CDPL.Pharm Package Reference

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

Classes
class	AromaticFeatureGenerator
	AromaticFeatureGenerator. More...
class	BasicFeature
	BasicFeature. More...
class	BasicPharmacophore
	BasicPharmacophore. More...
class	BoolDoubleFunctor
class	BoolFeature2Functor
class	BoolFeature2Matrix4DFunctor
class	BoolFeature4Functor
class	BoolFeatureFunctor
class	BoolSearchHitDoubleFunctor
class	BoolSizeType2Functor
class	CDFBZ2FeatureContainerOutputHandler
	A handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL. More...
class	CDFBZ2FeatureContainerWriter
class	CDFBZ2PharmacophoreInputHandler
	A handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...
class	CDFBZ2PharmacophoreReader
class	CDFFeatureContainerOutputHandler
	A handler for the output of feature container data in the native I/O format of the CDPL. More...
class	CDFFeatureContainerWriter
	A writer for feature container data in the native I/O format of the CDPL. More...
class	CDFGZFeatureContainerOutputHandler
	A handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL. More...
class	CDFGZFeatureContainerWriter
class	CDFGZPharmacophoreInputHandler
	A handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL. More...
class	CDFGZPharmacophoreReader
class	CDFPharmacophoreInputHandler
	A handler for the input of pharmacophore data in the native I/O format of the CDPL. More...
class	CDFPharmacophoreReader
	A reader for pharmacophore data in the native I/O format of the CDPL. More...
class	CationPiInteractionConstraint
	CationPiInteractionConstraint. More...
class	CationPiInteractionScore
	CationPiInteractionScore. More...
class	CompoundPharmacophoreReader
	CompoundDataReader. 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
	DefaultInteractionAnalyzer. More...
class	DefaultPharmacophoreGenerator
	DefaultPharmacophoreGenerator. More...
class	DoubleDouble2Functor
class	DoubleDoubleFunctor
class	DoubleFeature2Functor
class	DoubleFeature2Matrix4DFunctor
class	DoubleFeature2UIntFunctor
class	DoubleFeatureFunctor
class	DoubleSearchHitFunctor
class	Feature
	Feature. More...
class	Feature3DCoordinatesFunction
	A generic wrapper class used to store a user-defined Pharm.Feature 3D-coordinates function. More...
class	FeatureContainer
	FeatureContainer. More...
class	FeatureContainerIOManager
	A singleton class that serves as a global registry for Pharm.FeatureContainerInputHandler and Pharm.FeatureContainerOutputHandler implementation instances. More...
class	FeatureContainerOutputHandler
	A 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
	An interface for writing data objects of type Pharm.FeatureContainer to an arbitrary data sink. More...
class	FeatureDistanceConstraint
	FeatureDistanceConstraint. More...
class	FeatureDistanceScore
	FeatureDistanceScore. More...
class	FeatureGenerator
	FeatureGenerator. More...
class	FeatureGeometry
	Provides constants for the specification of the generic geometry of a pharmacophore feature. More...
class	FeatureGeometryMatchFunctor
	FeatureGeometryMatchFunctor. More...
class	FeatureInteractionScore
	FeatureInteractionScore. More...
class	FeatureInteractionScoreCombiner
	FeatureInteractionScoreCombiner. More...
class	FeatureMapping
	A data type for the storage and lookup of arbitrary feature to feature mappings. More...
class	FeaturePairDistanceMatchFunctor
	FeaturePairDistanceMatchFunctor. More...
class	FeaturePositionMatchFunctor
	FeaturePositionMatchFunctor. 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
	FeatureSet. More...
class	FeatureType
	Provides constants for the specification of the generic type of a pharmacophore feature. More...
class	FeatureTypeHistogram
	A data type for the storage of feature type histograms of pharmacophores. More...
class	FeatureTypeMatchFunctor
	FeatureTypeMatchFunctor. More...
class	FileCDFBZ2FeatureContainerWriter
class	FileCDFBZ2PharmacophoreReader
class	FileCDFFeatureContainerWriter
class	FileCDFGZFeatureContainerWriter
class	FileCDFGZPharmacophoreReader
class	FileCDFPharmacophoreReader
class	FilePMLFeatureContainerWriter
class	FilePMLPharmacophoreReader
class	FileScreeningHitCollector
	FileScreeningHitCollector. More...
class	HBondAcceptorFeatureGenerator
	HBondAcceptorFeatureGenerator. More...
class	HBondDonorFeatureGenerator
	HBondDonorFeatureGenerator. More...
class	HBondingInteractionConstraint
	HBondingInteractionConstraint. More...
class	HBondingInteractionScore
	HBondingInteractionScore. More...
class	HydrophobicAtomFeatureGenerator
	HydrophobicAtomFeatureGenerator. More...
class	HydrophobicFeatureGenerator
	HydrophobicFeatureGenerator. More...
class	HydrophobicInteractionConstraint
	HydrophobicInteractionConstraint. More...
class	HydrophobicInteractionScore
	HydrophobicInteractionScore. More...
class	InteractionAnalyzer
	InteractionAnalyzer. More...
class	InteractionConstraintConnector
	InteractionConstraintConnector. More...
class	InteractionPharmacophoreGenerator
	InteractionPharmacophoreGenerator. More...
class	IonicInteractionConstraint
	IonicInteractionConstraint. More...
class	IonicInteractionScore
	IonicInteractionScore. More...
class	NegIonizableFeatureGenerator
	NegIonizableFeatureGenerator. More...
class	OrthogonalPiPiInteractionConstraint
	OrthogonalPiPiInteractionConstraint. More...
class	OrthogonalPiPiInteractionScore
	OrthogonalPiPiInteractionScore. More...
class	PMLFeatureContainerOutputHandler
	A handler for the output of pharmacophore data in the native I/O format of LigandScout. More...
class	PMLFeatureContainerWriter
	A writer for feature container data in the native I/O format of LigandScout. More...
class	PMLPharmacophoreInputHandler
	A handler for the input of pharmacophore data in the native I/O format of LigandScout. More...
class	PMLPharmacophoreReader
	A reader for pharmacophore data in the native I/O format of LigandScout. More...
class	PSDMolecularGraphOutputHandler
	A handler for the output of molecular graph dara in the PSD-format of the CDPL. More...
class	PSDMolecularGraphWriter
	A writer for molecular graph data in the PSD-format of the CDPL. More...
class	PSDMoleculeInputHandler
	A handler for the input of molecule data in the PSD-format of the CDPL. More...
class	PSDMoleculeReader
	A reader for molecule data in the PSD-format of the CDPL. More...
class	PSDPharmacophoreInputHandler
	A handler for the input of pharmacophore data in the PSD-format of the CDPL. More...
class	PSDPharmacophoreReader
	A reader for pharmacophore data in the PSD-format of the CDPL. More...
class	PSDScreeningDBAccessor
	A class for accessing pharmacophore screening databases in the built-in optimized format. More...
class	PSDScreeningDBCreator
	A class for the creation of optimized pharmacophore screening databases. More...
class	ParallelPiPiInteractionConstraint
	ParallelPiPiInteractionConstraint. More...
class	ParallelPiPiInteractionScore
	ParallelPiPiInteractionScore. More...
class	PatternBasedFeatureGenerator
	PatternBasedFeatureGenerator. More...
class	Pharmacophore
	Abstract base class for mutable containers of Pharm.Feature instances representing a pharmacophore model. More...
class	PharmacophoreAlignment
	PharmacophoreAlignment. More...
class	PharmacophoreFitScore
	PharmacophoreFitScore. More...
class	PharmacophoreFitScreeningScore
	PharmacophoreFitScreeningScore. More...
class	PharmacophoreGenerator
	PharmacophoreGenerator. More...
class	PharmacophoreIOManager
	A singleton class that serves as a global registry for Pharm.PharmacophoreInputHandler and Pharm.PharmacophoreOutputHandler implementation instances. More...
class	PharmacophoreInputHandler
	A 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
	An interface for reading data objects of type Pharm.Pharmacophore from an arbitrary data source. More...
class	PosIonizableFeatureGenerator
	PosIonizableFeatureGenerator. More...
class	ScreeningDBAccessor
	A class for accessing the data stored in pharmacophore screening databases. More...
class	ScreeningDBCreator
	A class for the creation of optimized pharmacophore screening databases. More...
class	ScreeningProcessor
	ScreeningProcessor. More...
class	SpatialFeatureAlignment
class	SpatialFeatureMapping
	SpatialFeatureMapping. More...
class	TopologicalFeatureAlignment
class	XBondAcceptorFeatureGenerator
	XBondAcceptorFeatureGenerator. More...
class	XBondDonorFeatureGenerator
	XBondDonorFeatureGenerator. More...
class	XBondingInteractionConstraint
	XBondingInteractionConstraint. More...
class	XBondingInteractionScore
	XBondingInteractionScore. More...

Functions
None	setDisabledFlag (Feature feature, bool flag)
bool	hasDisabledFlag (Feature feature)
bool	getDisabledFlag (Feature feature)
None	clearDisabledFlag (Feature feature)
str	getEnvironmentResidueAtomInfo (Feature feature)
str	getEnvironmentResidueInfo (Feature feature)
None	setEnvironmentSubstructure (Feature feature, Chem.Fragment substruct)
bool	hasEnvironmentSubstructure (Feature feature)
Chem.Fragment	getEnvironmentSubstructure (Feature feature)
None	clearEnvironmentSubstructure (Feature feature)
None	getFeatureAtoms (FeatureContainer cntnr, Chem.Fragment atoms, bool append=False)
int	getFeatureCount (FeatureContainer cntnr)
int	getFeatureCount (FeatureContainer cntnr, int type)
str	getFeatureTypeString (int ftr_type)
None	getFeatures (FeatureSet ftr_set, FeatureMapping mapping, bool first)
None	setGeometry (Feature feature, int geom)
bool	hasGeometry (Feature feature)
int	getGeometry (Feature feature)
None	clearGeometry (Feature feature)
None	setHydrophobicity (Feature feature, float hyd)
bool	hasHydrophobicity (Feature feature)
float	getHydrophobicity (Feature feature)
None	clearHydrophobicity (Feature feature)
None	setLength (Feature feature, float length)
bool	hasLength (Feature feature)
float	getLength (Feature feature)
None	clearLength (Feature feature)
None	setName (FeatureContainer cntnr, str name)
bool	hasName (FeatureContainer cntnr)
str	getName (FeatureContainer cntnr)
None	clearName (FeatureContainer cntnr)
None	setOptionalFlag (Feature feature, bool flag)
bool	hasOptionalFlag (Feature feature)
bool	getOptionalFlag (Feature feature)
None	clearOptionalFlag (Feature feature)
None	setOrientation (Feature feature, Math.Vector3D orient)
bool	hasOrientation (Feature feature)
Math.Vector3D	getOrientation (Feature feature)
None	clearOrientation (Feature feature)
None	clearOrientations (FeatureContainer cntnr, bool fix_geom=True)
None	setSubstructure (Feature feature, Chem.Fragment substruct)
bool	hasSubstructure (Feature feature)
Chem.Fragment	getSubstructure (Feature feature)
None	clearSubstructure (Feature feature)
None	setTolerance (Feature feature, float tol)
bool	hasTolerance (Feature feature)
float	getTolerance (Feature feature)
None	clearTolerance (Feature feature)
None	setType (Feature feature, int type)
bool	hasType (Feature feature)
int	getType (Feature feature)
None	clearType (Feature feature)
None	setWeight (Feature feature, float weight)
bool	hasWeight (Feature feature)
float	getWeight (Feature feature)
None	clearWeight (Feature feature)
bool	checkForExclusionVolumeClashes (FeatureContainer ftr_cntnr, Chem.AtomContainer atom_cntnr, Chem.Atom3DCoordinatesFunction coords_func, Math.Matrix4D xform, float vdw_factor=1.0)
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)
None	createExclusionVolumes (Pharmacophore pharm, FeatureContainer cntnr, float tol=0.0, float min_dist=0.0, bool rel_dist=True, bool append=True)
None	generateFeatureTypeHistogram (FeatureContainer cntnr, FeatureTypeHistogram hist, bool append=False)
str	generateFeatureTypeHistogramString (FeatureContainer cntnr)
None	generateInteractionPharmacophore (Pharmacophore pharm, FeatureMapping iactions, bool append=False)
None	prepareForPharmacophoreGeneration (Chem.Molecule mol, bool calc_hyd=True, bool from_logp=False)
bool	removeExclusionVolumesWithClashes (Pharmacophore pharm, Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, float vdw_scaling_fact=1.0)
bool	removeFeaturesWithType (FeatureContainer cntnr, FeatureSet tgt_set, int type, bool append=False)
bool	removeFeaturesWithType (FeatureSet ftr_set, int type)
bool	removeFeaturesWithType (Pharmacophore pharm, int type)
bool	removePositionalDuplicates (FeatureContainer cntnr, FeatureSet tgt_set, float pos_tol=0.0, bool append=False)
bool	removePositionalDuplicates (FeatureSet ftr_set, float pos_tol=0.0)
bool	removePositionalDuplicates (Pharmacophore pharm, float pos_tol=0.0)
bool	resizeExclusionVolumesWithClashes (Pharmacophore pharm, Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, float vdw_scaling_fact=1.0)
None	transform3DCoordinates (FeatureContainer cntnr, Math.Matrix4D mtx)
None	setCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr, bool single_prec)
bool	hasCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
bool	getCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
None	clearCDFOutputSinglePrecisionFloatsParameter (Base.ControlParameterContainer cntnr)
None	setPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr, bool allow)
bool	hasPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr)
bool	getPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr)
None	clearPSDAllowDuplicatesParameter (Base.ControlParameterContainer cntnr)
None	setPSDCreationModeParameter (Base.ControlParameterContainer cntnr, Mode mode)
bool	hasPSDCreationModeParameter (Base.ControlParameterContainer cntnr)
Mode	getPSDCreationModeParameter (Base.ControlParameterContainer cntnr)
None	clearPSDCreationModeParameter (Base.ControlParameterContainer cntnr)
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)

Detailed Description

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

Function Documentation

setDisabledFlag()

None CDPL.Pharm.setDisabledFlag	(	Feature	feature,
		bool	flag
	)

Parameters

feature
flag

hasDisabledFlag()

bool CDPL.Pharm.hasDisabledFlag

(

Feature

feature

)

Parameters

feature

Returns

getDisabledFlag()

bool CDPL.Pharm.getDisabledFlag

(

Feature

feature

)

Parameters

feature

Returns

clearDisabledFlag()

None CDPL.Pharm.clearDisabledFlag

(

Feature

feature

)

Parameters

feature

getEnvironmentResidueAtomInfo()

str CDPL.Pharm.getEnvironmentResidueAtomInfo

(

Feature

feature

)

Parameters

feature

Returns

getEnvironmentResidueInfo()

str CDPL.Pharm.getEnvironmentResidueInfo

(

Feature

feature

)

Parameters

feature

Returns

setEnvironmentSubstructure()

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

Parameters

feature
substruct

hasEnvironmentSubstructure()

bool CDPL.Pharm.hasEnvironmentSubstructure

(

Feature

feature

)

Parameters

feature

Returns

getEnvironmentSubstructure()

Chem.Fragment CDPL.Pharm.getEnvironmentSubstructure

(

Feature

feature

)

Parameters

feature

Returns

clearEnvironmentSubstructure()

None CDPL.Pharm.clearEnvironmentSubstructure

(

Feature

feature

)

Parameters

feature

getFeatureAtoms()

None CDPL.Pharm.getFeatureAtoms	(	FeatureContainer	cntnr,
		Chem.Fragment	atoms,
		bool	append = False
	)

Parameters

cntnr
atoms
append

getFeatureCount() [1/2]

int CDPL.Pharm.getFeatureCount

(

FeatureContainer

cntnr

)

Parameters

cntnr

Returns

getFeatureCount() [2/2]

int CDPL.Pharm.getFeatureCount	(	FeatureContainer	cntnr,
		int	type
	)

Parameters

cntnr
type

Returns

getFeatureTypeString()

str CDPL.Pharm.getFeatureTypeString

(

int

ftr_type

)

Parameters

ftr_type

Returns

getFeatures()

None CDPL.Pharm.getFeatures	(	FeatureSet	ftr_set,
		FeatureMapping	mapping,
		bool	first
	)

Parameters

ftr_set
mapping
first

setGeometry()

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

Parameters

feature
geom

hasGeometry()

bool CDPL.Pharm.hasGeometry

(

Feature

feature

)

Parameters

feature

Returns

getGeometry()

int CDPL.Pharm.getGeometry

(

Feature

feature

)

Parameters

feature

Returns

clearGeometry()

None CDPL.Pharm.clearGeometry

(

Feature

feature

)

Parameters

feature

setHydrophobicity()

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

Parameters

feature
hyd

hasHydrophobicity()

bool CDPL.Pharm.hasHydrophobicity

(

Feature

feature

)

Parameters

feature

Returns

getHydrophobicity()

float CDPL.Pharm.getHydrophobicity

(

Feature

feature

)

Parameters

feature

Returns

clearHydrophobicity()

None CDPL.Pharm.clearHydrophobicity

(

Feature

feature

)

Parameters

feature

setLength()

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

Parameters

feature
length

hasLength()

bool CDPL.Pharm.hasLength

(

Feature

feature

)

Parameters

feature

Returns

getLength()

float CDPL.Pharm.getLength

(

Feature

feature

)

Parameters

feature

Returns

clearLength()

None CDPL.Pharm.clearLength

(

Feature

feature

)

Parameters

feature

setName()

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

Parameters

cntnr
name

hasName()

bool CDPL.Pharm.hasName

(

FeatureContainer

cntnr

)

Parameters

cntnr

Returns

getName()

str CDPL.Pharm.getName

(

FeatureContainer

cntnr

)

Parameters

cntnr

Returns

clearName()

None CDPL.Pharm.clearName

(

FeatureContainer

cntnr

)

Parameters

cntnr

setOptionalFlag()

None CDPL.Pharm.setOptionalFlag	(	Feature	feature,
		bool	flag
	)

Parameters

feature
flag

hasOptionalFlag()

bool CDPL.Pharm.hasOptionalFlag

(

Feature

feature

)

Parameters

feature

Returns

getOptionalFlag()

bool CDPL.Pharm.getOptionalFlag

(

Feature

feature

)

Parameters

feature

Returns

clearOptionalFlag()

None CDPL.Pharm.clearOptionalFlag

(

Feature

feature

)

Parameters

feature

setOrientation()

None CDPL.Pharm.setOrientation	(	Feature	feature,
		Math.Vector3D	orient
	)

Parameters

feature
orient

hasOrientation()

bool CDPL.Pharm.hasOrientation

(

Feature

feature

)

Parameters

feature

Returns

getOrientation()

Math.Vector3D CDPL.Pharm.getOrientation

(

Feature

feature

)

Parameters

feature

Returns

clearOrientation()

None CDPL.Pharm.clearOrientation

(

Feature

feature

)

Parameters

feature

clearOrientations()

None CDPL.Pharm.clearOrientations	(	FeatureContainer	cntnr,
		bool	fix_geom = True
	)

Parameters

cntnr
fix_geom

setSubstructure()

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

Parameters

feature
substruct

hasSubstructure()

bool CDPL.Pharm.hasSubstructure

(

Feature

feature

)

Parameters

feature

Returns

getSubstructure()

Chem.Fragment CDPL.Pharm.getSubstructure

(

Feature

feature

)

Parameters

feature

Returns

clearSubstructure()

None CDPL.Pharm.clearSubstructure

(

Feature

feature

)

Parameters

feature

setTolerance()

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

Parameters

feature
tol

hasTolerance()

bool CDPL.Pharm.hasTolerance

(

Feature

feature

)

Parameters

feature

Returns

getTolerance()

float CDPL.Pharm.getTolerance

(

Feature

feature

)

Parameters

feature

Returns

clearTolerance()

None CDPL.Pharm.clearTolerance

(

Feature

feature

)

Parameters

feature

setType()

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

Parameters

feature
type

hasType()

bool CDPL.Pharm.hasType

(

Feature

feature

)

Parameters

feature

Returns

getType()

int CDPL.Pharm.getType

(

Feature

feature

)

Parameters

feature

Returns

clearType()

None CDPL.Pharm.clearType

(

Feature

feature

)

Parameters

feature

setWeight()

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

Parameters

feature
weight

hasWeight()

bool CDPL.Pharm.hasWeight

(

Feature

feature

)

Parameters

feature

Returns

getWeight()

float CDPL.Pharm.getWeight

(

Feature

feature

)

Parameters

feature

Returns

clearWeight()

None CDPL.Pharm.clearWeight

(

Feature

feature

)

Parameters

feature

checkForExclusionVolumeClashes()

bool CDPL.Pharm.checkForExclusionVolumeClashes	(	FeatureContainer	ftr_cntnr,
		Chem.AtomContainer	atom_cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		Math.Matrix4D	xform,
		float	vdw_factor = 1.0
	)

Parameters

ftr_cntnr
atom_cntnr
coords_func
xform
vdw_factor

Returns

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
	)

Parameters

pharm
cntnr
coords_func
tol
min_dist
rel_dist
append

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
	)

Parameters

pharm
cntnr
tol
min_dist
rel_dist
append

generateFeatureTypeHistogram()

None CDPL.Pharm.generateFeatureTypeHistogram	(	FeatureContainer	cntnr,
		FeatureTypeHistogram	hist,
		bool	append = False
	)

Parameters

cntnr
hist
append

generateFeatureTypeHistogramString()

str CDPL.Pharm.generateFeatureTypeHistogramString

(

FeatureContainer

cntnr

)

Parameters

cntnr

Returns

generateInteractionPharmacophore()

None CDPL.Pharm.generateInteractionPharmacophore	(	Pharmacophore	pharm,
		FeatureMapping	iactions,
		bool	append = False
	)

Parameters

pharm
iactions
append

prepareForPharmacophoreGeneration()

None CDPL.Pharm.prepareForPharmacophoreGeneration	(	Chem.Molecule	mol,
		bool	calc_hyd = True,
		bool	from_logp = False
	)

Parameters

mol
calc_hyd
from_logp

removeExclusionVolumesWithClashes()

bool CDPL.Pharm.removeExclusionVolumesWithClashes	(	Pharmacophore	pharm,
		Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	vdw_scaling_fact = 1.0
	)

Parameters

pharm
cntnr
coords_func
vdw_scaling_fact

Returns

removeFeaturesWithType() [1/3]

bool CDPL.Pharm.removeFeaturesWithType	(	FeatureContainer	cntnr,
		FeatureSet	tgt_set,
		int	type,
		bool	append = False
	)

Parameters

cntnr
tgt_set
type
append

Returns

removeFeaturesWithType() [2/3]

bool CDPL.Pharm.removeFeaturesWithType	(	FeatureSet	ftr_set,
		int	type
	)

Parameters

ftr_set
type

Returns

removeFeaturesWithType() [3/3]

bool CDPL.Pharm.removeFeaturesWithType	(	Pharmacophore	pharm,
		int	type
	)

Parameters

pharm
type

Returns

removePositionalDuplicates() [1/3]

bool CDPL.Pharm.removePositionalDuplicates	(	FeatureContainer	cntnr,
		FeatureSet	tgt_set,
		float	pos_tol = 0.0,
		bool	append = False
	)

Parameters

cntnr
tgt_set
pos_tol
append

Returns

removePositionalDuplicates() [2/3]

bool CDPL.Pharm.removePositionalDuplicates	(	FeatureSet	ftr_set,
		float	pos_tol = 0.0
	)

Parameters

ftr_set
pos_tol

Returns

removePositionalDuplicates() [3/3]

bool CDPL.Pharm.removePositionalDuplicates	(	Pharmacophore	pharm,
		float	pos_tol = 0.0
	)

Parameters

pharm
pos_tol

Returns

resizeExclusionVolumesWithClashes()

bool CDPL.Pharm.resizeExclusionVolumesWithClashes	(	Pharmacophore	pharm,
		Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	vdw_scaling_fact = 1.0
	)

Parameters

pharm
cntnr
coords_func
vdw_scaling_fact

Returns

transform3DCoordinates()

None CDPL.Pharm.transform3DCoordinates	(	FeatureContainer	cntnr,
		Math.Matrix4D	mtx
	)

Parameters

cntnr
mtx

setCDFOutputSinglePrecisionFloatsParameter()

None CDPL.Pharm.setCDFOutputSinglePrecisionFloatsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	single_prec
	)

Parameters

cntnr
single_prec

hasCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Pharm.hasCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getCDFOutputSinglePrecisionFloatsParameter()

bool CDPL.Pharm.getCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearCDFOutputSinglePrecisionFloatsParameter()

None CDPL.Pharm.clearCDFOutputSinglePrecisionFloatsParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setPSDAllowDuplicatesParameter()

None CDPL.Pharm.setPSDAllowDuplicatesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	allow
	)

Parameters

cntnr
allow

hasPSDAllowDuplicatesParameter()

bool CDPL.Pharm.hasPSDAllowDuplicatesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getPSDAllowDuplicatesParameter()

bool CDPL.Pharm.getPSDAllowDuplicatesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearPSDAllowDuplicatesParameter()

None CDPL.Pharm.clearPSDAllowDuplicatesParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setPSDCreationModeParameter()

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

Parameters

cntnr
mode

hasPSDCreationModeParameter()

bool CDPL.Pharm.hasPSDCreationModeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getPSDCreationModeParameter()

Mode CDPL.Pharm.getPSDCreationModeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearPSDCreationModeParameter()

None CDPL.Pharm.clearPSDCreationModeParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

setStrictErrorCheckingParameter()

None CDPL.Pharm.setStrictErrorCheckingParameter	(	Base.ControlParameterContainer	cntnr,
		bool	strict
	)

Parameters

cntnr
strict

hasStrictErrorCheckingParameter()

bool CDPL.Pharm.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

getStrictErrorCheckingParameter()

bool CDPL.Pharm.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr

Returns

clearStrictErrorCheckingParameter()

None CDPL.Pharm.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Parameters

cntnr