Chemical Data Processing Library C++ API - Version 1.1.1
Public Types | Public Member Functions | Static Public Attributes | List of all members
CDPL::Pharm::HydrophobicAtomFeatureGenerator Class Reference

HydrophobicAtomFeatureGenerator. More...

#include <HydrophobicAtomFeatureGenerator.hpp>

+ Inheritance diagram for CDPL::Pharm::HydrophobicAtomFeatureGenerator:

Public Types

typedef std::shared_ptr< HydrophobicAtomFeatureGeneratorSharedPointer
 
- 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< PatternBasedFeatureGeneratorSharedPointer
 
- Public Types inherited from CDPL::Pharm::FeatureGenerator
typedef std::shared_ptr< FeatureGeneratorSharedPointer
 

Public Member Functions

 HydrophobicAtomFeatureGenerator ()
 Constructs the HydrophobicAtomFeatureGenerator instance. More...
 
 HydrophobicAtomFeatureGenerator (const HydrophobicAtomFeatureGenerator &gen)
 Constructs a copy of the HydrophobicAtomFeatureGenerator instance gen. More...
 
 HydrophobicAtomFeatureGenerator (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)
 Perceives hydrophobic group features of the molecular graph a\ molgraph and adds them to the pharmacophore pharm. More...
 
 ~HydrophobicAtomFeatureGenerator ()
 
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 setHydrophobicityThreshold (double thresh)
 Specifies the minimum hydrophobicity of an atom that is required for the generation of a new feature. More...
 
double getHydrophobicityThreshold () const
 Returns the minimum hydrophobicity of an atom that is required for the generation of a new feature. More...
 
HydrophobicAtomFeatureGeneratoroperator= (const HydrophobicAtomFeatureGenerator &gen)
 Copies the HydrophobicAtomFeatureGenerator 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...
 
PatternBasedFeatureGeneratoroperator= (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::Atom3DCoordinatesFunctiongetAtom3DCoordinatesFunction () const
 Returns the function that was registered for the retrieval of atom 3D-coordinates. More...
 

Static Public Attributes

static constexpr double DEF_HYD_THRESHOLD = 0.5
 
static constexpr double DEF_FEATURE_TOL = 1.5
 
static constexpr unsigned int DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC
 
static constexpr unsigned int DEF_FEATURE_GEOM = FeatureGeometry::SPHERE
 

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...
 
FeatureGeneratoroperator= (const FeatureGenerator &gen)
 

Detailed Description

HydrophobicAtomFeatureGenerator.

See also
[CATA]

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ HydrophobicAtomFeatureGenerator() [1/3]

CDPL::Pharm::HydrophobicAtomFeatureGenerator::HydrophobicAtomFeatureGenerator ( )

Constructs the HydrophobicAtomFeatureGenerator instance.

◆ HydrophobicAtomFeatureGenerator() [2/3]

CDPL::Pharm::HydrophobicAtomFeatureGenerator::HydrophobicAtomFeatureGenerator ( const HydrophobicAtomFeatureGenerator gen)

Constructs a copy of the HydrophobicAtomFeatureGenerator instance gen.

Parameters
genThe HydrophobicAtomFeatureGenerator to copy.

◆ HydrophobicAtomFeatureGenerator() [3/3]

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

Perceives hydrophobic group features of the molecular graph a\ molgraph and adds them to the pharmacophore pharm.

Parameters
molgraphThe molecular graph for which to perceive the features.
pharmThe output pharmacophore where to add the generated features.

◆ ~HydrophobicAtomFeatureGenerator()

CDPL::Pharm::HydrophobicAtomFeatureGenerator::~HydrophobicAtomFeatureGenerator ( )

Destructor.

Member Function Documentation

◆ setFeatureType()

void CDPL::Pharm::HydrophobicAtomFeatureGenerator::setFeatureType ( unsigned int  type)

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

Parameters
typeThe value of the feature type property.
Note
The default type is specified by the constant HydrophobicAtomFeatureGenerator::DEF_FEATURE_TYPE.
See also
FeatureProperty::TYPE

◆ getFeatureType()

unsigned int CDPL::Pharm::HydrophobicAtomFeatureGenerator::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::HydrophobicAtomFeatureGenerator::setFeatureTolerance ( double  tol)

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

Parameters
tolThe value of the feature tolerance property.
Note
The default value is specified by the constant HydrophobicAtomFeatureGenerator::DEF_FEATURE_TOL.
See also
FeatureProperty::TOLERANCE

◆ getFeatureTolerance()

double CDPL::Pharm::HydrophobicAtomFeatureGenerator::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::HydrophobicAtomFeatureGenerator::setFeatureGeometry ( unsigned int  geom)

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

Parameters
geomThe value of the feature geometry property.
Note
The default type is specified by the constant HydrophobicAtomFeatureGenerator::DEF_FEATURE_GEOM.
See also
FeatureProperty::GEOMETRY

◆ getFeatureGeometry()

unsigned int CDPL::Pharm::HydrophobicAtomFeatureGenerator::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

◆ setHydrophobicityThreshold()

void CDPL::Pharm::HydrophobicAtomFeatureGenerator::setHydrophobicityThreshold ( double  thresh)

Specifies the minimum hydrophobicity of an atom that is required for the generation of a new feature.

Parameters
threshThe minimum atom hydrophobicity.
Note
The default value is specified by the constant HydrophobicAtomFeatureGenerator::DEF_HYD_THRESHOLD.

◆ getHydrophobicityThreshold()

double CDPL::Pharm::HydrophobicAtomFeatureGenerator::getHydrophobicityThreshold ( ) const

Returns the minimum hydrophobicity of an atom that is required for the generation of a new feature.

Returns
The specified minimum atom hydrophobicity.

◆ operator=()

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

Copies the HydrophobicAtomFeatureGenerator instance gen.

Parameters
genThe HydrophobicAtomFeatureGenerator to copy.
Returns
A reference to itself.

◆ clone()

FeatureGenerator::SharedPointer CDPL::Pharm::HydrophobicAtomFeatureGenerator::clone ( ) const
virtual

Member Data Documentation

◆ DEF_HYD_THRESHOLD

constexpr double CDPL::Pharm::HydrophobicAtomFeatureGenerator::DEF_HYD_THRESHOLD = 0.5
staticconstexpr

◆ DEF_FEATURE_TOL

constexpr double CDPL::Pharm::HydrophobicAtomFeatureGenerator::DEF_FEATURE_TOL = 1.5
staticconstexpr

◆ DEF_FEATURE_TYPE

constexpr unsigned int CDPL::Pharm::HydrophobicAtomFeatureGenerator::DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC
staticconstexpr

◆ DEF_FEATURE_GEOM

constexpr unsigned int CDPL::Pharm::HydrophobicAtomFeatureGenerator::DEF_FEATURE_GEOM = FeatureGeometry::SPHERE
staticconstexpr

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