CDPL::Pharm::AromaticFeatureGenerator Class Reference

AromaticFeatureGenerator. More...

#include <AromaticFeatureGenerator.hpp>

Inheritance diagram for CDPL::Pharm::AromaticFeatureGenerator:

Public Member Functions
	AromaticFeatureGenerator ()
	Constructs the AromaticFeatureGenerator instance. More...
	AromaticFeatureGenerator (const AromaticFeatureGenerator &gen)
	Constructs a copy of the AromaticFeatureGenerator instance gen. More...
	AromaticFeatureGenerator (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)
	Perceives aromatic ring features of the molecular graph a\ molgraph and adds them to the pharmacophore pharm. More...
	~AromaticFeatureGenerator ()
void	setFeatureType (unsigned int type)
	Specifies the value of the feature type property that has to be set on newly generated features. More...
unsigned int	getFeatureType () const
	Returns the value of the feature type property that gets set on newly generated features. More...
void	setFeatureGeometry (unsigned int geom)
	Specifies the value of the feature geometry property that has to be set on newly generated features. More...
unsigned int	getFeatureGeometry () const
	Returns the value of the feature geometry property that gets set on newly generated features. More...
void	setFeatureTolerance (double tol)
	Specifies the value of the feature tolerance property that has to be set on newly generated features. More...
double	getFeatureTolerance () const
	Returns the value of the feature tolerance property that gets set on newly generated features. More...
AromaticFeatureGenerator &	operator= (const AromaticFeatureGenerator &gen)
	Replaces the current set include/exclude patterns and attributes by a copy of the AromaticFeatureGenerator instance gen. More...
FeatureGenerator::SharedPointer	clone () const
Public Member Functions inherited from CDPL::Pharm::PatternBasedFeatureGenerator
	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...

Static Public Attributes
static constexpr double	DEF_FEATURE_TOL = 0.9
static constexpr unsigned int	DEF_FEATURE_TYPE = FeatureType::AROMATIC
static constexpr unsigned int	DEF_FEATURE_GEOM = FeatureGeometry::PLANE

Additional Inherited Members
Public Types inherited from CDPL::Pharm::PatternBasedFeatureGenerator
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
Protected Types inherited from CDPL::Pharm::PatternBasedFeatureGenerator
typedef std::vector< const Chem::Atom * >	AtomList
Protected Member Functions inherited from CDPL::Pharm::PatternBasedFeatureGenerator
double	calcVecFeatureOrientation (const AtomList &, const AtomList &, Math::Vector3D &) const
bool	calcPlaneFeatureOrientation (const AtomList &, Math::Vector3D &, Math::Vector3D &)
bool	calcCentroid (const AtomList &, Math::Vector3D &) const
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

AromaticFeatureGenerator.

Constructor & Destructor Documentation

AromaticFeatureGenerator() [1/3]

CDPL::Pharm::AromaticFeatureGenerator::AromaticFeatureGenerator

(

)

Constructs the AromaticFeatureGenerator instance.

AromaticFeatureGenerator() [2/3]

CDPL::Pharm::AromaticFeatureGenerator::AromaticFeatureGenerator

(

const AromaticFeatureGenerator &

gen

)

Constructs a copy of the AromaticFeatureGenerator instance gen.

Parameters

gen	The AromaticFeatureGenerator instance to copy.

AromaticFeatureGenerator() [3/3]

CDPL::Pharm::AromaticFeatureGenerator::AromaticFeatureGenerator	(	const Chem::MolecularGraph &	molgraph,
		Pharmacophore &	pharm
	)

Perceives aromatic ring features of the molecular graph a\ molgraph 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.

~AromaticFeatureGenerator()

CDPL::Pharm::AromaticFeatureGenerator::~AromaticFeatureGenerator

(

)

Destructor.

Member Function Documentation

setFeatureType()

void CDPL::Pharm::AromaticFeatureGenerator::setFeatureType

(

unsigned int

type

)

Specifies the value of the feature type property that has to be set on newly generated features.

Parameters

type	The value of the feature type property.

Note

The default type is specified by the constant AromaticFeatureGenerator::DEF_FEATURE_TYPE.

See also

FeatureProperty::TYPE

getFeatureType()

unsigned int CDPL::Pharm::AromaticFeatureGenerator::getFeatureType

(

)

const

Returns the value of the feature type property that gets set on newly generated features.

Returns

The used value of the feature type property.

See also

FeatureProperty::TYPE

setFeatureGeometry()

void CDPL::Pharm::AromaticFeatureGenerator::setFeatureGeometry

(

unsigned int

geom

)

Specifies the value of the feature geometry property that has to be set on newly generated features.

Parameters

geom	The value of the feature geometry property.

Note

The default type is specified by the constant AromaticFeatureGenerator::DEF_FEATURE_GEOM.

See also

FeatureProperty::GEOMETRY

getFeatureGeometry()

unsigned int CDPL::Pharm::AromaticFeatureGenerator::getFeatureGeometry

(

)

const

Returns the value of the feature geometry property that gets set on newly generated features.

Returns

The used value of the feature geometry property.

See also

FeatureProperty::GEOMETRY

setFeatureTolerance()

void CDPL::Pharm::AromaticFeatureGenerator::setFeatureTolerance

(

double

tol

)

Specifies the value of the feature tolerance property that has to be set on newly generated features.

Parameters

tol	The value of the feature tolerance property.

Note

The default value is specified by the constant AromaticFeatureGenerator::DEF_FEATURE_TOL.

See also

FeatureProperty::TOLERANCE

getFeatureTolerance()

double CDPL::Pharm::AromaticFeatureGenerator::getFeatureTolerance

(

)

const

Returns the value of the feature tolerance property that gets set on newly generated features.

Returns

The value of the feature tolerance property.

See also

FeatureProperty::TOLERANCE

operator=()

AromaticFeatureGenerator& CDPL::Pharm::AromaticFeatureGenerator::operator=

(

const AromaticFeatureGenerator &

gen

)

Replaces the current set include/exclude patterns and attributes by a copy of the AromaticFeatureGenerator instance gen.

Parameters

gen	The AromaticFeatureGenerator instance to copy.

Returns

A reference to itself.

clone()

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

virtual

Implements CDPL::Pharm::FeatureGenerator.

Member Data Documentation

DEF_FEATURE_TOL

constexpr double CDPL::Pharm::AromaticFeatureGenerator::DEF_FEATURE_TOL = 0.9

staticconstexpr

DEF_FEATURE_TYPE

constexpr unsigned int CDPL::Pharm::AromaticFeatureGenerator::DEF_FEATURE_TYPE = FeatureType::AROMATIC

staticconstexpr

DEF_FEATURE_GEOM

constexpr unsigned int CDPL::Pharm::AromaticFeatureGenerator::DEF_FEATURE_GEOM = FeatureGeometry::PLANE

staticconstexpr

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

• AromaticFeatureGenerator.hpp