Chemical Data Processing Library C++ API - Version 1.1.1
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HydrophobicFeatureGenerator. More...
#include <HydrophobicFeatureGenerator.hpp>
Public Types | |
typedef std::shared_ptr< HydrophobicFeatureGenerator > | SharedPointer |
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< PatternBasedFeatureGenerator > | SharedPointer |
Public Types inherited from CDPL::Pharm::FeatureGenerator | |
typedef std::shared_ptr< FeatureGenerator > | SharedPointer |
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 a\ molgraph and adds them to the pharmacophore pharm. More... | |
~HydrophobicFeatureGenerator () | |
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 |
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... | |
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... | |
Static Public Attributes | |
static constexpr double | DEF_HYD_THRESHOLD_RING = 2.0 |
static constexpr double | DEF_HYD_THRESHOLD_CHAIN = 0.8 |
static constexpr double | DEF_HYD_THRESHOLD_GROUP = 0.8 |
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... | |
FeatureGenerator & | operator= (const FeatureGenerator &gen) |
typedef std::shared_ptr<HydrophobicFeatureGenerator> CDPL::Pharm::HydrophobicFeatureGenerator::SharedPointer |
CDPL::Pharm::HydrophobicFeatureGenerator::HydrophobicFeatureGenerator | ( | ) |
Constructs the HydrophobicFeatureGenerator
instance.
CDPL::Pharm::HydrophobicFeatureGenerator::HydrophobicFeatureGenerator | ( | const HydrophobicFeatureGenerator & | gen | ) |
Constructs a copy of the HydrophobicFeatureGenerator
instance gen.
gen | The HydrophobicFeatureGenerator to copy. |
CDPL::Pharm::HydrophobicFeatureGenerator::HydrophobicFeatureGenerator | ( | const Chem::MolecularGraph & | molgraph, |
Pharmacophore & | pharm | ||
) |
Perceives hydrophobic group features of the molecular graph a\ 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. |
CDPL::Pharm::HydrophobicFeatureGenerator::~HydrophobicFeatureGenerator | ( | ) |
Destructor.
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.
type | The value of the feature type property. |
unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::getFeatureType | ( | ) | const |
Returns the value of the feature type property that gets set on newly generated features.
void CDPL::Pharm::HydrophobicFeatureGenerator::setFeatureTolerance | ( | double | tol | ) |
Specifies the value of the feature tolerance property that has to be set on newly generated features.
tol | The value of the feature tolerance property. |
double CDPL::Pharm::HydrophobicFeatureGenerator::getFeatureTolerance | ( | ) | const |
Returns the value of the feature tolerance property that gets set on newly generated features.
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.
geom | The value of the feature geometry property. |
unsigned int CDPL::Pharm::HydrophobicFeatureGenerator::getFeatureGeometry | ( | ) | const |
Returns the value of the feature geometry property that gets set on newly generated features.
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.
thresh | The minimum total atom hydrophobicity. |
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.
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.
thresh | The minimum total atom hydrophobicity. |
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.
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.
thresh | The minimum total atom hydrophobicity. |
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.
HydrophobicFeatureGenerator& CDPL::Pharm::HydrophobicFeatureGenerator::operator= | ( | const HydrophobicFeatureGenerator & | gen | ) |
Copies the HydrophobicFeatureGenerator
instance gen.
gen | The HydrophobicFeatureGenerator to copy. |
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virtual |
Implements CDPL::Pharm::FeatureGenerator.
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