CDPL::Pharm::PatternBasedFeatureGenerator Class Reference

PatternBasedFeatureGenerator. 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 }
typedef std::shared_ptr< PatternBasedFeatureGenerator >	SharedPointer
Public Types inherited from CDPL::Pharm::FeatureGenerator
typedef std::shared_ptr< FeatureGenerator >	SharedPointer

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 &pattern, unsigned int type, double tol, unsigned int geom, double length=1.0)
	Appends a new feature include pattern to the current set of patterns. More...
void	addExcludePattern (const Chem::MolecularGraph::SharedPointer &pattern)
	Appends a new feature include 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
Public Member Functions inherited from CDPL::Pharm::FeatureGenerator
	FeatureGenerator ()
	Constructs the FeatureGenerator instance. More...
virtual	~FeatureGenerator ()
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)

Detailed Description

PatternBasedFeatureGenerator.

Member Typedef Documentation

SharedPointer

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

AtomList

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

protected

Member Enumeration Documentation

PatternAtomLabelFlag

enum CDPL::Pharm::PatternBasedFeatureGenerator::PatternAtomLabelFlag

Enumerator
FEATURE_ATOM_FLAG
POS_REF_ATOM_FLAG
GEOM_REF_ATOM1_FLAG
GEOM_REF_ATOM2_FLAG

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 &	pattern,
		unsigned int	type,
		double	tol,
		unsigned int	geom,
		double	length = 1.0
	)

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

Parameters

pattern	The substructure search pattern of the feature.
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 &

pattern

)

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

Parameters

pattern

The substructure search pattern of the feature.

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

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

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

• PatternBasedFeatureGenerator.hpp