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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Pharm::FeatureGenerator implementation that perceives negative ionizable group features by matching a built-in set of SMARTS-like substructure patterns. More...
#include <NegIonizableFeatureGenerator.hpp>
Inheritance diagram for CDPL::Pharm::NegIonizableFeatureGenerator:Public Member Functions | |
| NegIonizableFeatureGenerator (bool chgd_groups_only) | |
Constructs the NegIonizableFeatureGenerator instance. More... | |
| NegIonizableFeatureGenerator (const Chem::MolecularGraph &molgraph, Pharmacophore &pharm, bool chgd_groups_only) | |
| Perceives the negative ionizable group features of the molecular graph molgraph and adds them to the pharmacophore pharm. 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... | |
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 } |
| 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... | |
| 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 |
| 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) |
| Copy assignment operator. More... | |
Pharm::FeatureGenerator implementation that perceives negative ionizable group features by matching a built-in set of SMARTS-like substructure patterns.
| CDPL::Pharm::NegIonizableFeatureGenerator::NegIonizableFeatureGenerator | ( | bool | chgd_groups_only | ) |
Constructs the NegIonizableFeatureGenerator instance.
| chgd_groups_only | true if features shall be generated only for explicitly charged groups, and false if features shall be generated for both charged and ionizable neutral groups. |
| CDPL::Pharm::NegIonizableFeatureGenerator::NegIonizableFeatureGenerator | ( | const Chem::MolecularGraph & | molgraph, |
| Pharmacophore & | pharm, | ||
| bool | chgd_groups_only | ||
| ) |
Perceives the negative ionizable group features of the molecular graph molgraph 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. |
| chgd_groups_only | true if features shall be generated only for explicitly charged groups, and false if features shall be generated for both charged and ionizable neutral groups. |
1.9.1