Contains classes and functions related to pharmacophore perception and pharmacophore applications.
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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...
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typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::BZip2OStream > | CDFBZ2FeatureContainerWriter |
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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...
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typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::BZip2IStream > | CDFBZ2PharmacophoreReader |
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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...
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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...
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typedef Util::CompressedDataWriter< CDFFeatureContainerWriter, Util::GZipOStream > | CDFGZFeatureContainerWriter |
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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...
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typedef Util::CompressedDataReader< CDFPharmacophoreReader, Util::GZipIStream > | CDFGZPharmacophoreReader |
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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...
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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...
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typedef Util::MultiFormatDataWriter< FeatureContainer > | FeatureContainerWriter |
| Writer for pharmacophore data in any supported format. More...
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typedef Util::MultiFormatDataReader< Pharmacophore > | PharmacophoreReader |
| Reader for pharmacophore data in any supported format. More...
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typedef Util::DefaultDataOutputHandler< PMLFeatureContainerWriter, DataFormat::PML > | PMLFeatureContainerOutputHandler |
| A handler for the output of pharmacophore data in the native I/O format of LigandScout. More...
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typedef Util::DefaultDataInputHandler< PMLPharmacophoreReader, DataFormat::PML > | PMLPharmacophoreInputHandler |
| A handler for the input of pharmacophore data in the native I/O format of LigandScout. More...
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CDPL_PHARM_API bool | getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict) |
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CDPL_PHARM_API bool | hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API bool | getCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | setCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec) |
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CDPL_PHARM_API bool | hasCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | clearCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API ScreeningDBCreator::Mode | getPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | setPSDCreationModeParameter (Base::ControlParameterContainer &cntnr, ScreeningDBCreator::Mode mode) |
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CDPL_PHARM_API bool | hasPSDCreationModeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | clearPSDCreationModeParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API bool | getPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | setPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr, bool allow) |
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CDPL_PHARM_API bool | hasPSDAllowDuplicatesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API void | clearPSDAllowDuplicatesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_PHARM_API const std::string & | getName (const FeatureContainer &cntnr) |
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CDPL_PHARM_API void | setName (FeatureContainer &cntnr, const std::string &name) |
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CDPL_PHARM_API void | clearName (FeatureContainer &cntnr) |
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CDPL_PHARM_API bool | hasName (const FeatureContainer &cntnr) |
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CDPL_PHARM_API std::size_t | getFeatureCount (const FeatureContainer &cntnr) |
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CDPL_PHARM_API std::size_t | getFeatureCount (const FeatureContainer &cntnr, unsigned int type) |
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CDPL_PHARM_API void | generateFeatureTypeHistogram (const FeatureContainer &cntnr, FeatureTypeHistogram &hist, bool append=false) |
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CDPL_PHARM_API void | generateFeatureTypeHistogramString (const FeatureContainer &cntnr, std::string &histo_str) |
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CDPL_PHARM_API void | transform3DCoordinates (FeatureContainer &cntnr, const Math::Matrix4D &mtx) |
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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) |
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CDPL_PHARM_API void | getFeatureAtoms (const FeatureContainer &cntnr, Chem::Fragment &atoms, bool append=false) |
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CDPL_PHARM_API unsigned int | getType (const Feature &feature) |
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CDPL_PHARM_API void | setType (Feature &feature, unsigned int type) |
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CDPL_PHARM_API void | clearType (Feature &feature) |
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CDPL_PHARM_API bool | hasType (const Feature &feature) |
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CDPL_PHARM_API unsigned int | getGeometry (const Feature &feature) |
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CDPL_PHARM_API void | setGeometry (Feature &feature, unsigned int geom) |
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CDPL_PHARM_API void | clearGeometry (Feature &feature) |
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CDPL_PHARM_API bool | hasGeometry (const Feature &feature) |
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CDPL_PHARM_API const Math::Vector3D & | getOrientation (const Feature &feature) |
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CDPL_PHARM_API void | setOrientation (Feature &feature, const Math::Vector3D &orient) |
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CDPL_PHARM_API void | clearOrientation (Feature &feature) |
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CDPL_PHARM_API bool | hasOrientation (const Feature &feature) |
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CDPL_PHARM_API double | getLength (const Feature &feature) |
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CDPL_PHARM_API void | setLength (Feature &feature, double length) |
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CDPL_PHARM_API void | clearLength (Feature &feature) |
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CDPL_PHARM_API bool | hasLength (const Feature &feature) |
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CDPL_PHARM_API double | getTolerance (const Feature &feature) |
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CDPL_PHARM_API void | setTolerance (Feature &feature, double tol) |
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CDPL_PHARM_API void | clearTolerance (Feature &feature) |
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CDPL_PHARM_API bool | hasTolerance (const Feature &feature) |
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CDPL_PHARM_API double | getWeight (const Feature &feature) |
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CDPL_PHARM_API void | setWeight (Feature &feature, double weight) |
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CDPL_PHARM_API void | clearWeight (Feature &feature) |
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CDPL_PHARM_API bool | hasWeight (const Feature &feature) |
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CDPL_PHARM_API const Chem::Fragment::SharedPointer & | getSubstructure (const Feature &feature) |
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CDPL_PHARM_API void | setSubstructure (Feature &feature, const Chem::Fragment::SharedPointer &substruct) |
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CDPL_PHARM_API void | clearSubstructure (Feature &feature) |
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CDPL_PHARM_API bool | hasSubstructure (const Feature &feature) |
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CDPL_PHARM_API bool | getDisabledFlag (const Feature &feature) |
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CDPL_PHARM_API void | setDisabledFlag (Feature &feature, bool flag) |
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CDPL_PHARM_API void | clearDisabledFlag (Feature &feature) |
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CDPL_PHARM_API bool | hasDisabledFlag (const Feature &feature) |
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CDPL_PHARM_API bool | getOptionalFlag (const Feature &feature) |
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CDPL_PHARM_API void | setOptionalFlag (Feature &feature, bool flag) |
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CDPL_PHARM_API void | clearOptionalFlag (Feature &feature) |
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CDPL_PHARM_API bool | hasOptionalFlag (const Feature &feature) |
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CDPL_PHARM_API double | getHydrophobicity (const Feature &feature) |
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CDPL_PHARM_API void | setHydrophobicity (Feature &feature, double hyd) |
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CDPL_PHARM_API void | clearHydrophobicity (Feature &feature) |
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CDPL_PHARM_API bool | hasHydrophobicity (const Feature &feature) |
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CDPL_PHARM_API void | getFeatures (FeatureSet &ftr_set, const FeatureMapping &mapping, bool first) |
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CDPL_PHARM_API void | prepareForPharmacophoreGeneration (Chem::Molecule &mol, bool calc_hyd=true, bool from_logp=false) |
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CDPL_PHARM_API void | generateInteractionPharmacophore (Pharmacophore &pharm, const FeatureMapping &iactions, bool append=false) |
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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) |
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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) |
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CDPL_PHARM_API bool | removeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0) |
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CDPL_PHARM_API bool | resizeExclusionVolumesWithClashes (Pharmacophore &pharm, const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, double vdw_scaling_fact=1.0) |
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CDPL_PHARM_API const std::string & | getFeatureTypeString (unsigned int ftr_type) |
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Contains classes and functions related to pharmacophore perception and pharmacophore applications.