.

◆ calcVecFeatureOrientation()

double CDPL::Pharm::PatternBasedFeatureGenerator::calcVecFeatureOrientation	(	const AtomList &	,
		const AtomList &	,
		Math::Vector3D &
	)		const

protected

◆ calcPlaneFeatureOrientation()

bool CDPL::Pharm::PatternBasedFeatureGenerator::calcPlaneFeatureOrientation	(	const AtomList &	,
		Math::Vector3D &	,
		Math::Vector3D &
	)

protected

◆ calcCentroid()

bool CDPL::Pharm::PatternBasedFeatureGenerator::calcCentroid	(	const AtomList &	,
		Math::Vector3D &
	)		const

protected

◆ addNonPatternFeatures()

virtual void CDPL::Pharm::PatternBasedFeatureGenerator::addNonPatternFeatures	(	const Chem::MolecularGraph &	molgraph,
		Pharmacophore &	pharm
	)

inlineprotectedvirtual

◆ isContainedInIncMatchList()

bool CDPL::Pharm::PatternBasedFeatureGenerator::isContainedInIncMatchList ( const Util::BitSet & ) const

protected

◆ isContainedInExMatchList()

bool CDPL::Pharm::PatternBasedFeatureGenerator::isContainedInExMatchList ( const Util::BitSet & ) const

protected

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

PatternBasedFeatureGenerator.hpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ AtomList

Member Enumeration Documentation

◆ PatternAtomLabelFlag

Constructor & Destructor Documentation

◆ PatternBasedFeatureGenerator() [1/2]

◆ PatternBasedFeatureGenerator() [2/2]

◆ ~PatternBasedFeatureGenerator()

Member Function Documentation

◆ addIncludePattern()

◆ addExcludePattern()

◆ clearIncludePatterns()

◆ clearExcludePatterns()

◆ generate()

◆ operator=()

◆ clone()

◆ calcVecFeatureOrientation()

◆ calcPlaneFeatureOrientation()

◆ calcCentroid()

◆ addNonPatternFeatures()

◆ isContainedInIncMatchList()

◆ isContainedInExMatchList()