Chemical Data Processing Library C++ API - Version 1.1.1
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PatternBasedFeatureGenerator. More...
#include <PatternBasedFeatureGenerator.hpp>
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) |
typedef std::shared_ptr<PatternBasedFeatureGenerator> CDPL::Pharm::PatternBasedFeatureGenerator::SharedPointer |
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CDPL::Pharm::PatternBasedFeatureGenerator::PatternBasedFeatureGenerator | ( | ) |
Constructs the PatternBasedFeatureGenerator
instance.
CDPL::Pharm::PatternBasedFeatureGenerator::PatternBasedFeatureGenerator | ( | const PatternBasedFeatureGenerator & | gen | ) |
Constructs a copy of the PatternBasedFeatureGenerator
instance gen.
gen | The PatternBasedFeatureGenerator instance to copy. |
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Virtual destructor.
void CDPL::Pharm::PatternBasedFeatureGenerator::addIncludePattern | ( | const Chem::MolecularGraph::SharedPointer & | pattern, |
unsigned int | type, | ||
double | tol, | ||
unsigned int | geom, | ||
double | length = 1.0 |
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Appends a new feature include pattern to the current set of patterns.
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. |
void CDPL::Pharm::PatternBasedFeatureGenerator::addExcludePattern | ( | const Chem::MolecularGraph::SharedPointer & | pattern | ) |
Appends a new feature include pattern to the current set of patterns.
pattern | The substructure search pattern of the feature. |
void CDPL::Pharm::PatternBasedFeatureGenerator::clearIncludePatterns | ( | ) |
Clears the current set of include patterns.
void CDPL::Pharm::PatternBasedFeatureGenerator::clearExcludePatterns | ( | ) |
Clears the current set of exclude patterns.
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Perceives pharmacophore features according to the specified include/exclude patterns and adds them to the pharmacophore pharm.
molgraph | The molecular graph for which to perceive the features. |
pharm | The output pharmacophore where to add the generated features. |
Implements CDPL::Pharm::FeatureGenerator.
PatternBasedFeatureGenerator& CDPL::Pharm::PatternBasedFeatureGenerator::operator= | ( | const PatternBasedFeatureGenerator & | gen | ) |
Replaces the current set include/exclude patterns by the patterns in the PatternBasedFeatureGenerator
instance gen.
gen | The PatternBasedFeatureGenerator instance providing the new patterns to use. |
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Implements CDPL::Pharm::FeatureGenerator.
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