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

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	BoolDoubleFunctor

class	BoolFeature2Functor

class	BoolFeature2Matrix4DFunctor

class	BoolFeature4Functor

class	BoolFeatureFunctor

class	BoolSearchHitDoubleFunctor

class	BoolSizeType2Functor

class	CDFBZ2FeatureContainerOutputHandler
	Handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL. More...

class	CDFBZ2FeatureContainerWriter
	Writer for bzip2-compressed feature container data in the native I/O format of the CDPL. More...

class	CDFBZ2PharmacophoreInputHandler
	Handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...

class	CDFBZ2PharmacophoreReader
	Reader for bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...

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

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

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

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

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

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

class	CDFPharmacophoreInputHandler
	Handler for the input of pharmacophore 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	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	CompoundPharmacophoreReader
	Composite Base.DataReader that aggregates several underlying readers and presents their records as one contiguous record stream. More...

class	ControlParameter
	Provides keys for built-in control-parameters. More...

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

class	DataFormat
	Provides preinitialized Base.DataFormat objects for all supported data formats. 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	DoubleDouble2Functor

class	DoubleDoubleFunctor

class	DoubleFeature2Functor

class	DoubleFeature2Matrix4DFunctor

class	DoubleFeature2UIntFunctor

class	DoubleFeatureFunctor

class	DoubleSearchHitFunctor

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

class	Feature3DCoordinatesFunction
	Generic wrapper class used to store a user-defined Pharm.Feature 3D-coordinates function. More...

class	FeatureContainer
	Abstract base class for containers holding a sequence of Pharm.Feature objects with associated properties (e.g. More...

class	FeatureContainerIOManager
	Singleton class that serves as a global registry for Pharm.FeatureContainerInputHandler and Pharm.FeatureContainerOutputHandler implementation instances. More...

class	FeatureContainerOutputHandler
	Factory interface providing methods for the creation of Pharm.FeatureContainerWriterBase instances for data output in a particular storage format. More...

class	FeatureContainerProperty
	Provides keys for built-in Pharm.FeatureContainer properties. More...

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

class	FeatureContainerWriter
	Writer for pharmacophore data in any supported format. More...

class	FeatureContainerWriterBase
	Interface for writing data objects of type Pharm.FeatureContainer to an arbitrary data sink. 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. More...

class	FeatureGeometry
	Provides constants for the specification of the generic geometry of a pharmacophore feature. 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. 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	FeatureProperty
	Provides keys for built-in Pharm.Feature properties. More...

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

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

class	FeatureType
	Provides constants for the specification of the generic type of a pharmacophore feature. 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	FileCDFBZ2FeatureContainerWriter

class	FileCDFBZ2PharmacophoreReader

class	FileCDFFeatureContainerWriter

class	FileCDFGZFeatureContainerWriter

class	FileCDFGZPharmacophoreReader

class	FileCDFPharmacophoreReader

class	FilePMLFeatureContainerWriter

class	FilePMLPharmacophoreReader

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-hydrogen-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	PMLFeatureContainerOutputHandler
	Handler for the output of pharmacophore data in the native I/O format of LigandScout. More...

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

class	PMLPharmacophoreInputHandler
	Handler for the input of pharmacophore 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	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	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	PharmacophoreIOManager
	Singleton class that serves as a global registry for Pharm.PharmacophoreInputHandler and Pharm.PharmacophoreOutputHandler implementation instances. More...

class	PharmacophoreInputHandler
	Factory interface providing methods for the creation of Pharm.PharmacophoreReaderBase instances for reading data provided in a particular storage format. More...

class	PharmacophoreReader
	Reader for pharmacophore data in any supported format. More...

class	PharmacophoreReaderBase
	Interface for reading data objects of type Pharm.Pharmacophore from an arbitrary data source. More...

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

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	TopologicalFeatureAlignment

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...

Functions
None	setDisabledFlag (Feature feature, bool flag)
	Sets the value of the Pharm.FeatureProperty.DISABLED_FLAG property of the feature feature to flag. More...

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

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

None	clearDisabledFlag (Feature feature)
	Clears the value of the Pharm.FeatureProperty.DISABLED_FLAG property of the feature feature. More...

str	getEnvironmentResidueAtomInfo (Feature feature)
	Generates a string describing the per-atom residue environment of the feature feature (residue names and atom names of interacting pocket atoms). More...

str	getEnvironmentResidueInfo (Feature feature)
	Generates a string describing the residue environment of the feature feature (residue names of interacting pocket residues). More...

None	setEnvironmentSubstructure (Feature feature, Chem.Fragment substruct)
	Sets the value of the Pharm.FeatureProperty.ENVIRONMENT_SUBSTRUCTURE property of the feature feature to substruct. More...

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

Chem.Fragment	getEnvironmentSubstructure (Feature feature)
	Returns the value of the Pharm.FeatureProperty.ENVIRONMENT_SUBSTRUCTURE property of the feature feature (interacting pocket residues). More...

None	clearEnvironmentSubstructure (Feature feature)
	Clears the value of the Pharm.FeatureProperty.ENVIRONMENT_SUBSTRUCTURE property of the feature feature. More...

None	getFeatureAtoms (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...

int	getFeatureCount (FeatureContainer cntnr)
	Returns the total number of features stored in the feature container cntnr. More...

int	getFeatureCount (FeatureContainer cntnr, int type)
	Returns the number of features in the feature container cntr whose type matches type. More...

str	getFeatureTypeString (int ftr_type)
	Returns a concise human-readable string (e.g. More...

None	getFeatures (FeatureSet ftr_set, FeatureMapping mapping, bool first)
	Extracts features from mapping into the feature set ftr_set. More...

None	setGeometry (Feature feature, int geom)
	Sets the value of the Pharm.FeatureProperty.GEOMETRY property of the feature feature to geom. More...

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

int	getGeometry (Feature feature)
	Returns the value of the Pharm.FeatureProperty.GEOMETRY property of the feature feature. More...

None	clearGeometry (Feature feature)
	Clears the value of the Pharm.FeatureProperty.GEOMETRY property of the feature feature. More...

None	setHydrophobicity (Feature feature, float hyd)
	Sets the value of the Pharm.FeatureProperty.HYDROPHOBICITY property of the feature feature to hyd. More...

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

float	getHydrophobicity (Feature feature)
	Returns the value of the Pharm.FeatureProperty.HYDROPHOBICITY property of the feature feature. More...

None	clearHydrophobicity (Feature feature)
	Clears the value of the Pharm.FeatureProperty.HYDROPHOBICITY property of the feature feature. More...

None	setLength (Feature feature, float length)
	Sets the value of the Pharm.FeatureProperty.LENGTH property of the feature feature to length. More...

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

float	getLength (Feature feature)
	Returns the value of the Pharm.FeatureProperty.LENGTH property of the feature feature. More...

None	clearLength (Feature feature)
	Clears the value of the Pharm.FeatureProperty.LENGTH property of the feature feature. More...

None	setName (FeatureContainer cntnr, str name)
	Sets the value of the Pharm.FeatureContainerProperty.NAME property of the feature container cntnr to name. More...

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

str	getName (FeatureContainer cntnr)
	Returns the value of the Pharm.FeatureContainerProperty.NAME property of the feature container cntnr. More...

None	clearName (FeatureContainer cntnr)
	Clears the value of the Pharm.FeatureContainerProperty.NAME property of the feature container cntnr. More...

None	setOptionalFlag (Feature feature, bool flag)
	Sets the value of the Pharm.FeatureProperty.OPTIONAL_FLAG property of the feature feature to flag. More...

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

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

None	clearOptionalFlag (Feature feature)
	Clears the value of the Pharm.FeatureProperty.OPTIONAL_FLAG property of the feature feature. More...

None	setOrientation (Feature feature, Math.Vector3D orient)
	Sets the value of the Pharm.FeatureProperty.ORIENTATION property of the feature feature to orient. More...

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

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

None	clearOrientation (Feature feature)
	Clears the value of the Pharm.FeatureProperty.ORIENTATION property of the feature feature. More...

None	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...

None	setSubstructure (Feature feature, Chem.Fragment substruct)
	Sets the value of the Pharm.FeatureProperty.SUBSTRUCTURE property of the feature feature to substruct. More...

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

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

None	clearSubstructure (Feature feature)
	Clears the value of the Pharm.FeatureProperty.SUBSTRUCTURE property of the feature feature. More...

None	setTolerance (Feature feature, float tol)
	Sets the value of the Pharm.FeatureProperty.TOLERANCE property of the feature feature to tol. More...

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

float	getTolerance (Feature feature)
	Returns the value of the Pharm.FeatureProperty.TOLERANCE property of the feature feature. More...

None	clearTolerance (Feature feature)
	Clears the value of the Pharm.FeatureProperty.TOLERANCE property of the feature feature. More...

None	setType (Feature feature, int type)
	Sets the value of the Pharm.FeatureProperty.TYPE property of the feature feature to type. More...

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

int	getType (Feature feature)
	Returns the value of the Pharm.FeatureProperty.TYPE property of the feature feature. More...

None	clearType (Feature feature)
	Clears the value of the Pharm.FeatureProperty.TYPE property of the feature feature. More...

None	setWeight (Feature feature, float weight)
	Sets the value of the Pharm.FeatureProperty.WEIGHT property of the feature feature to weight. More...

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

float	getWeight (Feature feature)
	Returns the value of the Pharm.FeatureProperty.WEIGHT property of the feature feature. More...

None	clearWeight (Feature feature)
	Clears the value of the Pharm.FeatureProperty.WEIGHT property of the feature feature. More...

bool	checkForExclusionVolumeClashes (FeatureContainer ftr_cntnr, Chem.AtomContainer atom_cntnr, Chem.Atom3DCoordinatesFunction coords_func, Math.Matrix4D xform, float 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...

None	createExclusionVolumes (Pharmacophore pharm, Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, float tol=0.0, float 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...

None	createExclusionVolumes (Pharmacophore pharm, FeatureContainer cntnr, float tol=0.0, float 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...

None	generateFeatureTypeHistogram (FeatureContainer cntnr, FeatureTypeHistogram hist, bool append=False)
	Computes a per-feature type frequency histogram of the features in the feature container cntr. More...

str	generateFeatureTypeHistogramString (FeatureContainer cntnr)

None	generateInteractionPharmacophore (Pharmacophore pharm, FeatureMapping iactions, bool append=False)
	Builds an interaction pharmacophore from the supplied feature mapping. More...

None	prepareForPharmacophoreGeneration (Chem.Molecule mol, bool calc_hyd=True, bool from_logp=False)
	Prepares the molecule mol for downstream pharmacophore generation. More...

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

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

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

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

bool	removePositionalDuplicates (FeatureContainer cntnr, FeatureSet tgt_set, float 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...

bool	removePositionalDuplicates (FeatureSet ftr_set, float 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...

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

bool	resizeExclusionVolumesWithClashes (Pharmacophore pharm, Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, float 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...

None	transform3DCoordinates (FeatureContainer cntnr, 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...

None	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...

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

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

None	clearCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
	Removes the Pharm.ControlParameter.CDF_OUTPUT_SINGLE_PRECISION_FLOATS parameter from cntnr. More...

None	setPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr, bool allow)
	Sets the value of the Pharm.ControlParameter.PSD_ALLOW_DUPLICATES parameter of cntnr to allow. More...

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

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

None	clearPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr)
	Removes the Pharm.ControlParameter.PSD_ALLOW_DUPLICATES parameter from cntnr. More...

None	setPSDCreationModeParameter (Base.ControlParameterContainer cntnr, Mode mode)
	Sets the value of the Pharm.ControlParameter.PSD_CREATION_MODE parameter of cntnr to mode. More...

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

Mode	getPSDCreationModeParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Pharm.ControlParameter.PSD_CREATION_MODE parameter stored in cntnr. More...

None	clearPSDCreationModeParameter (Base.ControlParameterContainer cntnr)
	Removes the Pharm.ControlParameter.PSD_CREATION_MODE parameter from cntnr. More...

None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
	Sets the value of the Pharm.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict. More...

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

bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Pharm.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr. More...

None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Removes the Pharm.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr. More...

Detailed Description

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

Function Documentation

◆ setDisabledFlag()

None 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.

◆ hasDisabledFlag()

bool CDPL.Pharm.hasDisabledFlag ( 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.

◆ getDisabledFlag()

bool CDPL.Pharm.getDisabledFlag ( 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.

◆ clearDisabledFlag()

None 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.

◆ getEnvironmentResidueAtomInfo()

str CDPL.Pharm.getEnvironmentResidueAtomInfo ( Feature feature )

Generates a string describing the per-atom residue environment of the feature feature (residue names and atom names of interacting pocket atoms).

Parameters

feature The feature.

Returns: The generated environment residue atom info string.

Since: 1.4

◆ getEnvironmentResidueInfo()

str CDPL.Pharm.getEnvironmentResidueInfo ( Feature feature )

Generates a string describing the residue environment of the feature feature (residue names of interacting pocket residues).

Parameters

feature The feature.

Returns: The generated environment residue info string.

Since: 1.3

◆ setEnvironmentSubstructure()

None CDPL.Pharm.setEnvironmentSubstructure	(	Feature	feature,
		Chem.Fragment	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.

◆ hasEnvironmentSubstructure()

bool CDPL.Pharm.hasEnvironmentSubstructure ( 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.

◆ getEnvironmentSubstructure()

Chem.Fragment CDPL.Pharm.getEnvironmentSubstructure ( Feature feature )

Returns the value of the Pharm.FeatureProperty.ENVIRONMENT_SUBSTRUCTURE property of the feature feature (interacting pocket residues).

Parameters

feature The feature for which to get the property value.

Returns: A shared reference to the environment substructure.

Since: 1.4

◆ clearEnvironmentSubstructure()

None 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.

◆ getFeatureAtoms()

None CDPL.Pharm.getFeatureAtoms	(	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.

◆ getFeatureCount() [1/2]

int CDPL.Pharm.getFeatureCount ( 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]

int CDPL.Pharm.getFeatureCount	(	FeatureContainer	cntnr,
		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.

◆ getFeatureTypeString()

str CDPL.Pharm.getFeatureTypeString ( 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 reference to the feature type string.

◆ getFeatures()

None CDPL.Pharm.getFeatures	(	FeatureSet	ftr_set,
		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.

◆ setGeometry()

None CDPL.Pharm.setGeometry	(	Feature	feature,
		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).

◆ hasGeometry()

bool CDPL.Pharm.hasGeometry ( 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.

◆ getGeometry()

int CDPL.Pharm.getGeometry ( 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).

◆ clearGeometry()

None 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.

◆ setHydrophobicity()

None CDPL.Pharm.setHydrophobicity	(	Feature	feature,
		float	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.

◆ hasHydrophobicity()

bool CDPL.Pharm.hasHydrophobicity ( 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.

◆ getHydrophobicity()

float CDPL.Pharm.getHydrophobicity ( 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.

◆ clearHydrophobicity()

None 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.

◆ setLength()

None CDPL.Pharm.setLength	(	Feature	feature,
		float	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.

◆ hasLength()

bool CDPL.Pharm.hasLength ( 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.

◆ getLength()

float CDPL.Pharm.getLength ( 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.

◆ clearLength()

None 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.

◆ setName()

None CDPL.Pharm.setName	(	FeatureContainer	cntnr,
		str	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.

◆ hasName()

bool CDPL.Pharm.hasName ( 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.

◆ getName()

str CDPL.Pharm.getName ( 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).

◆ clearName()

None 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.

◆ setOptionalFlag()

None 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.

◆ hasOptionalFlag()

bool CDPL.Pharm.hasOptionalFlag ( 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.

◆ getOptionalFlag()

bool CDPL.Pharm.getOptionalFlag ( 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.

◆ clearOptionalFlag()

None 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.

◆ setOrientation()

None CDPL.Pharm.setOrientation	(	Feature	feature,
		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.

◆ hasOrientation()

bool CDPL.Pharm.hasOrientation ( 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.

◆ getOrientation()

Math.Vector3D CDPL.Pharm.getOrientation ( 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 reference to the 3D orientation vector.

◆ clearOrientation()

None 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.

◆ clearOrientations()

None 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

◆ setSubstructure()

None CDPL.Pharm.setSubstructure	(	Feature	feature,
		Chem.Fragment	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.

◆ hasSubstructure()

bool CDPL.Pharm.hasSubstructure ( 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.

◆ getSubstructure()

Chem.Fragment CDPL.Pharm.getSubstructure ( 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: A shared reference to the feature substructure.

◆ clearSubstructure()

None 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.

◆ setTolerance()

None CDPL.Pharm.setTolerance	(	Feature	feature,
		float	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.

◆ hasTolerance()

bool CDPL.Pharm.hasTolerance ( 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.

◆ getTolerance()

float CDPL.Pharm.getTolerance ( 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.

◆ clearTolerance()

None 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.

◆ setType()

None CDPL.Pharm.setType	(	Feature	feature,
		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).

◆ hasType()

bool CDPL.Pharm.hasType ( 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.

◆ getType()

int CDPL.Pharm.getType ( 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).

◆ clearType()

None 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.

◆ setWeight()

None CDPL.Pharm.setWeight	(	Feature	feature,
		float	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.

◆ hasWeight()

bool CDPL.Pharm.hasWeight ( 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.

◆ getWeight()

float CDPL.Pharm.getWeight ( 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.

◆ clearWeight()

None 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.

◆ checkForExclusionVolumeClashes()

bool CDPL.Pharm.checkForExclusionVolumeClashes	(	FeatureContainer	ftr_cntnr,
		Chem.AtomContainer	atom_cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		Math.Matrix4D	xform,
		float	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 4x4 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.

◆ createExclusionVolumes() [1/2]

None CDPL.Pharm.createExclusionVolumes	(	Pharmacophore	pharm,
		Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	tol = `0.0`,
		float	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]

None CDPL.Pharm.createExclusionVolumes	(	Pharmacophore	pharm,
		FeatureContainer	cntnr,
		float	tol = `0.0`,
		float	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.

◆ generateFeatureTypeHistogram()

None CDPL.Pharm.generateFeatureTypeHistogram	(	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 → count).
append	If `False`, hist is cleared before the counts are accumulated.

◆ generateFeatureTypeHistogramString()

str CDPL.Pharm.generateFeatureTypeHistogramString ( FeatureContainer cntnr )

Parameters

cntnr

Returns

◆ generateInteractionPharmacophore()

None CDPL.Pharm.generateInteractionPharmacophore	(	Pharmacophore	pharm,
		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.

◆ prepareForPharmacophoreGeneration()

None 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].

◆ removeExclusionVolumesWithClashes()

bool CDPL.Pharm.removeExclusionVolumesWithClashes	(	Pharmacophore	pharm,
		Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	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.

◆ removeFeaturesWithType() [1/3]

bool CDPL.Pharm.removeFeaturesWithType	(	FeatureContainer	cntnr,
		FeatureSet	tgt_set,
		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

◆ removeFeaturesWithType() [2/3]

bool CDPL.Pharm.removeFeaturesWithType	(	FeatureSet	ftr_set,
		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

◆ removeFeaturesWithType() [3/3]

bool CDPL.Pharm.removeFeaturesWithType	(	Pharmacophore	pharm,
		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

◆ removePositionalDuplicates() [1/3]

bool CDPL.Pharm.removePositionalDuplicates	(	FeatureContainer	cntnr,
		FeatureSet	tgt_set,
		float	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

◆ removePositionalDuplicates() [2/3]

bool CDPL.Pharm.removePositionalDuplicates	(	FeatureSet	ftr_set,
		float	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

◆ removePositionalDuplicates() [3/3]

bool CDPL.Pharm.removePositionalDuplicates	(	Pharmacophore	pharm,
		float	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

◆ resizeExclusionVolumesWithClashes()

bool CDPL.Pharm.resizeExclusionVolumesWithClashes	(	Pharmacophore	pharm,
		Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	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.

◆ transform3DCoordinates()

None CDPL.Pharm.transform3DCoordinates	(	FeatureContainer	cntnr,
		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 4x4 transformation matrix.

◆ setCDFOutputSinglePrecisionFloatsParameter()

None 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()

bool CDPL.Pharm.hasCDFOutputSinglePrecisionFloatsParameter ( 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

◆ getCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Pharm.getCDFOutputSinglePrecisionFloatsParameter ( 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

◆ clearCDFOutputSinglePrecisionFloatsParameter()

None 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

◆ setPSDAllowDuplicatesParameter()

None 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()

bool CDPL.Pharm.hasPSDAllowDuplicatesParameter ( 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.

◆ getPSDAllowDuplicatesParameter()

bool CDPL.Pharm.getPSDAllowDuplicatesParameter ( 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.

◆ clearPSDAllowDuplicatesParameter()

None CDPL.Pharm.clearPSDAllowDuplicatesParameter ( Base.ControlParameterContainer cntnr )

Removes the Pharm.ControlParameter.PSD_ALLOW_DUPLICATES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ setPSDCreationModeParameter()

None CDPL.Pharm.setPSDCreationModeParameter	(	Base.ControlParameterContainer	cntnr,
		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()

bool CDPL.Pharm.hasPSDCreationModeParameter ( 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.

◆ getPSDCreationModeParameter()

Mode CDPL.Pharm.getPSDCreationModeParameter ( 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.

◆ clearPSDCreationModeParameter()

None CDPL.Pharm.clearPSDCreationModeParameter ( Base.ControlParameterContainer cntnr )

Removes the Pharm.ControlParameter.PSD_CREATION_MODE parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ setStrictErrorCheckingParameter()

None 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()

bool CDPL.Pharm.hasStrictErrorCheckingParameter ( 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.

◆ getStrictErrorCheckingParameter()

bool CDPL.Pharm.getStrictErrorCheckingParameter ( 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.

◆ clearStrictErrorCheckingParameter()

None CDPL.Pharm.clearStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

Removes the Pharm.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr The control-parameter container.

Classes

Functions

Detailed Description

Function Documentation

◆ setDisabledFlag()

◆ hasDisabledFlag()

◆ getDisabledFlag()

◆ clearDisabledFlag()

◆ getEnvironmentResidueAtomInfo()

◆ getEnvironmentResidueInfo()

◆ setEnvironmentSubstructure()

◆ hasEnvironmentSubstructure()

◆ getEnvironmentSubstructure()

◆ clearEnvironmentSubstructure()

◆ getFeatureAtoms()

◆ getFeatureCount() [1/2]

◆ getFeatureCount() [2/2]

◆ getFeatureTypeString()

◆ getFeatures()

◆ setGeometry()

◆ hasGeometry()

◆ getGeometry()

◆ clearGeometry()

◆ setHydrophobicity()

◆ hasHydrophobicity()

◆ getHydrophobicity()

◆ clearHydrophobicity()

◆ setLength()

◆ hasLength()

◆ getLength()

◆ clearLength()

◆ setName()

◆ hasName()

◆ getName()

◆ clearName()

◆ setOptionalFlag()

◆ hasOptionalFlag()

◆ getOptionalFlag()

◆ clearOptionalFlag()

◆ setOrientation()

◆ hasOrientation()

◆ getOrientation()

◆ clearOrientation()

◆ clearOrientations()

◆ setSubstructure()

◆ hasSubstructure()

◆ getSubstructure()

◆ clearSubstructure()

◆ setTolerance()

◆ hasTolerance()

◆ getTolerance()

◆ clearTolerance()

◆ setType()

◆ hasType()

◆ getType()

◆ clearType()

◆ setWeight()

◆ hasWeight()

◆ getWeight()

◆ clearWeight()

◆ checkForExclusionVolumeClashes()

◆ createExclusionVolumes() [1/2]

◆ createExclusionVolumes() [2/2]

◆ generateFeatureTypeHistogram()

◆ generateFeatureTypeHistogramString()

◆ generateInteractionPharmacophore()

◆ prepareForPharmacophoreGeneration()

◆ removeExclusionVolumesWithClashes()

◆ removeFeaturesWithType() [1/3]

◆ removeFeaturesWithType() [2/3]

◆ removeFeaturesWithType() [3/3]

◆ removePositionalDuplicates() [1/3]

◆ removePositionalDuplicates() [2/3]

◆ removePositionalDuplicates() [3/3]

◆ resizeExclusionVolumesWithClashes()

◆ transform3DCoordinates()

◆ setCDFOutputSinglePrecisionFloatsParameter()

◆ hasCDFOutputSinglePrecisionFloatsParameter()

◆ getCDFOutputSinglePrecisionFloatsParameter()

◆ clearCDFOutputSinglePrecisionFloatsParameter()