Chemical Data Processing Library C++ API - Version 1.1.1
Namespaces | Classes | Typedefs | Functions
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_BZ2CDFBZ2FeatureContainerOutputHandler
 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::BZip2OStreamCDFBZ2FeatureContainerWriter
 
typedef Util::DefaultDataInputHandler< CDFBZ2PharmacophoreReader, DataFormat::CDF_BZ2CDFBZ2PharmacophoreInputHandler
 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::BZip2IStreamCDFBZ2PharmacophoreReader
 
typedef Util::DefaultDataOutputHandler< CDFFeatureContainerWriter, DataFormat::CDFCDFFeatureContainerOutputHandler
 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_GZCDFGZFeatureContainerOutputHandler
 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::GZipOStreamCDFGZFeatureContainerWriter
 
typedef Util::DefaultDataInputHandler< CDFGZPharmacophoreReader, DataFormat::CDF_GZCDFGZPharmacophoreInputHandler
 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::GZipIStreamCDFGZPharmacophoreReader
 
typedef Util::DefaultDataInputHandler< CDFPharmacophoreReader, DataFormat::CDFCDFPharmacophoreInputHandler
 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< FeatureContainerFeatureContainerWriter
 Writer for pharmacophore data in any supported format. More...
 
typedef Util::MultiFormatDataReader< PharmacophorePharmacophoreReader
 Reader for pharmacophore data in any supported format. More...
 
typedef Util::DefaultDataOutputHandler< PMLFeatureContainerWriter, DataFormat::PMLPMLFeatureContainerOutputHandler
 A handler for the output of pharmacophore data in the native I/O format of LigandScout. More...
 
typedef Util::DefaultDataInputHandler< PMLPharmacophoreReader, DataFormat::PMLPMLPharmacophoreInputHandler
 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::Vector3DgetOrientation (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::SharedPointergetSubstructure (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

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

◆ CDFBZ2FeatureContainerWriter

◆ CDFBZ2PharmacophoreInputHandler

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

◆ CDFBZ2PharmacophoreReader

◆ CDFFeatureContainerOutputHandler

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

◆ CDFGZFeatureContainerOutputHandler

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

◆ CDFGZFeatureContainerWriter

◆ CDFGZPharmacophoreInputHandler

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

◆ CDFGZPharmacophoreReader

◆ CDFPharmacophoreInputHandler

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

◆ Feature3DCoordinatesFunction

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

◆ FeatureContainerWriter

Writer for pharmacophore data in any supported format.

◆ PharmacophoreReader

Reader for pharmacophore data in any supported format.

◆ PMLFeatureContainerOutputHandler

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

◆ 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)