Contains classes and functions related to pharmacophore perception and pharmacophore applications. More...

Namespaces
	ControlParameter
	Provides keys for built-in control-parameters.

	ControlParameterDefault
	Provides default values for built-in control-parameters.

	DataFormat
	Provides preinitialized Base::DataFormat objects for all supported data formats.

	FeatureContainerProperty
	Provides keys for built-in Pharm::FeatureContainer properties.

	FeatureContainerPropertyDefault
	Provides default values for built-in Pharm::FeatureContainer properties.

	FeatureGeometry
	Provides constants for the specification of the generic geometry of a pharmacophore feature.

	FeatureProperty
	Provides keys for built-in Pharm::Feature properties.

	FeaturePropertyDefault
	Provides default values for built-in Pharm::Feature properties.

	FeatureType
	Provides constants for the specification of the generic type of a pharmacophore feature.

Classes
class	AromaticFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives aromatic ring features by enumerating the aromatic SSSR subset of the input molecular graph. More...

class	BasicFeature
	Pharm::Feature implementation owned by a Pharm::BasicPharmacophore parent. More...

class	BasicPharmacophore
	Concrete Pharm::Pharmacophore implementation that owns its features as Pharm::BasicFeature instances managed through an internal object pool. More...

class	CationPiInteractionConstraint
	Constraint functor that tests whether an aromatic/cationic feature pair satisfies the geometric criteria for a cation-π interaction (center distance plus cation-to-ring-plane-normal angle). More...

class	CationPiInteractionScore
	Pharm::FeatureInteractionScore implementation that scores an aromatic/cationic feature pair by combining per-component scores for cation-to-ring-center distance and cation-displacement to ring-plane-normal angle. More...

class	CDFFeatureContainerWriter
	Writer for feature container data in the native I/O format of the CDPL. More...

class	CDFPharmacophoreReader
	Reader for pharmacophore data in the native I/O format of the CDPL. More...

class	DefaultInteractionAnalyzer
	Interaction analyzer pre-configured with the built-in default set of interaction constraints (hydrogen-bonding, ionic, aromatic-aromatic, cation-π, hydrophobic, halogen-bonding). More...

class	DefaultPharmacophoreGenerator
	Pharmacophore generator pre-configured with the built-in default set of feature generators. More...

class	Feature
	Abstract base class representing a single pharmacophore feature within a parent Pharm::Pharmacophore. More...

class	FeatureContainer
	Abstract base class for containers holding a sequence of Pharm::Feature objects with associated properties (e.g. a pharmacophore or feature set). More...

class	FeatureDistanceConstraint
	Constraint functor that accepts a pair of features whose 3D-position distance lies within a configured [min, max] interval. More...

class	FeatureDistanceScore
	Pharm::FeatureInteractionScore implementation that scores a feature pair based on whether their 3D-position distance falls within a configured [min, max] interval. More...

class	FeatureGenerator
	Abstract base class for generators that perceive one type of pharmacophore feature (e.g. an aromatic ring or H-bond donor) and append the perceived features to a Pharm::Pharmacophore. More...

class	FeatureGeometryMatchFunctor
	Match functor that quantifies the goodness of the spatial orientation match between two pharmacophore features, applying type-specific tolerances for H-bond donor/acceptor, halogen-bond donor/acceptor and aromatic features. More...

class	FeatureInteractionScore
	Abstract base class for scoring functors that quantify the strength of a directional pharmacophore-feature interaction (e.g. H-bond, ionic, π-π stacking) between two Pharm::Feature instances. More...

class	FeatureInteractionScoreCombiner
	Composite Pharm::FeatureInteractionScore that combines two underlying interaction scores via a user-supplied binary combination function (default: maximum). More...

class	FeatureMapping
	Data type for the storage and lookup of arbitrary feature to feature mappings. More...

class	FeaturePairDistanceMatchFunctor
	Match functor that tests whether two feature pairs share a compatible inter-feature distance, with the compatibility relation switched between query-mode (asymmetric) and non-query-mode (symmetric). More...

class	FeaturePositionMatchFunctor
	Match functor that quantifies the goodness of the 3D-position match between two pharmacophore features by comparing their separation against the configured per-feature tolerance. More...

class	FeatureSet
	Concrete Pharm::FeatureContainer implementation that stores references to existing Pharm::Feature instances. More...

class	FeatureTypeHistogram
	Data type for the storage of feature type histograms of pharmacophores. More...

class	FeatureTypeMatchFunctor
	Match functor that accepts a feature pair when both features share the same Pharm::FeatureType identifier. More...

class	FileScreeningHitCollector
	Hit-callback functor for use with Pharm::ScreeningProcessor that writes each accepted hit molecule (optionally aligned and annotated with score/database properties) to a Base::DataWriter sink. More...

class	HBondAcceptorFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives H-bond acceptor features by matching a built-in set of SMARTS patterns. More...

class	HBondDonorFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives H-bond donor features by matching a built-in set of SMARTS patterns. More...

class	HBondingInteractionConstraint
	Constraint functor that tests whether a Pharm::Feature pair satisfies geometric H-bond criteria (H-bond length plus acceptor-H-donor and H-bond direction to acceptor vector angles). More...

class	HBondingInteractionScore
	Pharm::FeatureInteractionScore implementation that scores a donor/acceptor feature pair by combining per-component scores for H-bond length, acceptor-H-donor angle and H-bond direction to acceptor vector angle. More...

class	HydrophobicAtomFeatureGenerator
	Pharm::FeatureGenerator implementation that emits one hydrophobic feature per atom whose individual hydrophobicity exceeds a configurable threshold. More...

class	HydrophobicFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives hydrophobic features by grouping atoms into rings, chains and small fragment groups whose total atom hydrophobicity exceeds the per-class threshold. More...

class	HydrophobicInteractionConstraint
	Pharm::FeatureDistanceConstraint specialization that accepts a hydrophobic feature pair when its center distance lies within the typical hydrophobic interaction range. More...

class	HydrophobicInteractionScore
	Pharm::FeatureDistanceScore specialization that scores a hydrophobic feature pair based on its center distance in the typical hydrophobic interaction range. More...

class	InteractionAnalyzer
	Analyzer that detects pairwise interactions between features of two Pharm::FeatureContainer instances based on user-registered per-feature-type-pair interaction constraint functions. More...

class	InteractionConstraintConnector
	Composite feature-interaction constraint that combines two underlying constraint functions via a logical conjunction or disjunction. More...

class	InteractionPharmacophoreGenerator
	Driver that generates an interaction pharmacophore by perceiving a core pharmacophore on a ligand, an environment pharmacophore on the surrounding pocket residues, analyzing the inter-feature interactions and emitting features representing the detected interactions (optionally with exclusion volumes). More...

class	IonicInteractionConstraint
	Pharm::FeatureDistanceConstraint specialization that accepts an oppositely-charged ionic feature pair when its center distance lies within the typical salt-bridge range. More...

class	IonicInteractionScore
	Pharm::FeatureDistanceScore specialization that scores an oppositely-charged ionic feature pair based on its center distance in the typical salt-bridge range. More...

class	NegIonizableFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives negative ionizable group features by matching a built-in set of SMARTS patterns. More...

class	OrthogonalPiPiInteractionConstraint
	Constraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for an orthogonal (T-shaped) π-π interaction (horizontal/vertical center separations plus ring-normal angle). More...

class	OrthogonalPiPiInteractionScore
	Pharm::FeatureInteractionScore implementation that scores an aromatic feature pair for an orthogonal (T-shaped) π-π interaction by combining per-component scores for horizontal/vertical center separations and ring-plane-normal angle. More...

class	ParallelPiPiInteractionConstraint
	Constraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for a parallel (sandwich/displaced) π-π interaction (vertical/horizontal center separations plus ring-normal angle). More...

class	ParallelPiPiInteractionScore
	Pharm::FeatureInteractionScore implementation that scores an aromatic feature pair for a parallel (sandwich/displaced) π-π interaction by combining per-component scores for vertical/horizontal center separations and ring-plane-normal angle. More...

class	PatternBasedFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives pharmacophore features by substructure pattern matching, with separate include and exclude pattern lists. More...

class	Pharmacophore
	Abstract base class for mutable containers of Pharm::Feature instances representing a pharmacophore model. More...

class	PharmacophoreAlignment
	Pharmacophore alignment driver — a Chem::SpatialEntityAlignment specialization for Pharm::Feature objects that aligns two feature sets according to their type, geometry and 3D positions. More...

class	PharmacophoreFitScore
	Scoring functor that quantifies how well a candidate set of features fits a reference pharmacophore, combining feature-match count, per-feature position deviation and geometry-match contributions. More...

class	PharmacophoreFitScreeningScore
	Pharm::PharmacophoreFitScore specialization that scores a Pharm::ScreeningProcessor::SearchHit by applying the underlying pharmacophore-fit score to its query and hit features. More...

class	PharmacophoreGenerator
	Base class for pharmacophore generators that orchestrate per-feature-type Pharm::FeatureGenerator instances to produce the features of a Pharm::Pharmacophore from a Chem::MolecularGraph. More...

class	PMLFeatureContainerWriter
	Writer for feature container data in the native I/O format of LigandScout. More...

class	PMLPharmacophoreReader
	Reader for pharmacophore data in the native I/O format of LigandScout. More...

class	PosIonizableFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives positive ionizable group features by matching a built-in set of SMARTS patterns. More...

class	PSDMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the CDPL PSD-format. More...

class	PSDMolecularGraphWriter
	Writer for molecular graph data in the CDPL PSD-format. More...

class	PSDMoleculeInputHandler
	Handler for the input of molecule data in the CDPL PSD-format. More...

class	PSDMoleculeReader
	Reader for molecule data in the CDPL PSD-format. More...

class	PSDPharmacophoreInputHandler
	Handler for the input of pharmacophore data in the CDPL PSD-format. More...

class	PSDPharmacophoreReader
	Reader for pharmacophore data in the CDPL PSD-format. More...

class	PSDScreeningDBAccessor
	Pharm::ScreeningDBAccessor implementation that reads pharmacophore screening databases stored in the built-in optimized PSD format. More...

class	PSDScreeningDBCreator
	Pharm::ScreeningDBCreator implementation that builds optimized pharmacophore screening databases in the built-in PSD format. More...

class	ScreeningDBAccessor
	Abstract base class for accessors that read the data stored in pharmacophore screening databases. More...

class	ScreeningDBCreator
	Abstract base class for creators that build optimized pharmacophore screening databases. More...

class	ScreeningProcessor
	High-level driver for pharmacophore-based screening of a Pharm::ScreeningDBAccessor-backed database against a query feature container, reporting alignment hits via a user-supplied callback. More...

class	SpatialFeatureMapping
	Pharm::FeatureMapping specialization that perceives a reference-to-aligned feature mapping based on type, position and geometry compatibility under a given transformation, caching per-pair position and geometry match scores for later retrieval. More...

class	XBondAcceptorFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives halogen-bond acceptor features by matching a built-in set of SMARTS patterns. More...

class	XBondDonorFeatureGenerator
	Pharm::FeatureGenerator implementation that perceives halogen-bond donor features by matching a built-in set of SMARTS patterns. More...

class	XBondingInteractionConstraint
	Constraint functor that tests whether a halogen-bond donor/acceptor feature pair satisfies the geometric criteria for a halogen bond (halogen-acceptor distance plus the two characteristic angles). More...

class	XBondingInteractionScore
	Pharm::FeatureInteractionScore implementation that scores a halogen-bond donor/acceptor feature pair by combining per-component scores for halogen-acceptor distance, acceptor-halogen-bound-atom angle and acceptor direction angle. More...

Typedefs
typedef Util::DefaultDataOutputHandler< CDFBZ2FeatureContainerWriter, DataFormat::CDF_BZ2 >	CDFBZ2FeatureContainerOutputHandler
	Handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL. More...

typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::BZip2OStream >	CDFBZ2FeatureContainerWriter
	Writer for bzip2-compressed feature container data in the native I/O format of the CDPL. More...

typedef Util::DefaultDataInputHandler< CDFBZ2PharmacophoreReader, DataFormat::CDF_BZ2 >	CDFBZ2PharmacophoreInputHandler
	Handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...

typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::BZip2IStream >	CDFBZ2PharmacophoreReader
	Reader for bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...

typedef Util::DefaultDataOutputHandler< CDFFeatureContainerWriter, DataFormat::CDF >	CDFFeatureContainerOutputHandler
	Handler for the output of feature container data in the native I/O format of the CDPL. More...

typedef Util::DefaultDataOutputHandler< CDFGZFeatureContainerWriter, DataFormat::CDF_GZ >	CDFGZFeatureContainerOutputHandler
	Handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL. More...

typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::GZipOStream >	CDFGZFeatureContainerWriter
	Writer for gzip-compressed feature container data in the native I/O format of the CDPL. More...

typedef Util::DefaultDataInputHandler< CDFGZPharmacophoreReader, DataFormat::CDF_GZ >	CDFGZPharmacophoreInputHandler
	Handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL. More...

typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::GZipIStream >	CDFGZPharmacophoreReader
	Reader for gzip-compressed pharmacophore data in the native I/O format of the CDPL. More...

typedef Util::DefaultDataInputHandler< CDFPharmacophoreReader, DataFormat::CDF >	CDFPharmacophoreInputHandler
	Handler for the input of pharmacophore data in the native I/O format of the CDPL. More...

typedef std::function< const Math::Vector3D &(const Pharm::Feature &)>	Feature3DCoordinatesFunction
	Generic wrapper class used to store a user-defined Pharm::Feature 3D-coordinates function. More...

typedef std::function< bool(const Feature &, const Feature &)>	FeatureCompareFunction
	Generic wrapper class used to store a user-defined feature compare function. More...

typedef Util::MultiFormatDataWriter< FeatureContainer >	FeatureContainerWriter
	Writer for pharmacophore data in any supported format. More...

typedef Util::MultiFormatDataReader< Pharmacophore >	PharmacophoreReader
	Reader for pharmacophore data in any supported format. More...

typedef Util::DefaultDataOutputHandler< PMLFeatureContainerWriter, DataFormat::PML >	PMLFeatureContainerOutputHandler
	Handler for the output of pharmacophore data in the native I/O format of LigandScout. More...

typedef Util::DefaultDataInputHandler< PMLPharmacophoreReader, DataFormat::PML >	PMLPharmacophoreInputHandler
	Handler for the input of pharmacophore data in the native I/O format of LigandScout. More...

Functions
CDPL_PHARM_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr. More...

CDPL_PHARM_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
	Sets the value of the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict. More...

CDPL_PHARM_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr is set. More...

CDPL_PHARM_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
	Removes the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr. More...

CDPL_PHARM_API bool	getCDFOutputSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr. More...

CDPL_PHARM_API void	setCDFOutputSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec)
	Sets the value of the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec. More...

CDPL_PHARM_API bool	hasCDFOutputSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set. More...

CDPL_PHARM_API void	clearCDFOutputSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr. More...

CDPL_PHARM_API ScreeningDBCreator::Mode	getPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Pharm::ControlParameter::PSD_CREATION_MODE parameter stored in cntnr. More...

CDPL_PHARM_API void	setPSDCreationModeParameter (Base::ControlParameterContainer &cntnr, ScreeningDBCreator::Mode mode)
	Sets the value of the Pharm::ControlParameter::PSD_CREATION_MODE parameter of cntnr to mode. More...

CDPL_PHARM_API bool	hasPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Pharm::ControlParameter::PSD_CREATION_MODE parameter of cntnr is set. More...

CDPL_PHARM_API void	clearPSDCreationModeParameter (Base::ControlParameterContainer &cntnr)
	Removes the Pharm::ControlParameter::PSD_CREATION_MODE parameter from cntnr. More...

CDPL_PHARM_API bool	getPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter stored in cntnr. More...

CDPL_PHARM_API void	setPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr, bool allow)
	Sets the value of the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter of cntnr to allow. More...

CDPL_PHARM_API bool	hasPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter of cntnr is set. More...

CDPL_PHARM_API void	clearPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter from cntnr. More...

CDPL_PHARM_API const std::string &	getName (const FeatureContainer &cntnr)
	Returns the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr. More...

CDPL_PHARM_API void	setName (FeatureContainer &cntnr, const std::string &name)
	Sets the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr to name. More...

CDPL_PHARM_API void	clearName (FeatureContainer &cntnr)
	Clears the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr. More...

CDPL_PHARM_API bool	hasName (const FeatureContainer &cntnr)
	Tells whether the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr is set. More...

CDPL_PHARM_API std::size_t	getFeatureCount (const FeatureContainer &cntnr)
	Returns the total number of features stored in the feature container cntnr. More...

CDPL_PHARM_API std::size_t	getFeatureCount (const FeatureContainer &cntnr, unsigned int type)
	Returns the number of features in the feature container cntr whose type matches type. More...

CDPL_PHARM_API void	generateFeatureTypeHistogram (const FeatureContainer &cntnr, FeatureTypeHistogram &hist, bool append=false)
	Computes a per-feature type frequency histogram of the features in the feature container cntr. More...

CDPL_PHARM_API void	generateFeatureTypeHistogramString (const FeatureContainer &cntnr, std::string &histo_str)
	Generates a string representation of the feature type histogram of the feature container cntr. More...

CDPL_PHARM_API void	clearOrientations (FeatureContainer &cntnr, bool fix_geom=true)
	Clears the orientation property of every feature in the feature container cntr and (optionally) resets each feature's geometry property. More...

CDPL_PHARM_API bool	removePositionalDuplicates (const FeatureContainer &cntnr, FeatureSet &tgt_set, double pos_tol=0.0, bool append=false)
	Copies the features in the feature container cntr into tgt_set, suppressing features that share both type and 3D position with an already collected feature. More...

CDPL_PHARM_API bool	removeFeaturesWithType (const FeatureContainer &cntnr, FeatureSet &tgt_set, unsigned int type, bool append=false)
	Copies the features in the feature container cntr into tgt_set, skipping every feature whose type matches type. More...

CDPL_PHARM_API void	transform3DCoordinates (FeatureContainer &cntnr, const Math::Matrix4D &mtx)
	Applies the affine transformation mtx to the 3D position property and, if set, the orientation property of every feature in the feature container cntr. More...

CDPL_PHARM_API bool	checkForExclusionVolumeClashes (const FeatureContainer &ftr_cntnr, const Chem::AtomContainer &atom_cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, const Math::Matrix4D &xform, double vdw_factor=1.0)
	Tests whether the exclusion volume features in ftr_cntnr remain clash-free with respect to the transformed atom positions of atom_cntnr. More...

CDPL_PHARM_API void	getFeatureAtoms (const FeatureContainer &cntnr, Chem::Fragment &atoms, bool append=false)
	Collects the atoms of the molecular substructures underlying the features of the feature container cntr into atoms. More...

CDPL_PHARM_API unsigned int	getType (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::TYPE property of the feature feature. More...

CDPL_PHARM_API void	setType (Feature &feature, unsigned int type)
	Sets the value of the Pharm::FeatureProperty::TYPE property of the feature feature to type. More...

CDPL_PHARM_API void	clearType (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::TYPE property of the feature feature. More...

CDPL_PHARM_API bool	hasType (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::TYPE property of the feature feature is set. More...

CDPL_PHARM_API unsigned int	getGeometry (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature. More...

CDPL_PHARM_API void	setGeometry (Feature &feature, unsigned int geom)
	Sets the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature to geom. More...

CDPL_PHARM_API void	clearGeometry (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature. More...

CDPL_PHARM_API bool	hasGeometry (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::GEOMETRY property of the feature feature is set. More...

CDPL_PHARM_API const Math::Vector3D &	getOrientation (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature. More...

CDPL_PHARM_API void	setOrientation (Feature &feature, const Math::Vector3D &orient)
	Sets the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature to orient. More...

CDPL_PHARM_API void	clearOrientation (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature. More...

CDPL_PHARM_API bool	hasOrientation (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::ORIENTATION property of the feature feature is set. More...

CDPL_PHARM_API double	getLength (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::LENGTH property of the feature feature. More...

CDPL_PHARM_API void	setLength (Feature &feature, double length)
	Sets the value of the Pharm::FeatureProperty::LENGTH property of the feature feature to length. More...

CDPL_PHARM_API void	clearLength (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::LENGTH property of the feature feature. More...

CDPL_PHARM_API bool	hasLength (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::LENGTH property of the feature feature is set. More...

CDPL_PHARM_API double	getTolerance (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature. More...

CDPL_PHARM_API void	setTolerance (Feature &feature, double tol)
	Sets the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature to tol. More...

CDPL_PHARM_API void	clearTolerance (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature. More...

CDPL_PHARM_API bool	hasTolerance (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::TOLERANCE property of the feature feature is set. More...

CDPL_PHARM_API double	getWeight (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature. More...

CDPL_PHARM_API void	setWeight (Feature &feature, double weight)
	Sets the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature to weight. More...

CDPL_PHARM_API void	clearWeight (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature. More...

CDPL_PHARM_API bool	hasWeight (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::WEIGHT property of the feature feature is set. More...

CDPL_PHARM_API const Chem::Fragment::SharedPointer &	getSubstructure (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature (the underlying atoms/bonds). More...

CDPL_PHARM_API void	setSubstructure (Feature &feature, const Chem::Fragment::SharedPointer &substruct)
	Sets the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature to substruct. More...

CDPL_PHARM_API void	clearSubstructure (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature. More...

CDPL_PHARM_API bool	hasSubstructure (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature is set. More...

CDPL_PHARM_API std::string	getEnvironmentResidueInfo (const Feature &feature)
	Generates a string describing the environment residues associated with the feature feature. More...

CDPL_PHARM_API std::string &	getEnvironmentResidueInfo (const Feature &feature, std::string &info)
	Generates a string describing the environment residues associated with the feature feature. More...

CDPL_PHARM_API std::string	getEnvironmentResidueAtomInfo (const Feature &feature)
	Generates a string describing the environment residue atoms associated with the feature feature. More...

CDPL_PHARM_API std::string &	getEnvironmentResidueAtomInfo (const Feature &feature, std::string &info)
	Generates a string describing the environment residue atoms associated with the feature feature. More...

CDPL_PHARM_API const Chem::Fragment::SharedPointer &	getEnvironmentSubstructure (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature. More...

CDPL_PHARM_API void	setEnvironmentSubstructure (Feature &feature, const Chem::Fragment::SharedPointer &substruct)
	Sets the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature to substruct. More...

CDPL_PHARM_API void	clearEnvironmentSubstructure (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature. More...

CDPL_PHARM_API bool	hasEnvironmentSubstructure (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature is set. More...

CDPL_PHARM_API bool	getDisabledFlag (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature. More...

CDPL_PHARM_API void	setDisabledFlag (Feature &feature, bool flag)
	Sets the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature to flag. More...

CDPL_PHARM_API void	clearDisabledFlag (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature. More...

CDPL_PHARM_API bool	hasDisabledFlag (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature is set. More...

CDPL_PHARM_API bool	getOptionalFlag (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature. More...

CDPL_PHARM_API void	setOptionalFlag (Feature &feature, bool flag)
	Sets the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature to flag. More...

CDPL_PHARM_API void	clearOptionalFlag (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature. More...

CDPL_PHARM_API bool	hasOptionalFlag (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature is set. More...

CDPL_PHARM_API double	getHydrophobicity (const Feature &feature)
	Returns the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature. More...

CDPL_PHARM_API void	setHydrophobicity (Feature &feature, double hyd)
	Sets the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature to hyd. More...

CDPL_PHARM_API void	clearHydrophobicity (Feature &feature)
	Clears the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature. More...

CDPL_PHARM_API bool	hasHydrophobicity (const Feature &feature)
	Tells whether the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature is set. More...

CDPL_PHARM_API void	getFeatures (FeatureSet &ftr_set, const FeatureMapping &mapping, bool first)
	Extracts features from mapping into the feature set ftr_set. More...

CDPL_PHARM_API bool	removePositionalDuplicates (FeatureSet &ftr_set, double pos_tol=0.0)
	Removes features from the feature set ftr_set whose 3D position duplicates that of another feature of the same type. More...

CDPL_PHARM_API bool	removeFeaturesWithType (FeatureSet &ftr_set, unsigned int type)
	Removes features of the given type from the feature set ftr_set. More...

CDPL_PHARM_API void	prepareForPharmacophoreGeneration (Chem::Molecule &mol, bool calc_hyd=true, bool from_logp=false)
	Prepares the molecule mol for downstream pharmacophore generation.. More...

CDPL_PHARM_API bool	removePositionalDuplicates (Pharmacophore &pharm, double pos_tol=0.0)
	Removes positional duplicate features from the pharmacophore pharm in place. More...

CDPL_PHARM_API bool	removeFeaturesWithType (Pharmacophore &pharm, unsigned int type)
	Removes every feature in the pharmacophore pharm whose type matches type. More...

CDPL_PHARM_API void	generateInteractionPharmacophore (Pharmacophore &pharm, const FeatureMapping &iactions, bool append=false)
	Builds an interaction pharmacophore from the supplied feature mapping. More...

CDPL_PHARM_API void	createExclusionVolumes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double tol=0.0, double min_dist=0.0, bool rel_dist=true, bool append=true)
	Creates exclusion volume features at the 3D positions of the atoms in cntnr and appends them to the pharmacophore pharm. More...

CDPL_PHARM_API void	createExclusionVolumes (Pharmacophore &pharm, const FeatureContainer &cntnr, double tol=0.0, double min_dist=0.0, bool rel_dist=true, bool append=true)
	Creates exclusion volume features at the 3D positions of the features in cntnr and appends them to the pharmacophore pharm. More...

CDPL_PHARM_API bool	removeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0)
	Removes every exclusion volume feature from the pharmacophore pharm whose tolerance sphere clashes with any atom of cntnr. More...

CDPL_PHARM_API bool	resizeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0)
	Shrinks the tolerance of every exclusion volume feature in the pharmacophore pharm whose tolerance sphere clashes with any atom of cntnr. More...

CDPL_PHARM_API const std::string &	getFeatureTypeString (unsigned int ftr_type)
	Returns a concise human-readable string (e.g. "HBD" for H-bond donor) for the given numeric feature type identifier ftr_type. More...

Detailed Description

Contains classes and functions related to pharmacophore perception and pharmacophore applications.

Typedef Documentation

◆ CDFBZ2FeatureContainerOutputHandler

typedef Util::DefaultDataOutputHandler<CDFBZ2FeatureContainerWriter, DataFormat::CDF_BZ2> CDPL::Pharm::CDFBZ2FeatureContainerOutputHandler

Handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL.

◆ CDFBZ2FeatureContainerWriter

typedef Util::CompressedDataWriter<CDFFeatureContainerWriter, Util::BZip2OStream> CDPL::Pharm::CDFBZ2FeatureContainerWriter

Writer for bzip2-compressed feature container data in the native I/O format of the CDPL.

◆ CDFBZ2PharmacophoreInputHandler

typedef Util::DefaultDataInputHandler<CDFBZ2PharmacophoreReader, DataFormat::CDF_BZ2> CDPL::Pharm::CDFBZ2PharmacophoreInputHandler

Handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL.

◆ CDFBZ2PharmacophoreReader

typedef Util::CompressedDataReader<CDFPharmacophoreReader, Util::BZip2IStream> CDPL::Pharm::CDFBZ2PharmacophoreReader

Reader for bzip2-compressed pharmacophore data in the native I/O format of the CDPL.

◆ CDFFeatureContainerOutputHandler

typedef Util::DefaultDataOutputHandler<CDFFeatureContainerWriter, DataFormat::CDF> CDPL::Pharm::CDFFeatureContainerOutputHandler

Handler for the output of feature container data in the native I/O format of the CDPL.

◆ CDFGZFeatureContainerOutputHandler

typedef Util::DefaultDataOutputHandler<CDFGZFeatureContainerWriter, DataFormat::CDF_GZ> CDPL::Pharm::CDFGZFeatureContainerOutputHandler

Handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL.

◆ CDFGZFeatureContainerWriter

typedef Util::CompressedDataWriter<CDFFeatureContainerWriter, Util::GZipOStream> CDPL::Pharm::CDFGZFeatureContainerWriter

Writer for gzip-compressed feature container data in the native I/O format of the CDPL.

◆ CDFGZPharmacophoreInputHandler

typedef Util::DefaultDataInputHandler<CDFGZPharmacophoreReader, DataFormat::CDF_GZ> CDPL::Pharm::CDFGZPharmacophoreInputHandler

Handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL.

◆ CDFGZPharmacophoreReader

typedef Util::CompressedDataReader<CDFPharmacophoreReader, Util::GZipIStream> CDPL::Pharm::CDFGZPharmacophoreReader

Reader for gzip-compressed pharmacophore data in the native I/O format of the CDPL.

◆ CDFPharmacophoreInputHandler

typedef Util::DefaultDataInputHandler<CDFPharmacophoreReader, DataFormat::CDF> CDPL::Pharm::CDFPharmacophoreInputHandler

Handler for the input of pharmacophore data in the native I/O format of the CDPL.

◆ Feature3DCoordinatesFunction

typedef std::function<const Math::Vector3D&(const Pharm::Feature&)> CDPL::Pharm::Feature3DCoordinatesFunction

Generic wrapper class used to store a user-defined Pharm::Feature 3D-coordinates function.

◆ FeatureCompareFunction

typedef std::function<bool(const Feature&, const Feature&)> CDPL::Pharm::FeatureCompareFunction

Generic wrapper class used to store a user-defined feature compare function.

◆ FeatureContainerWriter

typedef Util::MultiFormatDataWriter<FeatureContainer> CDPL::Pharm::FeatureContainerWriter

Writer for pharmacophore data in any supported format.

◆ PharmacophoreReader

typedef Util::MultiFormatDataReader<Pharmacophore> CDPL::Pharm::PharmacophoreReader

Reader for pharmacophore data in any supported format.

◆ PMLFeatureContainerOutputHandler

typedef Util::DefaultDataOutputHandler<PMLFeatureContainerWriter, DataFormat::PML> CDPL::Pharm::PMLFeatureContainerOutputHandler

Handler for the output of pharmacophore data in the native I/O format of LigandScout.

◆ PMLPharmacophoreInputHandler

typedef Util::DefaultDataInputHandler<PMLPharmacophoreReader, DataFormat::PML> CDPL::Pharm::PMLPharmacophoreInputHandler

Handler for the input of pharmacophore data in the native I/O format of LigandScout.

Function Documentation

◆ getStrictErrorCheckingParameter()

CDPL_PHARM_API bool CDPL::Pharm::getStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

Returns the value of the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr The control-parameter container.

Returns: true if strict error checking is enabled, and false otherwise.

◆ setStrictErrorCheckingParameter()

CDPL_PHARM_API void CDPL::Pharm::setStrictErrorCheckingParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	strict
	)

Sets the value of the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict.

Parameters

cntnr	The control-parameter container.
strict	`true` to enable strict error checking, and `false` to disable it.

◆ hasStrictErrorCheckingParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

Tells whether the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr is set.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearStrictErrorCheckingParameter()

CDPL_PHARM_API void CDPL::Pharm::clearStrictErrorCheckingParameter ( Base::ControlParameterContainer & cntnr )

Removes the Pharm::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getCDFOutputSinglePrecisionFloatsParameter()

CDPL_PHARM_API bool CDPL::Pharm::getCDFOutputSinglePrecisionFloatsParameter ( const Base::ControlParameterContainer & cntnr )

Returns the value of the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter stored in cntnr.

Parameters

cntnr The control-parameter container.

Returns: true if CDF output uses single-precision floats, and false otherwise.

Since: 1.2

◆ setCDFOutputSinglePrecisionFloatsParameter()

CDPL_PHARM_API void CDPL::Pharm::setCDFOutputSinglePrecisionFloatsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	single_prec
	)

Sets the value of the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr to single_prec.

Parameters

cntnr	The control-parameter container.
single_prec	`true` to write single-precision floats, and `false` to write double-precision floats.

Since: 1.2

◆ hasCDFOutputSinglePrecisionFloatsParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasCDFOutputSinglePrecisionFloatsParameter ( const Base::ControlParameterContainer & cntnr )

Tells whether the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter of cntnr is set.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

Since: 1.2

◆ clearCDFOutputSinglePrecisionFloatsParameter()

CDPL_PHARM_API void CDPL::Pharm::clearCDFOutputSinglePrecisionFloatsParameter ( Base::ControlParameterContainer & cntnr )

Removes the Pharm::ControlParameter::CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr.

Parameters

cntnr The control-parameter container.

Since: 1.2

◆ getPSDCreationModeParameter()

CDPL_PHARM_API ScreeningDBCreator::Mode CDPL::Pharm::getPSDCreationModeParameter ( const Base::ControlParameterContainer & cntnr )

Returns the value of the Pharm::ControlParameter::PSD_CREATION_MODE parameter stored in cntnr.

Parameters

cntnr The control-parameter container.

Returns: The Pharm::ScreeningDBCreator::Mode value.

◆ setPSDCreationModeParameter()

CDPL_PHARM_API void CDPL::Pharm::setPSDCreationModeParameter	(	Base::ControlParameterContainer &	cntnr,
		ScreeningDBCreator::Mode	mode
	)

Sets the value of the Pharm::ControlParameter::PSD_CREATION_MODE parameter of cntnr to mode.

Parameters

cntnr	The control-parameter container.
mode	The new Pharm::ScreeningDBCreator::Mode value.

◆ hasPSDCreationModeParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasPSDCreationModeParameter ( const Base::ControlParameterContainer & cntnr )

Tells whether the Pharm::ControlParameter::PSD_CREATION_MODE parameter of cntnr is set.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPSDCreationModeParameter()

CDPL_PHARM_API void CDPL::Pharm::clearPSDCreationModeParameter ( Base::ControlParameterContainer & cntnr )

Removes the Pharm::ControlParameter::PSD_CREATION_MODE parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPSDAllowDuplicatesParameter()

CDPL_PHARM_API bool CDPL::Pharm::getPSDAllowDuplicatesParameter ( const Base::ControlParameterContainer & cntnr )

Returns the value of the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter stored in cntnr.

Parameters

cntnr The control-parameter container.

Returns: true if duplicate database entries are allowed, and false otherwise.

◆ setPSDAllowDuplicatesParameter()

CDPL_PHARM_API void CDPL::Pharm::setPSDAllowDuplicatesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	allow
	)

Sets the value of the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter of cntnr to allow.

Parameters

cntnr	The control-parameter container.
allow	`true` to allow duplicate database entries, and `false` to reject them.

◆ hasPSDAllowDuplicatesParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasPSDAllowDuplicatesParameter ( const Base::ControlParameterContainer & cntnr )

Tells whether the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter of cntnr is set.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPSDAllowDuplicatesParameter()

CDPL_PHARM_API void CDPL::Pharm::clearPSDAllowDuplicatesParameter ( Base::ControlParameterContainer & cntnr )

Removes the Pharm::ControlParameter::PSD_ALLOW_DUPLICATES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getName()

CDPL_PHARM_API const std::string& CDPL::Pharm::getName ( const FeatureContainer & cntnr )

Returns the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr.

Parameters

cntnr The feature container for which to return the property value.

Returns: The name (or an empty string if the property is not set).

◆ setName()

CDPL_PHARM_API void CDPL::Pharm::setName	(	FeatureContainer &	cntnr,
		const std::string &	name
	)

Sets the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr to name.

Parameters

cntnr	The feature container for which to set the property value.
name	The new name.

◆ clearName()

CDPL_PHARM_API void CDPL::Pharm::clearName ( FeatureContainer & cntnr )

Clears the value of the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr.

Parameters

cntnr The feature container for which to clear the property value.

◆ hasName()

CDPL_PHARM_API bool CDPL::Pharm::hasName ( const FeatureContainer & cntnr )

Tells whether the Pharm::FeatureContainerProperty::NAME property of the feature container cntnr is set.

Parameters

cntnr The feature container for which to query the property value.

Returns: true if the name property is set, and false otherwise.

◆ getFeatureCount() [1/2]

CDPL_PHARM_API std::size_t CDPL::Pharm::getFeatureCount ( const FeatureContainer & cntnr )

Returns the total number of features stored in the feature container cntnr.

Parameters

cntnr The feature container.

Returns: The number of stored features.

◆ getFeatureCount() [2/2]

CDPL_PHARM_API std::size_t CDPL::Pharm::getFeatureCount	(	const FeatureContainer &	cntnr,
		unsigned int	type
	)

Returns the number of features in the feature container cntr whose type matches type.

Parameters

cntnr	The feature container.
type	The feature type to count.

Returns: The number of features of the specified type.

◆ generateFeatureTypeHistogram()

CDPL_PHARM_API void CDPL::Pharm::generateFeatureTypeHistogram	(	const FeatureContainer &	cntnr,
		FeatureTypeHistogram &	hist,
		bool	append = `false`
	)

Computes a per-feature type frequency histogram of the features in the feature container cntr.

Parameters

cntnr	The feature container.
hist	The output histogram (feature type to count).
append	If `false`, hist is cleared before the counts are accumulated.

◆ generateFeatureTypeHistogramString()

CDPL_PHARM_API void CDPL::Pharm::generateFeatureTypeHistogramString	(	const FeatureContainer &	cntnr,
		std::string &	histo_str
	)

Generates a string representation of the feature type histogram of the feature container cntr.

The generated string is a human readable comma separated list of entries of the form Name(count).

Parameters

cntnr	The feature container.
histo_str	The output string.

◆ clearOrientations()

CDPL_PHARM_API void CDPL::Pharm::clearOrientations	(	FeatureContainer &	cntnr,
		bool	fix_geom = `true`
	)

Clears the orientation property of every feature in the feature container cntr and (optionally) resets each feature's geometry property.

Parameters

cntnr	The feature container.
fix_geom	If `true`, the geometry property of each feature is set to Pharm::FeatureGeometry::SPHERE after clearing the orientation.

Since: 1.2

◆ removePositionalDuplicates() [1/3]

CDPL_PHARM_API bool CDPL::Pharm::removePositionalDuplicates	(	const FeatureContainer &	cntnr,
		FeatureSet &	tgt_set,
		double	pos_tol = `0.0`,
		bool	append = `false`
	)

Copies the features in the feature container cntr into tgt_set, suppressing features that share both type and 3D position with an already collected feature.

Two features count as duplicates if they have identical type and their position vectors either match exactly (pos_tol ≤ 0) or lie within pos_tol from each other. When a duplicate is detected, the feature with the larger position tolerance is retained.

Parameters

cntnr	The feature container providing the input features.
tgt_set	The feature set receiving the deduplicated features.
pos_tol	The position-equality tolerance in Ångstrom. Values ≤ 0 require an exact position match.
append	If `false`, tgt_set is cleared before adding any features.

Returns: true if at least one duplicate was detected, and false otherwise.

Since: 1.2

◆ removeFeaturesWithType() [1/3]

CDPL_PHARM_API bool CDPL::Pharm::removeFeaturesWithType	(	const FeatureContainer &	cntnr,
		FeatureSet &	tgt_set,
		unsigned int	type,
		bool	append = `false`
	)

Copies the features in the feature container cntr into tgt_set, skipping every feature whose type matches type.

Parameters

cntnr	The feature container providing the input features.
tgt_set	The feature set receiving the filtered features.
type	The feature type to exclude (see namespace Pharm::FeatureType).
append	If `false`, tgt_set is cleared before adding any features.

Returns: true if at least one feature was excluded, and false otherwise.

Since: 1.2

◆ transform3DCoordinates()

CDPL_PHARM_API void CDPL::Pharm::transform3DCoordinates	(	FeatureContainer &	cntnr,
		const Math::Matrix4D &	mtx
	)

Applies the affine transformation mtx to the 3D position property and, if set, the orientation property of every feature in the feature container cntr.

Parameters

cntnr	The feature container to transform.
mtx	The 4×4 transformation matrix.

◆ checkForExclusionVolumeClashes()

CDPL_PHARM_API bool CDPL::Pharm::checkForExclusionVolumeClashes	(	const FeatureContainer &	ftr_cntnr,
		const Chem::AtomContainer &	atom_cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		const Math::Matrix4D &	xform,
		double	vdw_factor = `1.0`
	)

Tests whether the exclusion volume features in ftr_cntnr remain clash-free with respect to the transformed atom positions of atom_cntnr.

Each enabled feature of type Pharm::FeatureType::EXCLUSION_VOLUME is checked against every atom of atom_cntnr: a clash is reported as soon as the distance between feature and atom is smaller than the sum of the feature's position tolerance and vdw_factor times the atom's Van der Waals radius.

Parameters

ftr_cntnr	The feature container providing the exclusion volume features.
atom_cntnr	The atom container providing the test atoms.
coords_func	The function returning the 3D coordinates of an atom.
xform	The 4×4 transformation applied to the atom coordinates before the clash test.
vdw_factor	Scaling factor for the per-atom Van der Waals radii. If ≤ 0 the atoms are treated as point particles.

Returns: true if no clash is detected, and false otherwise.

◆ getFeatureAtoms()

CDPL_PHARM_API void CDPL::Pharm::getFeatureAtoms	(	const FeatureContainer &	cntnr,
		Chem::Fragment &	atoms,
		bool	append = `false`
	)

Collects the atoms of the molecular substructures underlying the features of the feature container cntr into atoms.

Features without an associated substructure (see Pharm::hasSubstructure()) are silently skipped.

Parameters

cntnr	The feature container providing the features.
atoms	The output fragment receiving the contributing atoms.
append	If `false`, atoms is cleared before any atoms are added.

◆ getType()

CDPL_PHARM_API unsigned int CDPL::Pharm::getType ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::TYPE property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The feature type identifier (see namespace Pharm::FeatureType).

◆ setType()

CDPL_PHARM_API void CDPL::Pharm::setType	(	Feature &	feature,
		unsigned int	type
	)

Sets the value of the Pharm::FeatureProperty::TYPE property of the feature feature to type.

Parameters

feature	The feature for which to set the property value.
type	The new feature type identifier (see namespace Pharm::FeatureType).

◆ clearType()

CDPL_PHARM_API void CDPL::Pharm::clearType ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::TYPE property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasType()

CDPL_PHARM_API bool CDPL::Pharm::hasType ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::TYPE property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the type property is set, and false otherwise.

◆ getGeometry()

CDPL_PHARM_API unsigned int CDPL::Pharm::getGeometry ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The feature geometry identifier (see namespace Pharm::FeatureGeometry).

◆ setGeometry()

CDPL_PHARM_API void CDPL::Pharm::setGeometry	(	Feature &	feature,
		unsigned int	geom
	)

Sets the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature to geom.

Parameters

feature	The feature for which to set the property value.
geom	The new feature geometry identifier (see namespace Pharm::FeatureGeometry).

◆ clearGeometry()

CDPL_PHARM_API void CDPL::Pharm::clearGeometry ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::GEOMETRY property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasGeometry()

CDPL_PHARM_API bool CDPL::Pharm::hasGeometry ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::GEOMETRY property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the geometry property is set, and false otherwise.

◆ getOrientation()

CDPL_PHARM_API const Math::Vector3D& CDPL::Pharm::getOrientation ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: A const reference to the 3D orientation vector.

◆ setOrientation()

CDPL_PHARM_API void CDPL::Pharm::setOrientation	(	Feature &	feature,
		const Math::Vector3D &	orient
	)

Sets the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature to orient.

Parameters

feature	The feature for which to set the property value.
orient	The new 3D orientation vector.

◆ clearOrientation()

CDPL_PHARM_API void CDPL::Pharm::clearOrientation ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::ORIENTATION property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasOrientation()

CDPL_PHARM_API bool CDPL::Pharm::hasOrientation ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::ORIENTATION property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the orientation property is set, and false otherwise.

◆ getLength()

CDPL_PHARM_API double CDPL::Pharm::getLength ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::LENGTH property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The length value.

◆ setLength()

CDPL_PHARM_API void CDPL::Pharm::setLength	(	Feature &	feature,
		double	length
	)

Sets the value of the Pharm::FeatureProperty::LENGTH property of the feature feature to length.

Parameters

feature	The feature for which to set the property value.
length	The new length value.

◆ clearLength()

CDPL_PHARM_API void CDPL::Pharm::clearLength ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::LENGTH property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasLength()

CDPL_PHARM_API bool CDPL::Pharm::hasLength ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::LENGTH property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the length property is set, and false otherwise.

◆ getTolerance()

CDPL_PHARM_API double CDPL::Pharm::getTolerance ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The tolerance value.

◆ setTolerance()

CDPL_PHARM_API void CDPL::Pharm::setTolerance	(	Feature &	feature,
		double	tol
	)

Sets the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature to tol.

Parameters

feature	The feature for which to set the property value.
tol	The new tolerance value.

◆ clearTolerance()

CDPL_PHARM_API void CDPL::Pharm::clearTolerance ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::TOLERANCE property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasTolerance()

CDPL_PHARM_API bool CDPL::Pharm::hasTolerance ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::TOLERANCE property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the tolerance property is set, and false otherwise.

◆ getWeight()

CDPL_PHARM_API double CDPL::Pharm::getWeight ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The weight value.

◆ setWeight()

CDPL_PHARM_API void CDPL::Pharm::setWeight	(	Feature &	feature,
		double	weight
	)

Sets the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature to weight.

Parameters

feature	The feature for which to set the property value.
weight	The new weight value.

◆ clearWeight()

CDPL_PHARM_API void CDPL::Pharm::clearWeight ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::WEIGHT property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasWeight()

CDPL_PHARM_API bool CDPL::Pharm::hasWeight ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::WEIGHT property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the weight property is set, and false otherwise.

◆ getSubstructure()

CDPL_PHARM_API const Chem::Fragment::SharedPointer& CDPL::Pharm::getSubstructure ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature (the underlying atoms/bonds).

Parameters

feature The feature for which to get the property value.

Returns: The stored feature substructure.

◆ setSubstructure()

CDPL_PHARM_API void CDPL::Pharm::setSubstructure	(	Feature &	feature,
		const Chem::Fragment::SharedPointer &	substruct
	)

Sets the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature to substruct.

Parameters

feature	The feature for which to set the property value.
substruct	The new feature substructure.

◆ clearSubstructure()

CDPL_PHARM_API void CDPL::Pharm::clearSubstructure ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasSubstructure()

CDPL_PHARM_API bool CDPL::Pharm::hasSubstructure ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::SUBSTRUCTURE property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the substructure property is set, and false otherwise.

◆ getEnvironmentResidueInfo() [1/2]

CDPL_PHARM_API std::string CDPL::Pharm::getEnvironmentResidueInfo ( const Feature & feature )

Generates a string describing the environment residues associated with the feature feature.

Parameters

feature The feature.

Returns: The generated environment residue info string.

Since: 1.3

◆ getEnvironmentResidueInfo() [2/2]

CDPL_PHARM_API std::string& CDPL::Pharm::getEnvironmentResidueInfo	(	const Feature &	feature,
		std::string &	info
	)

Generates a string describing the environment residues associated with the feature feature.

Parameters

feature	The feature.
info	Will store the generated environment residue info string.

Returns: A reference to info.

Since: 1.4

◆ getEnvironmentResidueAtomInfo() [1/2]

CDPL_PHARM_API std::string CDPL::Pharm::getEnvironmentResidueAtomInfo ( const Feature & feature )

Generates a string describing the environment residue atoms associated with the feature feature.

Parameters

feature The feature.

Returns: The generated environment residue atom info string.

Since: 1.4

◆ getEnvironmentResidueAtomInfo() [2/2]

CDPL_PHARM_API std::string& CDPL::Pharm::getEnvironmentResidueAtomInfo	(	const Feature &	feature,
		std::string &	info
	)

Generates a string describing the environment residue atoms associated with the feature feature.

Parameters

feature	The feature.
info	Will store the generated environment residue atom info string.

Returns: A reference to info.

Since: 1.4

◆ getEnvironmentSubstructure()

CDPL_PHARM_API const Chem::Fragment::SharedPointer& CDPL::Pharm::getEnvironmentSubstructure ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The stored environment substructure.

Since: 1.4

◆ setEnvironmentSubstructure()

CDPL_PHARM_API void CDPL::Pharm::setEnvironmentSubstructure	(	Feature &	feature,
		const Chem::Fragment::SharedPointer &	substruct
	)

Sets the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature to substruct.

Parameters

feature	The feature for which to set the property value.
substruct	The new environment substructure.

◆ clearEnvironmentSubstructure()

CDPL_PHARM_API void CDPL::Pharm::clearEnvironmentSubstructure ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasEnvironmentSubstructure()

CDPL_PHARM_API bool CDPL::Pharm::hasEnvironmentSubstructure ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::ENVIRONMENT_SUBSTRUCTURE property of the feature feature is set.

Parameters

feature The feature.

Returns: true if the environment substructure property is set, and false otherwise.

◆ getDisabledFlag()

CDPL_PHARM_API bool CDPL::Pharm::getDisabledFlag ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: true if the feature is flagged as disabled, and false otherwise.

◆ setDisabledFlag()

CDPL_PHARM_API void CDPL::Pharm::setDisabledFlag	(	Feature &	feature,
		bool	flag
	)

Sets the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature to flag.

Parameters

feature	The feature for which to set the property value.
flag	The new disabled flag value.

◆ clearDisabledFlag()

CDPL_PHARM_API void CDPL::Pharm::clearDisabledFlag ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasDisabledFlag()

CDPL_PHARM_API bool CDPL::Pharm::hasDisabledFlag ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::DISABLED_FLAG property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the disabled flag is set, and false otherwise.

◆ getOptionalFlag()

CDPL_PHARM_API bool CDPL::Pharm::getOptionalFlag ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: true if the feature is flagged as optional, and false otherwise.

◆ setOptionalFlag()

CDPL_PHARM_API void CDPL::Pharm::setOptionalFlag	(	Feature &	feature,
		bool	flag
	)

Sets the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature to flag.

Parameters

feature	The feature for which to set the property value.
flag	The new optional flag value.

◆ clearOptionalFlag()

CDPL_PHARM_API void CDPL::Pharm::clearOptionalFlag ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasOptionalFlag()

CDPL_PHARM_API bool CDPL::Pharm::hasOptionalFlag ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::OPTIONAL_FLAG property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the optional flag is set, and false otherwise.

◆ getHydrophobicity()

CDPL_PHARM_API double CDPL::Pharm::getHydrophobicity ( const Feature & feature )

Returns the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature.

Parameters

feature The feature for which to get the property value.

Returns: The hydrophobicity value.

◆ setHydrophobicity()

CDPL_PHARM_API void CDPL::Pharm::setHydrophobicity	(	Feature &	feature,
		double	hyd
	)

Sets the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature to hyd.

Parameters

feature	The feature for which to set the property value.
hyd	The new hydrophobicity value.

◆ clearHydrophobicity()

CDPL_PHARM_API void CDPL::Pharm::clearHydrophobicity ( Feature & feature )

Clears the value of the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature.

Parameters

feature The feature for which to clear the property value.

◆ hasHydrophobicity()

CDPL_PHARM_API bool CDPL::Pharm::hasHydrophobicity ( const Feature & feature )

Tells whether the Pharm::FeatureProperty::HYDROPHOBICITY property of the feature feature is set.

Parameters

feature The feature for which to query the property value.

Returns: true if the hydrophobicity property is set, and false otherwise.

◆ getFeatures()

CDPL_PHARM_API void CDPL::Pharm::getFeatures	(	FeatureSet &	ftr_set,
		const FeatureMapping &	mapping,
		bool	first
	)

Extracts features from mapping into the feature set ftr_set.

Parameters

ftr_set	The output feature set.
mapping	The feature mapping.
first	If `true`, the first feature of each mapping pair is added. Otherwise, the second feature.

◆ removePositionalDuplicates() [2/3]

CDPL_PHARM_API bool CDPL::Pharm::removePositionalDuplicates	(	FeatureSet &	ftr_set,
		double	pos_tol = `0.0`
	)

Removes features from the feature set ftr_set whose 3D position duplicates that of another feature of the same type.

Parameters

ftr_set	The feature set to clean (modified in place).
pos_tol	The positional tolerance below which two features are considered duplicates.

Returns: true if at least one feature was removed, and false otherwise.

Since: 1.2

◆ removeFeaturesWithType() [2/3]

CDPL_PHARM_API bool CDPL::Pharm::removeFeaturesWithType	(	FeatureSet &	ftr_set,
		unsigned int	type
	)

Removes features of the given type from the feature set ftr_set.

Parameters

ftr_set	The feature set to clean (modified in place).
type	The feature type to remove (see namespace Pharm::FeatureType).

Returns: true if at least one feature was removed, and false otherwise.

Since: 1.2

◆ prepareForPharmacophoreGeneration()

CDPL_PHARM_API void CDPL::Pharm::prepareForPharmacophoreGeneration	(	Chem::Molecule &	mol,
		bool	calc_hyd = `true`,
		bool	from_logp = `false`
	)

Prepares the molecule mol for downstream pharmacophore generation..

The molecule gets prepared by completing its hydrogens, perceiving the SSSR, ring flags, implicit H counts, hybridization states and aromaticity, generating 3D coordinates for newly added hydrogens and (optionally) calculating per-atom hydrophobicities. Failures of the hydrogen 3D-coordinate or residue sequence info derivation steps are silently caught and ignored. All other exceptions propagate.

Parameters

mol	The molecule to prepare (modified in place).
calc_hyd	If `true`, atom hydrophobicities are also calculated and stored as atom properties.
from_logp	If `true` and calc_hyd is set, the hydrophobicities are derived from the XLogP [XLOGP] atom contributions instead of the Greene algorithm [CATA].

◆ removePositionalDuplicates() [3/3]

CDPL_PHARM_API bool CDPL::Pharm::removePositionalDuplicates	(	Pharmacophore &	pharm,
		double	pos_tol = `0.0`
	)

Removes positional duplicate features from the pharmacophore pharm in place.

Two features count as duplicates if they have identical type and their position vectors either match exactly (pos_tol ≤ 0) or lie within pos_tol from each other. When a duplicate is detected, the feature with the larger position tolerance is retained.

Parameters

pharm	The pharmacophore to deduplicate.
pos_tol	The position-equality tolerance in Ångstrom. Values ≤ 0 require an exact position match.

Returns: true if at least one feature was removed, and false otherwise.

Since: 1.2

◆ removeFeaturesWithType() [3/3]

CDPL_PHARM_API bool CDPL::Pharm::removeFeaturesWithType	(	Pharmacophore &	pharm,
		unsigned int	type
	)

Removes every feature in the pharmacophore pharm whose type matches type.

Parameters

pharm	The pharmacophore to filter.
type	The feature type to remove (see namespace Pharm::FeatureType).

Returns: true if at least one feature was removed, and false otherwise.

Since: 1.2

◆ generateInteractionPharmacophore()

CDPL_PHARM_API void CDPL::Pharm::generateInteractionPharmacophore	(	Pharmacophore &	pharm,
		const FeatureMapping &	iactions,
		bool	append = `false`
	)

Builds an interaction pharmacophore from the supplied feature mapping.

At least one output feature per interacting ligand feature is emitted. For H-bond donor/acceptor and X-bonding interactions separate vector features are output. The environment substructure properties of the output features are set to the (combined) substructures covered by the interacting target features.

Parameters

pharm	The output pharmacophore where to add the generated features.
iactions	The feature mapping describing the interactions.
append	If `false`, the pharmacophore pharm is cleared before any features are added.

◆ createExclusionVolumes() [1/2]

CDPL_PHARM_API void CDPL::Pharm::createExclusionVolumes	(	Pharmacophore &	pharm,
		const Chem::AtomContainer &	cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		double	tol = `0.0`,
		double	min_dist = `0.0`,
		bool	rel_dist = `true`,
		bool	append = `true`
	)

Creates exclusion volume features at the 3D positions of the atoms in cntnr and appends them to the pharmacophore pharm.

Parameters

pharm	The pharmacophore receiving the new exclusion volumes.
cntnr	The atom container providing the seed positions.
coords_func	The function returning the 3D coordinates of an atom.
tol	The position tolerance to assign to new exclusion volumes (if ≤ 0 the per-atom VdW radius is used).
min_dist	Minimum distance (rel_dist controls absolute vs. tolerance-corrected) that a new exclusion volume must keep from existing ones.
rel_dist	If `true`, the per-pair tolerance sum is subtracted from the pair distance before testing against min_dist. Otherwise, the absolute distance is tested.
append	If `false`, the pharmacophore pharm is cleared before any exclusion volumes are added.

◆ createExclusionVolumes() [2/2]

CDPL_PHARM_API void CDPL::Pharm::createExclusionVolumes	(	Pharmacophore &	pharm,
		const FeatureContainer &	cntnr,
		double	tol = `0.0`,
		double	min_dist = `0.0`,
		bool	rel_dist = `true`,
		bool	append = `true`
	)

Creates exclusion volume features at the 3D positions of the features in cntnr and appends them to the pharmacophore pharm.

Parameters

pharm	The pharmacophore receiving the new exclusion volumes.
cntnr	The feature container providing the seed positions.
tol	The position tolerance to assign to new exclusion volumes (if ≤ 0 the per-feature tolerance is used).
min_dist	Minimum distance (rel_dist controls absolute vs. tolerance-corrected) that a new exclusion volume must keep from existing ones.
rel_dist	If `true`, the per-pair tolerance sum is subtracted from the pair distance before testing against min_dist. Otherwise, the absolute distance is tested.
append	If `false`, the pharmacophore pharm is cleared before any exclusion volumes are added.

◆ removeExclusionVolumesWithClashes()

CDPL_PHARM_API bool CDPL::Pharm::removeExclusionVolumesWithClashes	(	Pharmacophore &	pharm,
		const Chem::AtomContainer &	cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		double	vdw_scaling_fact = `1.0`
	)

Removes every exclusion volume feature from the pharmacophore pharm whose tolerance sphere clashes with any atom of cntnr.

Parameters

pharm	The pharmacophore to filter.
cntnr	The atom container providing the clash partners.
coords_func	The function returning the 3D coordinates of an atom.
vdw_scaling_fact	Scaling factor applied to the per-atom Van der Waals radius during the clash test.

Returns: true if at least one exclusion volume was removed, and false otherwise.

◆ resizeExclusionVolumesWithClashes()

CDPL_PHARM_API bool CDPL::Pharm::resizeExclusionVolumesWithClashes	(	Pharmacophore &	pharm,
		const Chem::AtomContainer &	cntnr,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		double	vdw_scaling_fact = `1.0`
	)

Shrinks the tolerance of every exclusion volume feature in the pharmacophore pharm whose tolerance sphere clashes with any atom of cntnr.

If the resulting tolerance falls below 0.25 then the exclusion volume feature is removed.

Parameters

pharm	The pharmacophore to modify.
cntnr	The atom container providing the clash partners.
coords_func	The function returning the 3D coordinates of an atom.
vdw_scaling_fact	Scaling factor applied to the per-atom Van der Waals radius during the clash test.

Returns: true if at least one exclusion volume was resized or removed, and false otherwise.

◆ getFeatureTypeString()

CDPL_PHARM_API const std::string& CDPL::Pharm::getFeatureTypeString ( unsigned int ftr_type )

Returns a concise human-readable string (e.g. "HBD" for H-bond donor) for the given numeric feature type identifier ftr_type.

Parameters

ftr_type The feature type identifier (see namespace Pharm::FeatureType).

Returns: A const reference to the feature type string.

Namespaces

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ CDFBZ2FeatureContainerOutputHandler

◆ CDFBZ2FeatureContainerWriter

◆ CDFBZ2PharmacophoreInputHandler

◆ CDFBZ2PharmacophoreReader

◆ CDFFeatureContainerOutputHandler

◆ CDFGZFeatureContainerOutputHandler

◆ CDFGZFeatureContainerWriter

◆ CDFGZPharmacophoreInputHandler

◆ CDFGZPharmacophoreReader

◆ CDFPharmacophoreInputHandler

◆ Feature3DCoordinatesFunction

◆ FeatureCompareFunction

◆ FeatureContainerWriter

◆ PharmacophoreReader

◆ PMLFeatureContainerOutputHandler

◆ PMLPharmacophoreInputHandler

Function Documentation

◆ getStrictErrorCheckingParameter()

◆ setStrictErrorCheckingParameter()

◆ hasStrictErrorCheckingParameter()

◆ clearStrictErrorCheckingParameter()

◆ getCDFOutputSinglePrecisionFloatsParameter()

◆ setCDFOutputSinglePrecisionFloatsParameter()

◆ hasCDFOutputSinglePrecisionFloatsParameter()

◆ clearCDFOutputSinglePrecisionFloatsParameter()

◆ getPSDCreationModeParameter()

◆ setPSDCreationModeParameter()

◆ hasPSDCreationModeParameter()

◆ clearPSDCreationModeParameter()

◆ getPSDAllowDuplicatesParameter()

◆ setPSDAllowDuplicatesParameter()

◆ hasPSDAllowDuplicatesParameter()

◆ clearPSDAllowDuplicatesParameter()

◆ getName()

◆ setName()

◆ clearName()

◆ hasName()

◆ getFeatureCount() [1/2]

◆ getFeatureCount() [2/2]

◆ generateFeatureTypeHistogram()

◆ generateFeatureTypeHistogramString()

◆ clearOrientations()

◆ removePositionalDuplicates() [1/3]

◆ removeFeaturesWithType() [1/3]

◆ transform3DCoordinates()

◆ checkForExclusionVolumeClashes()

◆ getFeatureAtoms()

◆ getType()

◆ setType()

◆ clearType()

◆ hasType()

◆ getGeometry()

◆ setGeometry()

◆ clearGeometry()

◆ hasGeometry()

◆ getOrientation()

◆ setOrientation()

◆ clearOrientation()

◆ hasOrientation()

◆ getLength()

◆ setLength()

◆ clearLength()

◆ hasLength()

◆ getTolerance()

◆ setTolerance()

◆ clearTolerance()

◆ hasTolerance()

◆ getWeight()

◆ setWeight()

◆ clearWeight()

◆ hasWeight()

◆ getSubstructure()

◆ setSubstructure()

◆ clearSubstructure()