CDPL::Pharm Namespace Reference

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

Namespaces
	ControlParameter
	Provides keys for built-in control-parameters.
	ControlParameterDefault
	Provides default values for built-in control-parameters.
	DataFormat
	Provides preinitialized Base::DataFormat objects for all supported data formats.
	FeatureContainerProperty
	Provides keys for built-in Pharm::FeatureContainer properties.
	FeatureContainerPropertyDefault
	Provides default values for built-in Pharm::FeatureContainer properties.
	FeatureGeometry
	Provides constants for the specification of the generic geometry of a pharmacophore feature.
	FeatureProperty
	Provides keys for built-in Pharm::Feature properties.
	FeaturePropertyDefault
	Provides default values for built-in Pharm::Feature properties.
	FeatureType
	Provides constants for the specification of the generic type of a pharmacophore feature.

Classes
class	AromaticFeatureGenerator
	AromaticFeatureGenerator. More...
class	BasicFeature
	BasicFeature. More...
class	BasicPharmacophore
	BasicPharmacophore. More...
class	CationPiInteractionConstraint
	CationPiInteractionConstraint. More...
class	CationPiInteractionScore
	CationPiInteractionScore. More...
class	CDFFeatureContainerWriter
	A writer for feature container 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	DefaultInteractionAnalyzer
	DefaultInteractionAnalyzer. More...
class	DefaultPharmacophoreGenerator
	DefaultPharmacophoreGenerator. More...
class	Feature
	Feature. More...
class	FeatureContainer
	FeatureContainer. More...
class	FeatureDistanceConstraint
	FeatureDistanceConstraint. More...
class	FeatureDistanceScore
	FeatureDistanceScore. More...
class	FeatureGenerator
	FeatureGenerator. 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	FeatureSet
	FeatureSet. More...
class	FeatureTypeHistogram
	A data type for the storage of feature type histograms of pharmacophores. More...
class	FeatureTypeMatchFunctor
	FeatureTypeMatchFunctor. More...
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	ParallelPiPiInteractionConstraint
	ParallelPiPiInteractionConstraint. More...
class	ParallelPiPiInteractionScore
	ParallelPiPiInteractionScore. More...
class	PatternBasedFeatureGenerator
	PatternBasedFeatureGenerator. More...
class	Pharmacophore
	Pharmacophore. More...
class	PharmacophoreAlignment
	PharmacophoreAlignment. More...
class	PharmacophoreFitScore
	PharmacophoreFitScore. More...
class	PharmacophoreFitScreeningScore
	PharmacophoreFitScreeningScore. More...
class	PharmacophoreGenerator
	PharmacophoreGenerator. More...
class	PMLFeatureContainerWriter
	A writer for feature container 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	PosIonizableFeatureGenerator
	PosIonizableFeatureGenerator. 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	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	SpatialFeatureMapping
	SpatialFeatureMapping. More...
class	XBondAcceptorFeatureGenerator
	XBondAcceptorFeatureGenerator. More...
class	XBondDonorFeatureGenerator
	XBondDonorFeatureGenerator. More...
class	XBondingInteractionConstraint
	XBondingInteractionConstraint. More...
class	XBondingInteractionScore
	XBondingInteractionScore. More...

Typedefs
typedef Util::DefaultDataOutputHandler< CDFBZ2FeatureContainerWriter, DataFormat::CDF_BZ2 >	CDFBZ2FeatureContainerOutputHandler
	A handler for the output of bzip2-compressed feature container data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::BZip2OStream >	CDFBZ2FeatureContainerWriter
typedef Util::DefaultDataInputHandler< CDFBZ2PharmacophoreReader, DataFormat::CDF_BZ2 >	CDFBZ2PharmacophoreInputHandler
	A handler for the input of bzip2-compressed pharmacophore data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::BZip2IStream >	CDFBZ2PharmacophoreReader
typedef Util::DefaultDataOutputHandler< CDFFeatureContainerWriter, DataFormat::CDF >	CDFFeatureContainerOutputHandler
	A handler for the output of feature container data in the native I/O format of the CDPL. More...
typedef Util::DefaultDataOutputHandler< CDFGZFeatureContainerWriter, DataFormat::CDF_GZ >	CDFGZFeatureContainerOutputHandler
	A handler for the output of gzip-compressed feature container data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::GZipOStream >	CDFGZFeatureContainerWriter
typedef Util::DefaultDataInputHandler< CDFGZPharmacophoreReader, DataFormat::CDF_GZ >	CDFGZPharmacophoreInputHandler
	A handler for the input of gzip-compressed pharmacophore data in the native I/O format of the CDPL. More...
typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::GZipIStream >	CDFGZPharmacophoreReader
typedef Util::DefaultDataInputHandler< CDFPharmacophoreReader, DataFormat::CDF >	CDFPharmacophoreInputHandler
	A handler for the input of pharmacophore data in the native I/O format of the CDPL. More...
typedef std::function< const Math::Vector3D &(const Pharm::Feature &)>	Feature3DCoordinatesFunction
	A generic wrapper class used to store a user-defined Pharm::Feature 3D-coordinates function. More...
typedef Util::MultiFormatDataWriter< FeatureContainer >	FeatureContainerWriter
	Writer for pharmacophore data in any supported format. More...
typedef Util::MultiFormatDataReader< Pharmacophore >	PharmacophoreReader
	Reader for pharmacophore data in any supported format. More...
typedef Util::DefaultDataOutputHandler< PMLFeatureContainerWriter, DataFormat::PML >	PMLFeatureContainerOutputHandler
	A handler for the output of pharmacophore data in the native I/O format of LigandScout. More...
typedef Util::DefaultDataInputHandler< PMLPharmacophoreReader, DataFormat::PML >	PMLPharmacophoreInputHandler
	A handler for the input of pharmacophore data in the native I/O format of LigandScout. More...

Functions
CDPL_PHARM_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
CDPL_PHARM_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API bool	getCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	setCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec)
CDPL_PHARM_API bool	hasCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	clearCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API ScreeningDBCreator::Mode	getPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	setPSDCreationModeParameter (Base::ControlParameterContainer &cntnr, ScreeningDBCreator::Mode mode)
CDPL_PHARM_API bool	hasPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	clearPSDCreationModeParameter (Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API bool	getPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	setPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr, bool allow)
CDPL_PHARM_API bool	hasPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API void	clearPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr)
CDPL_PHARM_API const std::string &	getName (const FeatureContainer &cntnr)
CDPL_PHARM_API void	setName (FeatureContainer &cntnr, const std::string &name)
CDPL_PHARM_API void	clearName (FeatureContainer &cntnr)
CDPL_PHARM_API bool	hasName (const FeatureContainer &cntnr)
CDPL_PHARM_API std::size_t	getFeatureCount (const FeatureContainer &cntnr)
CDPL_PHARM_API std::size_t	getFeatureCount (const FeatureContainer &cntnr, unsigned int type)
CDPL_PHARM_API void	generateFeatureTypeHistogram (const FeatureContainer &cntnr, FeatureTypeHistogram &hist, bool append=false)
CDPL_PHARM_API void	generateFeatureTypeHistogramString (const FeatureContainer &cntnr, std::string &histo_str)
CDPL_PHARM_API void	transform3DCoordinates (FeatureContainer &cntnr, const Math::Matrix4D &mtx)
CDPL_PHARM_API bool	checkForExclusionVolumeClashes (const FeatureContainer &ftr_cntnr, const Chem::AtomContainer &atom_cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, const Math::Matrix4D &xform, double vdw_factor=1.0)
CDPL_PHARM_API void	getFeatureAtoms (const FeatureContainer &cntnr, Chem::Fragment &atoms, bool append=false)
CDPL_PHARM_API unsigned int	getType (const Feature &feature)
CDPL_PHARM_API void	setType (Feature &feature, unsigned int type)
CDPL_PHARM_API void	clearType (Feature &feature)
CDPL_PHARM_API bool	hasType (const Feature &feature)
CDPL_PHARM_API unsigned int	getGeometry (const Feature &feature)
CDPL_PHARM_API void	setGeometry (Feature &feature, unsigned int geom)
CDPL_PHARM_API void	clearGeometry (Feature &feature)
CDPL_PHARM_API bool	hasGeometry (const Feature &feature)
CDPL_PHARM_API const Math::Vector3D &	getOrientation (const Feature &feature)
CDPL_PHARM_API void	setOrientation (Feature &feature, const Math::Vector3D &orient)
CDPL_PHARM_API void	clearOrientation (Feature &feature)
CDPL_PHARM_API bool	hasOrientation (const Feature &feature)
CDPL_PHARM_API double	getLength (const Feature &feature)
CDPL_PHARM_API void	setLength (Feature &feature, double length)
CDPL_PHARM_API void	clearLength (Feature &feature)
CDPL_PHARM_API bool	hasLength (const Feature &feature)
CDPL_PHARM_API double	getTolerance (const Feature &feature)
CDPL_PHARM_API void	setTolerance (Feature &feature, double tol)
CDPL_PHARM_API void	clearTolerance (Feature &feature)
CDPL_PHARM_API bool	hasTolerance (const Feature &feature)
CDPL_PHARM_API double	getWeight (const Feature &feature)
CDPL_PHARM_API void	setWeight (Feature &feature, double weight)
CDPL_PHARM_API void	clearWeight (Feature &feature)
CDPL_PHARM_API bool	hasWeight (const Feature &feature)
CDPL_PHARM_API const Chem::Fragment::SharedPointer &	getSubstructure (const Feature &feature)
CDPL_PHARM_API void	setSubstructure (Feature &feature, const Chem::Fragment::SharedPointer &substruct)
CDPL_PHARM_API void	clearSubstructure (Feature &feature)
CDPL_PHARM_API bool	hasSubstructure (const Feature &feature)
CDPL_PHARM_API bool	getDisabledFlag (const Feature &feature)
CDPL_PHARM_API void	setDisabledFlag (Feature &feature, bool flag)
CDPL_PHARM_API void	clearDisabledFlag (Feature &feature)
CDPL_PHARM_API bool	hasDisabledFlag (const Feature &feature)
CDPL_PHARM_API bool	getOptionalFlag (const Feature &feature)
CDPL_PHARM_API void	setOptionalFlag (Feature &feature, bool flag)
CDPL_PHARM_API void	clearOptionalFlag (Feature &feature)
CDPL_PHARM_API bool	hasOptionalFlag (const Feature &feature)
CDPL_PHARM_API double	getHydrophobicity (const Feature &feature)
CDPL_PHARM_API void	setHydrophobicity (Feature &feature, double hyd)
CDPL_PHARM_API void	clearHydrophobicity (Feature &feature)
CDPL_PHARM_API bool	hasHydrophobicity (const Feature &feature)
CDPL_PHARM_API void	getFeatures (FeatureSet &ftr_set, const FeatureMapping &mapping, bool first)
CDPL_PHARM_API void	prepareForPharmacophoreGeneration (Chem::Molecule &mol, bool calc_hyd=true, bool from_logp=false)
CDPL_PHARM_API void	generateInteractionPharmacophore (Pharmacophore &pharm, const FeatureMapping &iactions, bool append=false)
CDPL_PHARM_API void	createExclusionVolumes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double tol=0.0, double min_dist=0.0, bool rel_dist=true, bool append=true)
CDPL_PHARM_API void	createExclusionVolumes (Pharmacophore &pharm, const FeatureContainer &cntnr, double tol=0.0, double min_dist=0.0, bool rel_dist=true, bool append=true)
CDPL_PHARM_API bool	removeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0)
CDPL_PHARM_API bool	resizeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0)
CDPL_PHARM_API const std::string &	getFeatureTypeString (unsigned int ftr_type)

Detailed Description

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

Typedef Documentation

CDFBZ2FeatureContainerOutputHandler

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

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

CDFBZ2FeatureContainerWriter

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

CDFBZ2PharmacophoreInputHandler

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

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

CDFBZ2PharmacophoreReader

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

CDFFeatureContainerOutputHandler

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

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

CDFGZFeatureContainerOutputHandler

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

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

CDFGZFeatureContainerWriter

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

CDFGZPharmacophoreInputHandler

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

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

CDFGZPharmacophoreReader

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

CDFPharmacophoreInputHandler

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

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

Feature3DCoordinatesFunction

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

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

FeatureContainerWriter

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

Writer for pharmacophore data in any supported format.

PharmacophoreReader

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

Reader for pharmacophore data in any supported format.

PMLFeatureContainerOutputHandler

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

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

PMLPharmacophoreInputHandler

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

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

Function Documentation

getStrictErrorCheckingParameter()

CDPL_PHARM_API bool CDPL::Pharm::getStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

setStrictErrorCheckingParameter()

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

hasStrictErrorCheckingParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasStrictErrorCheckingParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearStrictErrorCheckingParameter()

CDPL_PHARM_API void CDPL::Pharm::clearStrictErrorCheckingParameter

(

Base::ControlParameterContainer &

cntnr

)

getCDFWriteSinglePrecisionFloatsParameter()

CDPL_PHARM_API bool CDPL::Pharm::getCDFWriteSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

setCDFWriteSinglePrecisionFloatsParameter()

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

hasCDFWriteSinglePrecisionFloatsParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasCDFWriteSinglePrecisionFloatsParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearCDFWriteSinglePrecisionFloatsParameter()

CDPL_PHARM_API void CDPL::Pharm::clearCDFWriteSinglePrecisionFloatsParameter

(

Base::ControlParameterContainer &

cntnr

)

getPSDCreationModeParameter()

CDPL_PHARM_API ScreeningDBCreator::Mode CDPL::Pharm::getPSDCreationModeParameter

(

const Base::ControlParameterContainer &

cntnr

)

setPSDCreationModeParameter()

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

hasPSDCreationModeParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasPSDCreationModeParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearPSDCreationModeParameter()

CDPL_PHARM_API void CDPL::Pharm::clearPSDCreationModeParameter

(

Base::ControlParameterContainer &

cntnr

)

getPSDAllowDuplicatesParameter()

CDPL_PHARM_API bool CDPL::Pharm::getPSDAllowDuplicatesParameter

(

const Base::ControlParameterContainer &

cntnr

)

setPSDAllowDuplicatesParameter()

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

hasPSDAllowDuplicatesParameter()

CDPL_PHARM_API bool CDPL::Pharm::hasPSDAllowDuplicatesParameter

(

const Base::ControlParameterContainer &

cntnr

)

clearPSDAllowDuplicatesParameter()

CDPL_PHARM_API void CDPL::Pharm::clearPSDAllowDuplicatesParameter

(

Base::ControlParameterContainer &

cntnr

)

getName()

CDPL_PHARM_API const std::string& CDPL::Pharm::getName

(

const FeatureContainer &

cntnr

)

setName()

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

clearName()

CDPL_PHARM_API void CDPL::Pharm::clearName

(

FeatureContainer &

cntnr

)

hasName()

CDPL_PHARM_API bool CDPL::Pharm::hasName

(

const FeatureContainer &

cntnr

)

getFeatureCount() [1/2]

CDPL_PHARM_API std::size_t CDPL::Pharm::getFeatureCount

(

const FeatureContainer &

cntnr

)

getFeatureCount() [2/2]

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

generateFeatureTypeHistogram()

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

generateFeatureTypeHistogramString()

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

transform3DCoordinates()

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

checkForExclusionVolumeClashes()

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

getFeatureAtoms()

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

getType()

CDPL_PHARM_API unsigned int CDPL::Pharm::getType

(

const Feature &

feature

)

setType()

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

clearType()

CDPL_PHARM_API void CDPL::Pharm::clearType

(

Feature &

feature

)

hasType()

CDPL_PHARM_API bool CDPL::Pharm::hasType

(

const Feature &

feature

)

getGeometry()

CDPL_PHARM_API unsigned int CDPL::Pharm::getGeometry

(

const Feature &

feature

)

setGeometry()

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

clearGeometry()

CDPL_PHARM_API void CDPL::Pharm::clearGeometry

(

Feature &

feature

)

hasGeometry()

CDPL_PHARM_API bool CDPL::Pharm::hasGeometry

(

const Feature &

feature

)

getOrientation()

CDPL_PHARM_API const Math::Vector3D& CDPL::Pharm::getOrientation

(

const Feature &

feature

)

setOrientation()

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

clearOrientation()

CDPL_PHARM_API void CDPL::Pharm::clearOrientation

(

Feature &

feature

)

hasOrientation()

CDPL_PHARM_API bool CDPL::Pharm::hasOrientation

(

const Feature &

feature

)

getLength()

CDPL_PHARM_API double CDPL::Pharm::getLength

(

const Feature &

feature

)

setLength()

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

clearLength()

CDPL_PHARM_API void CDPL::Pharm::clearLength

(

Feature &

feature

)

hasLength()

CDPL_PHARM_API bool CDPL::Pharm::hasLength

(

const Feature &

feature

)

getTolerance()

CDPL_PHARM_API double CDPL::Pharm::getTolerance

(

const Feature &

feature

)

setTolerance()

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

clearTolerance()

CDPL_PHARM_API void CDPL::Pharm::clearTolerance

(

Feature &

feature

)

hasTolerance()

CDPL_PHARM_API bool CDPL::Pharm::hasTolerance

(

const Feature &

feature

)

getWeight()

CDPL_PHARM_API double CDPL::Pharm::getWeight

(

const Feature &

feature

)

setWeight()

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

clearWeight()

CDPL_PHARM_API void CDPL::Pharm::clearWeight

(

Feature &

feature

)

hasWeight()

CDPL_PHARM_API bool CDPL::Pharm::hasWeight

(

const Feature &

feature

)

getSubstructure()

CDPL_PHARM_API const Chem::Fragment::SharedPointer& CDPL::Pharm::getSubstructure

(

const Feature &

feature

)

setSubstructure()

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

clearSubstructure()

CDPL_PHARM_API void CDPL::Pharm::clearSubstructure

(

Feature &

feature

)

hasSubstructure()

CDPL_PHARM_API bool CDPL::Pharm::hasSubstructure

(

const Feature &

feature

)

getDisabledFlag()

CDPL_PHARM_API bool CDPL::Pharm::getDisabledFlag

(

const Feature &

feature

)

setDisabledFlag()

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

clearDisabledFlag()

CDPL_PHARM_API void CDPL::Pharm::clearDisabledFlag

(

Feature &

feature

)

hasDisabledFlag()

CDPL_PHARM_API bool CDPL::Pharm::hasDisabledFlag

(

const Feature &

feature

)

getOptionalFlag()

CDPL_PHARM_API bool CDPL::Pharm::getOptionalFlag

(

const Feature &

feature

)

setOptionalFlag()

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

clearOptionalFlag()

CDPL_PHARM_API void CDPL::Pharm::clearOptionalFlag

(

Feature &

feature

)

hasOptionalFlag()

CDPL_PHARM_API bool CDPL::Pharm::hasOptionalFlag

(

const Feature &

feature

)

getHydrophobicity()

CDPL_PHARM_API double CDPL::Pharm::getHydrophobicity

(

const Feature &

feature

)

setHydrophobicity()

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

clearHydrophobicity()

CDPL_PHARM_API void CDPL::Pharm::clearHydrophobicity

(

Feature &

feature

)

hasHydrophobicity()

CDPL_PHARM_API bool CDPL::Pharm::hasHydrophobicity

(

const Feature &

feature

)

getFeatures()

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

prepareForPharmacophoreGeneration()

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

generateInteractionPharmacophore()

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

createExclusionVolumes() [1/2]

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

createExclusionVolumes() [2/2]

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

removeExclusionVolumesWithClashes()

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

resizeExclusionVolumesWithClashes()

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

getFeatureTypeString()

CDPL_PHARM_API const std::string& CDPL::Pharm::getFeatureTypeString

(

unsigned int

ftr_type

)