Pharm::FeatureGenerator implementation that perceives hydrophobic features by grouping atoms into rings, chains and small fragment groups whose total atom hydrophobicity exceeds the per-class threshold. More...

#include <HydrophobicFeatureGenerator.hpp>

Inheritance diagram for CDPL::Pharm::HydrophobicFeatureGenerator:

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

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 }
	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
	HydrophobicFeatureGenerator ()
	Constructs the `HydrophobicFeatureGenerator` instance. More...

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

	HydrophobicFeatureGenerator (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)
	Perceives hydrophobic group features of the molecular graph molgraph and adds them to the pharmacophore pharm. More...

	~HydrophobicFeatureGenerator ()
	Destructor. More...

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	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...

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	setRingHydrophobicityThreshold (double thresh)
	Specifies the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature. More...

double	getRingHydrophobicityThreshold () const
	Returns the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature. More...

void	setChainHydrophobicityThreshold (double thresh)
	Specifies the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature. More...

double	getChainHydrophobicityThreshold () const
	Returns the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature. More...

void	setGroupHydrophobicityThreshold (double thresh)
	Specifies the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature. More...

double	getGroupHydrophobicityThreshold () const
	Returns the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature. More...

HydrophobicFeatureGenerator &	operator= (const HydrophobicFeatureGenerator &gen)
	Copies the `HydrophobicFeatureGenerator` instance gen. More...

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

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 &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...

Static Public Attributes
static constexpr double	DEF_HYD_THRESHOLD_RING = 2.0
	Default minimum total atom hydrophobicity required for emitting a ring feature. More...

static constexpr double	DEF_HYD_THRESHOLD_CHAIN = 0.8
	Default minimum total atom hydrophobicity required for emitting a chain feature. More...

static constexpr double	DEF_HYD_THRESHOLD_GROUP = 0.8
	Default minimum total atom hydrophobicity required for emitting a group feature. More...

static constexpr double	DEF_FEATURE_TOL = 1.5
	Default value for the feature tolerance property of generated hydrophobic features. More...

static constexpr unsigned int	DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC
	Default value for the feature type property of generated hydrophobic features (Pharm::FeatureType::HYDROPHOBIC). More...

static constexpr unsigned int	DEF_FEATURE_GEOM = FeatureGeometry::SPHERE
	Default value for the feature geometry property of generated hydrophobic features (Pharm::FeatureGeometry::SPHERE). More...

Additional Inherited Members
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)
	Copy assignment operator. More...

Detailed Description

Pharm::FeatureGenerator implementation that perceives hydrophobic features by grouping atoms into rings, chains and small fragment groups whose total atom hydrophobicity exceeds the per-class threshold.

See also: [CATA]

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ HydrophobicFeatureGenerator() [1/3]

CDPL::Pharm::HydrophobicFeatureGenerator::HydrophobicFeatureGenerator ( )

Constructs the HydrophobicFeatureGenerator instance.

◆ HydrophobicFeatureGenerator() [2/3]

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

Constructs a copy of the HydrophobicFeatureGenerator instance gen.

Parameters

gen	The `HydrophobicFeatureGenerator` to copy.

◆ HydrophobicFeatureGenerator() [3/3]

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

Perceives hydrophobic group features of the molecular graph 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.

◆ ~HydrophobicFeatureGenerator()

CDPL::Pharm::HydrophobicFeatureGenerator::~HydrophobicFeatureGenerator ( )

Destructor.

Member Function Documentation

◆ setFeatureType()

void CDPL::Pharm::HydrophobicFeatureGenerator::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 HydrophobicFeatureGenerator::DEF_FEATURE_TYPE.

See also: FeatureProperty::TYPE

◆ getFeatureType()

unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::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

◆ setFeatureTolerance()

void CDPL::Pharm::HydrophobicFeatureGenerator::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 HydrophobicFeatureGenerator::DEF_FEATURE_TOL.

See also: FeatureProperty::TOLERANCE

◆ getFeatureTolerance()

double CDPL::Pharm::HydrophobicFeatureGenerator::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

◆ setFeatureGeometry()

void CDPL::Pharm::HydrophobicFeatureGenerator::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 HydrophobicFeatureGenerator::DEF_FEATURE_GEOM.

See also: FeatureProperty::GEOMETRY

◆ getFeatureGeometry()

unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::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

◆ setRingHydrophobicityThreshold()

void CDPL::Pharm::HydrophobicFeatureGenerator::setRingHydrophobicityThreshold ( double thresh )

Specifies the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_RING.

◆ getRingHydrophobicityThreshold()

double CDPL::Pharm::HydrophobicFeatureGenerator::getRingHydrophobicityThreshold ( ) const

Returns the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

◆ setChainHydrophobicityThreshold()

void CDPL::Pharm::HydrophobicFeatureGenerator::setChainHydrophobicityThreshold ( double thresh )

Specifies the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_CHAIN.

◆ getChainHydrophobicityThreshold()

double CDPL::Pharm::HydrophobicFeatureGenerator::getChainHydrophobicityThreshold ( ) const

Returns the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

◆ setGroupHydrophobicityThreshold()

void CDPL::Pharm::HydrophobicFeatureGenerator::setGroupHydrophobicityThreshold ( double thresh )

Specifies the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_GROUP.

◆ getGroupHydrophobicityThreshold()

double CDPL::Pharm::HydrophobicFeatureGenerator::getGroupHydrophobicityThreshold ( ) const

Returns the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

◆ operator=()

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

Copies the HydrophobicFeatureGenerator instance gen.

Parameters

gen	The `HydrophobicFeatureGenerator` to copy.

Returns: A reference to itself.

◆ clone()

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

virtual

Creates a deep copy of the HydrophobicFeatureGenerator instance.

Returns: A smart pointer to the cloned feature generator.

Implements CDPL::Pharm::FeatureGenerator.

Member Data Documentation

◆ DEF_HYD_THRESHOLD_RING

constexpr double CDPL::Pharm::HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_RING = 2.0

staticconstexpr

Default minimum total atom hydrophobicity required for emitting a ring feature.

◆ DEF_HYD_THRESHOLD_CHAIN

constexpr double CDPL::Pharm::HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_CHAIN = 0.8

staticconstexpr

Default minimum total atom hydrophobicity required for emitting a chain feature.

◆ DEF_HYD_THRESHOLD_GROUP

constexpr double CDPL::Pharm::HydrophobicFeatureGenerator::DEF_HYD_THRESHOLD_GROUP = 0.8

staticconstexpr

Default minimum total atom hydrophobicity required for emitting a group feature.

◆ DEF_FEATURE_TOL

constexpr double CDPL::Pharm::HydrophobicFeatureGenerator::DEF_FEATURE_TOL = 1.5

staticconstexpr

Default value for the feature tolerance property of generated hydrophobic features.

◆ DEF_FEATURE_TYPE

constexpr unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC

staticconstexpr

Default value for the feature type property of generated hydrophobic features (Pharm::FeatureType::HYDROPHOBIC).

◆ DEF_FEATURE_GEOM

constexpr unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::DEF_FEATURE_GEOM = FeatureGeometry::SPHERE

staticconstexpr

Default value for the feature geometry property of generated hydrophobic features (Pharm::FeatureGeometry::SPHERE).

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

HydrophobicFeatureGenerator.hpp

Public Types

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ HydrophobicFeatureGenerator() [1/3]

◆ HydrophobicFeatureGenerator() [2/3]

◆ HydrophobicFeatureGenerator() [3/3]

◆ ~HydrophobicFeatureGenerator()

Member Function Documentation

◆ setFeatureType()

◆ getFeatureType()

◆ setFeatureTolerance()

◆ getFeatureTolerance()

◆ setFeatureGeometry()

◆ getFeatureGeometry()

◆ setRingHydrophobicityThreshold()

◆ getRingHydrophobicityThreshold()

◆ setChainHydrophobicityThreshold()

◆ getChainHydrophobicityThreshold()

◆ setGroupHydrophobicityThreshold()

◆ getGroupHydrophobicityThreshold()

◆ operator=()

◆ clone()

Member Data Documentation

◆ DEF_HYD_THRESHOLD_RING

◆ DEF_HYD_THRESHOLD_CHAIN

◆ DEF_HYD_THRESHOLD_GROUP

◆ DEF_FEATURE_TOL

◆ DEF_FEATURE_TYPE

◆ DEF_FEATURE_GEOM