Chemical Data Processing Library C++ API - Version 1.1.1
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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< PatternBasedFeatureGeneratorSharedPointer
 
- Public Types inherited from CDPL::Pharm::FeatureGenerator
typedef std::shared_ptr< FeatureGeneratorSharedPointer
 

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...
 
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...
 

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...
 
FeatureGeneratoroperator= (const FeatureGenerator &gen)
 

Detailed Description

PatternBasedFeatureGenerator.

Member Typedef Documentation

◆ SharedPointer

◆ AtomList

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

Member Enumeration Documentation

◆ 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
genThe 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
patternThe substructure search pattern of the feature.
typeThe value of the type property of the feature.
tolThe value of the tolerance property of the feature.
geomThe value of the geometry property of the feature.
lengthThe 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
patternThe 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
molgraphThe molecular graph for which to perceive the features.
pharmThe 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
genThe PatternBasedFeatureGenerator instance providing the new patterns to use.
Returns
A reference to itself.

◆ clone()

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

◆ 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: