Contains classes and functions related to biological macromolecules. More...

Namespaces
	AtomProperty
	Provides keys for built-in Biomol::Atom properties.

	AtomPropertyDefault
	Provides default values for built-in Chem::Atom properties.

	AtomPropertyFlag
	Provides flags for the specification of basic Chem::Atom properties.

	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 biopolymer data formats.

	MolecularGraphProperty
	Provides keys for built-in Biomol::MolecularGraph properties.

	MolecularGraphPropertyDefault
	Provides default values for built-in Chem::MolecularGraph properties.

	PDBFormatVersion
	Provides constants for the specification of the Brookhaven Protein Data Bank (PDB) [PDB] format version.

	ResidueType

Classes
class	HierarchyView
	A data structure allowing a hierarchical view on biological macromolecules. More...

class	HierarchyViewChain
	HierarchyViewChain. More...

class	HierarchyViewFragment
	HierarchyViewFragment. More...

class	HierarchyViewModel
	HierarchyViewModel. More...

class	HierarchyViewNode
	HierarchyViewNode. More...

class	MMCIFData
	A data structure for the storage of imported MMCIF data (see [MMCIF]). More...

class	MMCIFMolecularGraphWriter

class	MMCIFMoleculeReader

class	MMTFMolecularGraphWriter
	A writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...

class	MMTFMoleculeReader
	A reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...

class	PDBData
	A data structure for the storage of imported PDB data records (see [CTFILE]). More...

class	PDBMolecularGraphWriter
	A writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

class	PDBMoleculeReader
	A reader for molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

class	ResidueDictionary
	A global dictionary for the lookup of meta-data associated with the residues in biological macromolecules. More...

class	ResidueList
	Implements the extraction of residues in biological macromolecules. More...

Typedefs
typedef Util::DefaultDataOutputHandler< MMCIFBZ2MolecularGraphWriter, DataFormat::MMCIF_BZ2 >	MMCIFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the MMCIF format. More...

typedef Util::CompressedDataWriter< MMCIFMolecularGraphWriter, Util::BZip2OStream >	MMCIFBZ2MolecularGraphWriter

typedef Util::DefaultDataInputHandler< MMCIFBZ2MoleculeReader, DataFormat::MMCIF_BZ2 >	MMCIFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the MMCIF format. More...

typedef Util::CompressedDataReader< MMCIFMoleculeReader, Util::BZip2IStream >	MMCIFBZ2MoleculeReader

typedef std::function< void(Biomol::MMCIFData &, const Chem::MolecularGraph &)>	MMCIFDataProcessingFunction
	A generic wrapper class used to store a user-defined function for the processing of Biomol::MMCIFData instances. More...

typedef Util::DefaultDataOutputHandler< MMCIFGZMolecularGraphWriter, DataFormat::MMCIF_GZ >	MMCIFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the MMCIF format. More...

typedef Util::CompressedDataWriter< MMCIFMolecularGraphWriter, Util::GZipOStream >	MMCIFGZMolecularGraphWriter

typedef Util::DefaultDataInputHandler< MMCIFGZMoleculeReader, DataFormat::MMCIF_GZ >	MMCIFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the MMCIF format. More...

typedef Util::CompressedDataReader< MMCIFMoleculeReader, Util::GZipIStream >	MMCIFGZMoleculeReader

typedef Util::DefaultDataOutputHandler< MMCIFMolecularGraphWriter, DataFormat::MMCIF >	MMCIFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the MMCIF format. More...

typedef Util::DefaultDataInputHandler< MMCIFMoleculeReader, DataFormat::MMCIF >	MMCIFMoleculeInputHandler
	A handler for the input of molecule data in the MMCIF format. More...

typedef Util::DefaultDataOutputHandler< MMTFBZ2MolecularGraphWriter, DataFormat::MMTF_BZ2 >	MMTFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...

typedef Util::CompressedDataWriter< MMTFMolecularGraphWriter, Util::BZip2OStream >	MMTFBZ2MolecularGraphWriter

typedef Util::DefaultDataInputHandler< MMTFBZ2MoleculeReader, DataFormat::MMTF_BZ2 >	MMTFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...

typedef Util::CompressedDataReader< MMTFMoleculeReader, Util::BZip2IStream >	MMTFBZ2MoleculeReader

typedef Util::DefaultDataOutputHandler< MMTFGZMolecularGraphWriter, DataFormat::MMTF_GZ >	MMTFGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...

typedef Util::CompressedDataWriter< MMTFMolecularGraphWriter, Util::GZipOStream >	MMTFGZMolecularGraphWriter

typedef Util::DefaultDataInputHandler< MMTFGZMoleculeReader, DataFormat::MMTF_GZ >	MMTFGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...

typedef Util::CompressedDataReader< MMTFMoleculeReader, Util::GZipIStream >	MMTFGZMoleculeReader

typedef Util::DefaultDataOutputHandler< MMTFMolecularGraphWriter, DataFormat::MMTF >	MMTFMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...

typedef Util::DefaultDataInputHandler< MMTFMoleculeReader, DataFormat::MMTF >	MMTFMoleculeInputHandler
	A handler for the input of molecule data in the Macromolecular Transmission Format (MMTF)y [MMTF]. More...

typedef Util::DefaultDataOutputHandler< PDBBZ2MolecularGraphWriter, DataFormat::PDB_BZ2 >	PDBBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

typedef Util::CompressedDataWriter< PDBMolecularGraphWriter, Util::BZip2OStream >	PDBBZ2MolecularGraphWriter

typedef Util::DefaultDataInputHandler< PDBBZ2MoleculeReader, DataFormat::PDB_BZ2 >	PDBBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

typedef Util::CompressedDataReader< PDBMoleculeReader, Util::BZip2IStream >	PDBBZ2MoleculeReader

typedef Util::DefaultDataOutputHandler< PDBGZMolecularGraphWriter, DataFormat::PDB_GZ >	PDBGZMolecularGraphOutputHandler
	A handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

typedef Util::CompressedDataWriter< PDBMolecularGraphWriter, Util::GZipOStream >	PDBGZMolecularGraphWriter

typedef Util::DefaultDataInputHandler< PDBGZMoleculeReader, DataFormat::PDB_GZ >	PDBGZMoleculeInputHandler
	A handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

typedef Util::CompressedDataReader< PDBMoleculeReader, Util::GZipIStream >	PDBGZMoleculeReader

typedef Util::DefaultDataOutputHandler< PDBMolecularGraphWriter, DataFormat::PDB >	PDBMolecularGraphOutputHandler
	A handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

typedef Util::DefaultDataInputHandler< PDBMoleculeReader, DataFormat::PDB >	PDBMoleculeInputHandler
	A handler for the input of molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

Functions
CDPL_BIOMOL_API const std::string &	getResidueAtomName (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueAtomName (Chem::Atom &atom, const std::string &name)

CDPL_BIOMOL_API void	clearResidueAtomName (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueAtomName (const Chem::Atom &atom)

CDPL_BIOMOL_API const std::string &	getResidueAltAtomName (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueAltAtomName (Chem::Atom &atom, const std::string &name)

CDPL_BIOMOL_API void	clearResidueAltAtomName (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueAltAtomName (const Chem::Atom &atom)

CDPL_BIOMOL_API bool	getResidueLeavingAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueLeavingAtomFlag (Chem::Atom &atom, bool leaving)

CDPL_BIOMOL_API void	clearResidueLeavingAtomFlag (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueLeavingAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API bool	getResidueLinkingAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueLinkingAtomFlag (Chem::Atom &atom, bool linking)

CDPL_BIOMOL_API void	clearResidueLinkingAtomFlag (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueLinkingAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API const std::string &	getResidueCode (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueCode (Chem::Atom &atom, const std::string &code)

CDPL_BIOMOL_API void	clearResidueCode (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueCode (const Chem::Atom &atom)

CDPL_BIOMOL_API long	getResidueSequenceNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueSequenceNumber (Chem::Atom &atom, long seq_no)

CDPL_BIOMOL_API void	clearResidueSequenceNumber (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueSequenceNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API char	getResidueInsertionCode (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setResidueInsertionCode (Chem::Atom &atom, char code)

CDPL_BIOMOL_API void	clearResidueInsertionCode (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasResidueInsertionCode (const Chem::Atom &atom)

CDPL_BIOMOL_API bool	getHeteroAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setHeteroAtomFlag (Chem::Atom &atom, bool is_het)

CDPL_BIOMOL_API void	clearHeteroAtomFlag (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasHeteroAtomFlag (const Chem::Atom &atom)

CDPL_BIOMOL_API const std::string &	getChainID (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setChainID (Chem::Atom &atom, const std::string &id)

CDPL_BIOMOL_API void	clearChainID (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasChainID (const Chem::Atom &atom)

CDPL_BIOMOL_API char	getAltLocationID (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setAltLocationID (Chem::Atom &atom, char id)

CDPL_BIOMOL_API void	clearAltLocationID (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasAltLocationID (const Chem::Atom &atom)

CDPL_BIOMOL_API const std::string &	getEntityID (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setEntityID (Chem::Atom &atom, const std::string &id)

CDPL_BIOMOL_API void	clearEntityID (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasEntityID (const Chem::Atom &atom)

CDPL_BIOMOL_API std::size_t	getModelNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setModelNumber (Chem::Atom &atom, std::size_t model_no)

CDPL_BIOMOL_API void	clearModelNumber (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasModelNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API long	getSerialNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setSerialNumber (Chem::Atom &atom, long serial_no)

CDPL_BIOMOL_API void	clearSerialNumber (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasSerialNumber (const Chem::Atom &atom)

CDPL_BIOMOL_API double	getOccupancy (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setOccupancy (Chem::Atom &atom, double occupancy)

CDPL_BIOMOL_API void	clearOccupancy (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasOccupancy (const Chem::Atom &atom)

CDPL_BIOMOL_API double	getBFactor (const Chem::Atom &atom)

CDPL_BIOMOL_API void	setBFactor (Chem::Atom &atom, double factor)

CDPL_BIOMOL_API void	clearBFactor (Chem::Atom &atom)

CDPL_BIOMOL_API bool	hasBFactor (const Chem::Atom &atom)

CDPL_BIOMOL_API bool	isPDBBackboneAtom (const Chem::Atom &atom)

CDPL_BIOMOL_API bool	matchesResidueInfo (const Chem::Atom &atom, const char res_code=0, const char chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0, const char *atom_name=0, long serial_no=IGNORE_SERIAL_NO)

CDPL_BIOMOL_API bool	areInSameResidue (const Chem::Atom &atom1, const Chem::Atom &atom2, unsigned int flags=AtomPropertyFlag::DEFAULT)

CDPL_BIOMOL_API void	extractResidueSubstructure (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, Chem::Fragment &res_substruct, bool cnctd_only=false, unsigned int flags=AtomPropertyFlag::DEFAULT, bool append=false)

CDPL_BIOMOL_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)

CDPL_BIOMOL_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check)

CDPL_BIOMOL_API bool	hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API const ResidueDictionary::SharedPointer &	getResidueDictionaryParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setResidueDictionaryParameter (Base::ControlParameterContainer &cntnr, const ResidueDictionary::SharedPointer &dict)

CDPL_BIOMOL_API bool	hasResidueDictionaryParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearResidueDictionaryParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getApplyDictFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setApplyDictFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasApplyDictFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearApplyDictFormalChargesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getApplyDictAtomTypesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setApplyDictAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasApplyDictAtomTypesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearApplyDictAtomTypesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getCalcMissingFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setCalcMissingFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)

CDPL_BIOMOL_API bool	hasCalcMissingFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearCalcMissingFormalChargesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPerceiveMissingBondOrdersParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPerceiveMissingBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive)

CDPL_BIOMOL_API bool	hasPerceiveMissingBondOrdersParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPerceiveMissingBondOrdersParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getCombineInterferingResidueCoordinatesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setCombineInterferingResidueCoordinatesParameter (Base::ControlParameterContainer &cntnr, bool comb)

CDPL_BIOMOL_API bool	hasCombineInterferingResidueCoordinatesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearCombineInterferingResidueCoordinatesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBApplyDictAtomBondingToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBApplyDictAtomBondingToStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasPDBApplyDictAtomBondingToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBApplyDictAtomBondingToStdResiduesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBApplyDictAtomBondingToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasPDBApplyDictAtomBondingToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBApplyDictBondOrdersToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBApplyDictBondOrdersToStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasPDBApplyDictBondOrdersToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBApplyDictBondOrdersToStdResiduesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBApplyDictBondOrdersToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasPDBApplyDictBondOrdersToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBIgnoreConectRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBIgnoreConectRecordsParameter (Base::ControlParameterContainer &cntnr, bool ignore)

CDPL_BIOMOL_API bool	hasPDBIgnoreConectRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBIgnoreConectRecordsParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBDeduceBondOrdersFromCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base::ControlParameterContainer &cntnr, bool deduce)

CDPL_BIOMOL_API bool	hasPDBDeduceBondOrdersFromCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBIgnoreFormalChargeFieldParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBIgnoreFormalChargeFieldParameter (Base::ControlParameterContainer &cntnr, bool ignore)

CDPL_BIOMOL_API bool	hasPDBIgnoreFormalChargeFieldParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBIgnoreFormalChargeFieldParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBEvaluateMASTERRecordParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBEvaluateMASTERRecordParameter (Base::ControlParameterContainer &cntnr, bool eval)

CDPL_BIOMOL_API bool	hasPDBEvaluateMASTERRecordParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBEvaluateMASTERRecordParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc)

CDPL_BIOMOL_API bool	hasPDBTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBTruncateLinesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBWriteFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBWriteFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool write)

CDPL_BIOMOL_API bool	hasPDBWriteFormalChargesParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBWriteFormalChargesParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBWriteCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBWriteCONECTRecordsParameter (Base::ControlParameterContainer &cntnr, bool write)

CDPL_BIOMOL_API bool	hasPDBWriteCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBWriteCONECTRecordsParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBWriteCONECTRecordsForAllBondsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBWriteCONECTRecordsForAllBondsParameter (Base::ControlParameterContainer &cntnr, bool write)

CDPL_BIOMOL_API bool	hasPDBWriteCONECTRecordsForAllBondsParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBWriteCONECTRecordsForAllBondsParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getPDBWriteCONECTRecordsReflectingBondOrderParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBWriteCONECTRecordsReflectingBondOrderParameter (Base::ControlParameterContainer &cntnr, bool write)

CDPL_BIOMOL_API bool	hasPDBWriteCONECTRecordsReflectingBondOrderParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBWriteCONECTRecordsReflectingBondOrderParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API unsigned int	getPDBFormatVersionParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setPDBFormatVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int ver)

CDPL_BIOMOL_API bool	hasPDBFormatVersionParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearPDBFormatVersionParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getMMCIFApplyDictAtomBondingParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setMMCIFApplyDictAtomBondingParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasMMCIFApplyDictAtomBondingParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearMMCIFApplyDictAtomBondingParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getMMCIFApplyDictBondOrdersParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setMMCIFApplyDictBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool apply)

CDPL_BIOMOL_API bool	hasMMCIFApplyDictBondOrdersParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearMMCIFApplyDictBondOrdersParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API bool	getMMCIFOutputBiopolymersAsChemCompParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setMMCIFOutputBiopolymersAsChemCompParameter (Base::ControlParameterContainer &cntnr, bool output)

CDPL_BIOMOL_API bool	hasMMCIFOutputBiopolymersAsChemCompParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearMMCIFOutputBiopolymersAsChemCompParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API const MMCIFDataProcessingFunction &	getMMCIFOutputDataPostprocFunctionParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	setMMCIFOutputDataPostprocFunctionParameter (Base::ControlParameterContainer &cntnr, const MMCIFDataProcessingFunction &func)

CDPL_BIOMOL_API bool	hasMMCIFOutputDataPostprocFunctionParameter (const Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API void	clearMMCIFOutputDataPostprocFunctionParameter (Base::ControlParameterContainer &cntnr)

CDPL_BIOMOL_API std::ostream &	operator<< (std::ostream &os, const MMCIFData &data)

CDPL_BIOMOL_API std::ostream &	operator<< (std::ostream &os, const MMCIFData::Category &cat)

CDPL_BIOMOL_API const std::string &	getResidueCode (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setResidueCode (Chem::MolecularGraph &molgraph, const std::string &code)

CDPL_BIOMOL_API void	clearResidueCode (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasResidueCode (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API long	getResidueSequenceNumber (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setResidueSequenceNumber (Chem::MolecularGraph &molgraph, long seq_no)

CDPL_BIOMOL_API void	clearResidueSequenceNumber (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasResidueSequenceNumber (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API char	getResidueInsertionCode (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setResidueInsertionCode (Chem::MolecularGraph &molgraph, char code)

CDPL_BIOMOL_API void	clearResidueInsertionCode (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasResidueInsertionCode (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API const std::string &	getChainID (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setChainID (Chem::MolecularGraph &molgraph, const std::string &id)

CDPL_BIOMOL_API void	clearChainID (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasChainID (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API std::size_t	getModelNumber (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setModelNumber (Chem::MolecularGraph &molgraph, std::size_t model_no)

CDPL_BIOMOL_API void	clearModelNumber (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasModelNumber (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API const PDBData::SharedPointer &	getPDBData (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setPDBData (Chem::MolecularGraph &molgraph, const PDBData::SharedPointer &data)

CDPL_BIOMOL_API void	clearPDBData (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasPDBData (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API const MMCIFData::SharedPointer &	getMMCIFData (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	setMMCIFData (Chem::MolecularGraph &molgraph, const MMCIFData::SharedPointer &data)

CDPL_BIOMOL_API void	clearMMCIFData (Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API bool	hasMMCIFData (const Chem::MolecularGraph &molgraph)

CDPL_BIOMOL_API void	extractResidueSubstructures (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent_molgraph, Chem::Fragment &res_substructs, bool cnctd_only=false, unsigned int flags=AtomPropertyFlag::DEFAULT, bool append=false)

CDPL_BIOMOL_API void	extractProximalAtoms (const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_atoms, double max_dist, bool inc_core_atoms=false, bool append=false)

CDPL_BIOMOL_API void	extractProximalAtoms (const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_atoms, const Chem::Atom3DCoordinatesFunction &coords_func, double max_dist, bool inc_core_atoms=false, bool append=false)

CDPL_BIOMOL_API void	extractEnvironmentResidues (const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_residues, double max_dist, bool append=false)

CDPL_BIOMOL_API void	extractEnvironmentResidues (const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_residues, const Chem::Atom3DCoordinatesFunction &coords_func, double max_dist, bool append=false)

CDPL_BIOMOL_API void	setHydrogenResidueSequenceInfo (Chem::MolecularGraph &molgraph, bool overwrite, unsigned int flags=AtomPropertyFlag::DEFAULT)

CDPL_BIOMOL_API bool	matchesResidueInfo (const Chem::MolecularGraph &molgraph, const char res_code=0, const char chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0)

CDPL_BIOMOL_API bool	combineInterferingResidueCoordinates (Chem::Molecule &mol, double max_ctr_dist=1.0)

template<typename Iter >
Iter	findResidueAtom (Iter it, Iter end, const char res_code=0, const char chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0, const char *atom_name=0, long serial_no=IGNORE_SERIAL_NO)

template<typename Iter >
Iter	findResidue (Iter it, Iter end, const char res_code=0, const char chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0, const char *atom_name=0, long serial_no=IGNORE_SERIAL_NO)

Variables
const long	IGNORE_SEQUENCE_NO = std::numeric_limits<long>::min()

const long	IGNORE_SERIAL_NO = std::numeric_limits<long>::min()

Detailed Description

Contains classes and functions related to biological macromolecules.

Typedef Documentation

◆ MMCIFBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMCIFBZ2MolecularGraphWriter, DataFormat::MMCIF_BZ2> CDPL::Biomol::MMCIFBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the MMCIF format.

Since: 1.2

◆ MMCIFBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<MMCIFMolecularGraphWriter, Util::BZip2OStream> CDPL::Biomol::MMCIFBZ2MolecularGraphWriter

Since: 1.2

◆ MMCIFBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMCIFBZ2MoleculeReader, DataFormat::MMCIF_BZ2> CDPL::Biomol::MMCIFBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the MMCIF format.

Since: 1.2

◆ MMCIFBZ2MoleculeReader

typedef Util::CompressedDataReader<MMCIFMoleculeReader, Util::BZip2IStream> CDPL::Biomol::MMCIFBZ2MoleculeReader

Since: 1.2

◆ MMCIFDataProcessingFunction

typedef std::function<void(Biomol::MMCIFData&, const Chem::MolecularGraph&)> CDPL::Biomol::MMCIFDataProcessingFunction

A generic wrapper class used to store a user-defined function for the processing of Biomol::MMCIFData instances.

◆ MMCIFGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMCIFGZMolecularGraphWriter, DataFormat::MMCIF_GZ> CDPL::Biomol::MMCIFGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the MMCIF format.

Since: 1.2

◆ MMCIFGZMolecularGraphWriter

typedef Util::CompressedDataWriter<MMCIFMolecularGraphWriter, Util::GZipOStream> CDPL::Biomol::MMCIFGZMolecularGraphWriter

Since: 1.2

◆ MMCIFGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMCIFGZMoleculeReader, DataFormat::MMCIF_GZ> CDPL::Biomol::MMCIFGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the MMCIF format.

Since: 1.2

◆ MMCIFGZMoleculeReader

typedef Util::CompressedDataReader<MMCIFMoleculeReader, Util::GZipIStream> CDPL::Biomol::MMCIFGZMoleculeReader

Since: 1.2

◆ MMCIFMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMCIFMolecularGraphWriter, DataFormat::MMCIF> CDPL::Biomol::MMCIFMolecularGraphOutputHandler

A handler for the output of molecular graph data in the MMCIF format.

Since: 1.2

◆ MMCIFMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMCIFMoleculeReader, DataFormat::MMCIF> CDPL::Biomol::MMCIFMoleculeInputHandler

A handler for the input of molecule data in the MMCIF format.

Since: 1.2

◆ MMTFBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMTFBZ2MolecularGraphWriter, DataFormat::MMTF_BZ2> CDPL::Biomol::MMTFBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<MMTFMolecularGraphWriter, Util::BZip2OStream> CDPL::Biomol::MMTFBZ2MolecularGraphWriter

◆ MMTFBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMTFBZ2MoleculeReader, DataFormat::MMTF_BZ2> CDPL::Biomol::MMTFBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format.

◆ MMTFBZ2MoleculeReader

typedef Util::CompressedDataReader<MMTFMoleculeReader, Util::BZip2IStream> CDPL::Biomol::MMTFBZ2MoleculeReader

◆ MMTFGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMTFGZMolecularGraphWriter, DataFormat::MMTF_GZ> CDPL::Biomol::MMTFGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFGZMolecularGraphWriter

typedef Util::CompressedDataWriter<MMTFMolecularGraphWriter, Util::GZipOStream> CDPL::Biomol::MMTFGZMolecularGraphWriter

◆ MMTFGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMTFGZMoleculeReader, DataFormat::MMTF_GZ> CDPL::Biomol::MMTFGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format.

◆ MMTFGZMoleculeReader

typedef Util::CompressedDataReader<MMTFMoleculeReader, Util::GZipIStream> CDPL::Biomol::MMTFGZMoleculeReader

◆ MMTFMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<MMTFMolecularGraphWriter, DataFormat::MMTF> CDPL::Biomol::MMTFMolecularGraphOutputHandler

A handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] format.

◆ MMTFMoleculeInputHandler

typedef Util::DefaultDataInputHandler<MMTFMoleculeReader, DataFormat::MMTF> CDPL::Biomol::MMTFMoleculeInputHandler

A handler for the input of molecule data in the Macromolecular Transmission Format (MMTF)y [MMTF].

◆ PDBBZ2MolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<PDBBZ2MolecularGraphWriter, DataFormat::PDB_BZ2> CDPL::Biomol::PDBBZ2MolecularGraphOutputHandler

A handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBBZ2MolecularGraphWriter

typedef Util::CompressedDataWriter<PDBMolecularGraphWriter, Util::BZip2OStream> CDPL::Biomol::PDBBZ2MolecularGraphWriter

◆ PDBBZ2MoleculeInputHandler

typedef Util::DefaultDataInputHandler<PDBBZ2MoleculeReader, DataFormat::PDB_BZ2> CDPL::Biomol::PDBBZ2MoleculeInputHandler

A handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBBZ2MoleculeReader

typedef Util::CompressedDataReader<PDBMoleculeReader, Util::BZip2IStream> CDPL::Biomol::PDBBZ2MoleculeReader

◆ PDBGZMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<PDBGZMolecularGraphWriter, DataFormat::PDB_GZ> CDPL::Biomol::PDBGZMolecularGraphOutputHandler

A handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBGZMolecularGraphWriter

typedef Util::CompressedDataWriter<PDBMolecularGraphWriter, Util::GZipOStream> CDPL::Biomol::PDBGZMolecularGraphWriter

◆ PDBGZMoleculeInputHandler

typedef Util::DefaultDataInputHandler<PDBGZMoleculeReader, DataFormat::PDB_GZ> CDPL::Biomol::PDBGZMoleculeInputHandler

A handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBGZMoleculeReader

typedef Util::CompressedDataReader<PDBMoleculeReader, Util::GZipIStream> CDPL::Biomol::PDBGZMoleculeReader

◆ PDBMolecularGraphOutputHandler

typedef Util::DefaultDataOutputHandler<PDBMolecularGraphWriter, DataFormat::PDB> CDPL::Biomol::PDBMolecularGraphOutputHandler

A handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBMoleculeInputHandler

typedef Util::DefaultDataInputHandler<PDBMoleculeReader, DataFormat::PDB> CDPL::Biomol::PDBMoleculeInputHandler

A handler for the input of molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format.

Function Documentation

◆ getResidueAtomName()

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getResidueAtomName ( const Chem::Atom & atom )

◆ setResidueAtomName()

CDPL_BIOMOL_API void CDPL::Biomol::setResidueAtomName	(	Chem::Atom &	atom,
		const std::string &	name
	)

◆ clearResidueAtomName()

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueAtomName ( Chem::Atom & atom )

◆ hasResidueAtomName()

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueAtomName ( const Chem::Atom & atom )

◆ getResidueAltAtomName()

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getResidueAltAtomName ( const Chem::Atom & atom )

◆ setResidueAltAtomName()

CDPL_BIOMOL_API void CDPL::Biomol::setResidueAltAtomName	(	Chem::Atom &	atom,
		const std::string &	name
	)

◆ clearResidueAltAtomName()

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueAltAtomName ( Chem::Atom & atom )

◆ hasResidueAltAtomName()

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueAltAtomName ( const Chem::Atom & atom )

◆ getResidueLeavingAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::getResidueLeavingAtomFlag ( const Chem::Atom & atom )

◆ setResidueLeavingAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::setResidueLeavingAtomFlag	(	Chem::Atom &	atom,
		bool	leaving
	)

◆ clearResidueLeavingAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueLeavingAtomFlag ( Chem::Atom & atom )

◆ hasResidueLeavingAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueLeavingAtomFlag ( const Chem::Atom & atom )

◆ getResidueLinkingAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::getResidueLinkingAtomFlag ( const Chem::Atom & atom )

◆ setResidueLinkingAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::setResidueLinkingAtomFlag	(	Chem::Atom &	atom,
		bool	linking
	)

◆ clearResidueLinkingAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueLinkingAtomFlag ( Chem::Atom & atom )

◆ hasResidueLinkingAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueLinkingAtomFlag ( const Chem::Atom & atom )

◆ getResidueCode() [1/2]

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getResidueCode ( const Chem::Atom & atom )

◆ setResidueCode() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueCode	(	Chem::Atom &	atom,
		const std::string &	code
	)

◆ clearResidueCode() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueCode ( Chem::Atom & atom )

◆ hasResidueCode() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueCode ( const Chem::Atom & atom )

◆ getResidueSequenceNumber() [1/2]

CDPL_BIOMOL_API long CDPL::Biomol::getResidueSequenceNumber ( const Chem::Atom & atom )

◆ setResidueSequenceNumber() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueSequenceNumber	(	Chem::Atom &	atom,
		long	seq_no
	)

◆ clearResidueSequenceNumber() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueSequenceNumber ( Chem::Atom & atom )

◆ hasResidueSequenceNumber() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueSequenceNumber ( const Chem::Atom & atom )

◆ getResidueInsertionCode() [1/2]

CDPL_BIOMOL_API char CDPL::Biomol::getResidueInsertionCode ( const Chem::Atom & atom )

◆ setResidueInsertionCode() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueInsertionCode	(	Chem::Atom &	atom,
		char	code
	)

◆ clearResidueInsertionCode() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueInsertionCode ( Chem::Atom & atom )

◆ hasResidueInsertionCode() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueInsertionCode ( const Chem::Atom & atom )

◆ getHeteroAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::getHeteroAtomFlag ( const Chem::Atom & atom )

◆ setHeteroAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::setHeteroAtomFlag	(	Chem::Atom &	atom,
		bool	is_het
	)

◆ clearHeteroAtomFlag()

CDPL_BIOMOL_API void CDPL::Biomol::clearHeteroAtomFlag ( Chem::Atom & atom )

◆ hasHeteroAtomFlag()

CDPL_BIOMOL_API bool CDPL::Biomol::hasHeteroAtomFlag ( const Chem::Atom & atom )

◆ getChainID() [1/2]

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getChainID ( const Chem::Atom & atom )

◆ setChainID() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::setChainID	(	Chem::Atom &	atom,
		const std::string &	id
	)

◆ clearChainID() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearChainID ( Chem::Atom & atom )

◆ hasChainID() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasChainID ( const Chem::Atom & atom )

◆ getAltLocationID()

CDPL_BIOMOL_API char CDPL::Biomol::getAltLocationID ( const Chem::Atom & atom )

◆ setAltLocationID()

CDPL_BIOMOL_API void CDPL::Biomol::setAltLocationID	(	Chem::Atom &	atom,
		char	id
	)

◆ clearAltLocationID()

CDPL_BIOMOL_API void CDPL::Biomol::clearAltLocationID ( Chem::Atom & atom )

◆ hasAltLocationID()

CDPL_BIOMOL_API bool CDPL::Biomol::hasAltLocationID ( const Chem::Atom & atom )

◆ getEntityID()

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getEntityID ( const Chem::Atom & atom )

Since: 1.2

◆ setEntityID()

CDPL_BIOMOL_API void CDPL::Biomol::setEntityID	(	Chem::Atom &	atom,
		const std::string &	id
	)

◆ clearEntityID()

CDPL_BIOMOL_API void CDPL::Biomol::clearEntityID ( Chem::Atom & atom )

◆ hasEntityID()

CDPL_BIOMOL_API bool CDPL::Biomol::hasEntityID ( const Chem::Atom & atom )

◆ getModelNumber() [1/2]

CDPL_BIOMOL_API std::size_t CDPL::Biomol::getModelNumber ( const Chem::Atom & atom )

◆ setModelNumber() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::setModelNumber	(	Chem::Atom &	atom,
		std::size_t	model_no
	)

◆ clearModelNumber() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearModelNumber ( Chem::Atom & atom )

◆ hasModelNumber() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasModelNumber ( const Chem::Atom & atom )

◆ getSerialNumber()

CDPL_BIOMOL_API long CDPL::Biomol::getSerialNumber ( const Chem::Atom & atom )

◆ setSerialNumber()

CDPL_BIOMOL_API void CDPL::Biomol::setSerialNumber	(	Chem::Atom &	atom,
		long	serial_no
	)

◆ clearSerialNumber()

CDPL_BIOMOL_API void CDPL::Biomol::clearSerialNumber ( Chem::Atom & atom )

◆ hasSerialNumber()

CDPL_BIOMOL_API bool CDPL::Biomol::hasSerialNumber ( const Chem::Atom & atom )

◆ getOccupancy()

CDPL_BIOMOL_API double CDPL::Biomol::getOccupancy ( const Chem::Atom & atom )

◆ setOccupancy()

CDPL_BIOMOL_API void CDPL::Biomol::setOccupancy	(	Chem::Atom &	atom,
		double	occupancy
	)

◆ clearOccupancy()

CDPL_BIOMOL_API void CDPL::Biomol::clearOccupancy ( Chem::Atom & atom )

◆ hasOccupancy()

CDPL_BIOMOL_API bool CDPL::Biomol::hasOccupancy ( const Chem::Atom & atom )

◆ getBFactor()

CDPL_BIOMOL_API double CDPL::Biomol::getBFactor ( const Chem::Atom & atom )

◆ setBFactor()

CDPL_BIOMOL_API void CDPL::Biomol::setBFactor	(	Chem::Atom &	atom,
		double	factor
	)

◆ clearBFactor()

CDPL_BIOMOL_API void CDPL::Biomol::clearBFactor ( Chem::Atom & atom )

◆ hasBFactor()

CDPL_BIOMOL_API bool CDPL::Biomol::hasBFactor ( const Chem::Atom & atom )

◆ isPDBBackboneAtom()

CDPL_BIOMOL_API bool CDPL::Biomol::isPDBBackboneAtom ( const Chem::Atom & atom )

◆ matchesResidueInfo() [1/2]

CDPL_BIOMOL_API bool CDPL::Biomol::matchesResidueInfo	(	const Chem::Atom &	atom,
		const char *	res_code = `0`,
		const char *	chain_id = `0`,
		long	res_seq_no = `IGNORE_SEQUENCE_NO`,
		char	ins_code = `0`,
		std::size_t	model_no = `0`,
		const char *	atom_name = `0`,
		long	serial_no = `IGNORE_SERIAL_NO`
	)

◆ areInSameResidue()

CDPL_BIOMOL_API bool CDPL::Biomol::areInSameResidue	(	const Chem::Atom &	atom1,
		const Chem::Atom &	atom2,
		unsigned int	flags = `AtomPropertyFlag::DEFAULT`
	)

◆ extractResidueSubstructure()

CDPL_BIOMOL_API void CDPL::Biomol::extractResidueSubstructure	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		Chem::Fragment &	res_substruct,
		bool	cnctd_only = `false`,
		unsigned int	flags = `AtomPropertyFlag::DEFAULT`,
		bool	append = `false`
	)

◆ getStrictErrorCheckingParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

◆ setStrictErrorCheckingParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setStrictErrorCheckingParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	strict
	)

◆ hasStrictErrorCheckingParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasStrictErrorCheckingParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearStrictErrorCheckingParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearStrictErrorCheckingParameter ( Base::ControlParameterContainer & cntnr )

◆ getCheckLineLengthParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getCheckLineLengthParameter ( const Base::ControlParameterContainer & cntnr )

◆ setCheckLineLengthParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setCheckLineLengthParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	check
	)

◆ hasCheckLineLengthParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasCheckLineLengthParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearCheckLineLengthParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearCheckLineLengthParameter ( Base::ControlParameterContainer & cntnr )

◆ getResidueDictionaryParameter()

CDPL_BIOMOL_API const ResidueDictionary::SharedPointer& CDPL::Biomol::getResidueDictionaryParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setResidueDictionaryParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setResidueDictionaryParameter	(	Base::ControlParameterContainer &	cntnr,
		const ResidueDictionary::SharedPointer &	dict
	)

◆ hasResidueDictionaryParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueDictionaryParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearResidueDictionaryParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueDictionaryParameter ( Base::ControlParameterContainer & cntnr )

◆ getApplyDictFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getApplyDictFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setApplyDictFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setApplyDictFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasApplyDictFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasApplyDictFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearApplyDictFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearApplyDictFormalChargesParameter ( Base::ControlParameterContainer & cntnr )

◆ getApplyDictAtomTypesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getApplyDictAtomTypesParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setApplyDictAtomTypesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setApplyDictAtomTypesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasApplyDictAtomTypesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasApplyDictAtomTypesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearApplyDictAtomTypesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearApplyDictAtomTypesParameter ( Base::ControlParameterContainer & cntnr )

◆ getCalcMissingFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getCalcMissingFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setCalcMissingFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setCalcMissingFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	calc
	)

◆ hasCalcMissingFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasCalcMissingFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearCalcMissingFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearCalcMissingFormalChargesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPerceiveMissingBondOrdersParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPerceiveMissingBondOrdersParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setPerceiveMissingBondOrdersParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPerceiveMissingBondOrdersParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	perceive
	)

◆ hasPerceiveMissingBondOrdersParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPerceiveMissingBondOrdersParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPerceiveMissingBondOrdersParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPerceiveMissingBondOrdersParameter ( Base::ControlParameterContainer & cntnr )

◆ getCombineInterferingResidueCoordinatesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getCombineInterferingResidueCoordinatesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setCombineInterferingResidueCoordinatesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setCombineInterferingResidueCoordinatesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	comb
	)

◆ hasCombineInterferingResidueCoordinatesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasCombineInterferingResidueCoordinatesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearCombineInterferingResidueCoordinatesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearCombineInterferingResidueCoordinatesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBApplyDictAtomBondingToStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBApplyDictAtomBondingToStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBApplyDictAtomBondingToStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBApplyDictAtomBondingToStdResiduesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasPDBApplyDictAtomBondingToStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBApplyDictAtomBondingToStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBApplyDictAtomBondingToStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBApplyDictAtomBondingToStdResiduesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBApplyDictAtomBondingToNonStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBApplyDictAtomBondingToNonStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBApplyDictAtomBondingToNonStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBApplyDictAtomBondingToNonStdResiduesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasPDBApplyDictAtomBondingToNonStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBApplyDictAtomBondingToNonStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBApplyDictAtomBondingToNonStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBApplyDictAtomBondingToNonStdResiduesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBApplyDictBondOrdersToStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBApplyDictBondOrdersToStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBApplyDictBondOrdersToStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBApplyDictBondOrdersToStdResiduesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasPDBApplyDictBondOrdersToStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBApplyDictBondOrdersToStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBApplyDictBondOrdersToStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBApplyDictBondOrdersToStdResiduesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBApplyDictBondOrdersToNonStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBApplyDictBondOrdersToNonStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBApplyDictBondOrdersToNonStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBApplyDictBondOrdersToNonStdResiduesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasPDBApplyDictBondOrdersToNonStdResiduesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBApplyDictBondOrdersToNonStdResiduesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBApplyDictBondOrdersToNonStdResiduesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBApplyDictBondOrdersToNonStdResiduesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBIgnoreConectRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBIgnoreConectRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBIgnoreConectRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBIgnoreConectRecordsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	ignore
	)

◆ hasPDBIgnoreConectRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBIgnoreConectRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBIgnoreConectRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBIgnoreConectRecordsParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBDeduceBondOrdersFromCONECTRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBDeduceBondOrdersFromCONECTRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBDeduceBondOrdersFromCONECTRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBDeduceBondOrdersFromCONECTRecordsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	deduce
	)

◆ hasPDBDeduceBondOrdersFromCONECTRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBDeduceBondOrdersFromCONECTRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBDeduceBondOrdersFromCONECTRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBDeduceBondOrdersFromCONECTRecordsParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBIgnoreFormalChargeFieldParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBIgnoreFormalChargeFieldParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBIgnoreFormalChargeFieldParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBIgnoreFormalChargeFieldParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	ignore
	)

◆ hasPDBIgnoreFormalChargeFieldParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBIgnoreFormalChargeFieldParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBIgnoreFormalChargeFieldParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBIgnoreFormalChargeFieldParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBEvaluateMASTERRecordParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBEvaluateMASTERRecordParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBEvaluateMASTERRecordParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBEvaluateMASTERRecordParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	eval
	)

◆ hasPDBEvaluateMASTERRecordParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBEvaluateMASTERRecordParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBEvaluateMASTERRecordParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBEvaluateMASTERRecordParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBTruncateLinesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBTruncateLinesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBTruncateLinesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBTruncateLinesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	trunc
	)

◆ hasPDBTruncateLinesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBTruncateLinesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBTruncateLinesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBTruncateLinesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBWriteFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBWriteFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBWriteFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBWriteFormalChargesParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

◆ hasPDBWriteFormalChargesParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBWriteFormalChargesParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBWriteFormalChargesParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBWriteFormalChargesParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBWriteCONECTRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBWriteCONECTRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBWriteCONECTRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBWriteCONECTRecordsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

◆ hasPDBWriteCONECTRecordsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBWriteCONECTRecordsParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBWriteCONECTRecordsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBWriteCONECTRecordsParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBWriteCONECTRecordsForAllBondsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBWriteCONECTRecordsForAllBondsParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBWriteCONECTRecordsForAllBondsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBWriteCONECTRecordsForAllBondsParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

◆ hasPDBWriteCONECTRecordsForAllBondsParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBWriteCONECTRecordsForAllBondsParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBWriteCONECTRecordsForAllBondsParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBWriteCONECTRecordsForAllBondsParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBWriteCONECTRecordsReflectingBondOrderParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getPDBWriteCONECTRecordsReflectingBondOrderParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBWriteCONECTRecordsReflectingBondOrderParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBWriteCONECTRecordsReflectingBondOrderParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	write
	)

◆ hasPDBWriteCONECTRecordsReflectingBondOrderParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBWriteCONECTRecordsReflectingBondOrderParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBWriteCONECTRecordsReflectingBondOrderParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBWriteCONECTRecordsReflectingBondOrderParameter ( Base::ControlParameterContainer & cntnr )

◆ getPDBFormatVersionParameter()

CDPL_BIOMOL_API unsigned int CDPL::Biomol::getPDBFormatVersionParameter ( const Base::ControlParameterContainer & cntnr )

◆ setPDBFormatVersionParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBFormatVersionParameter	(	Base::ControlParameterContainer &	cntnr,
		unsigned int	ver
	)

◆ hasPDBFormatVersionParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBFormatVersionParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearPDBFormatVersionParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBFormatVersionParameter ( Base::ControlParameterContainer & cntnr )

◆ getMMCIFApplyDictAtomBondingParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getMMCIFApplyDictAtomBondingParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setMMCIFApplyDictAtomBondingParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setMMCIFApplyDictAtomBondingParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasMMCIFApplyDictAtomBondingParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasMMCIFApplyDictAtomBondingParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearMMCIFApplyDictAtomBondingParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearMMCIFApplyDictAtomBondingParameter ( Base::ControlParameterContainer & cntnr )

◆ getMMCIFApplyDictBondOrdersParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getMMCIFApplyDictBondOrdersParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setMMCIFApplyDictBondOrdersParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setMMCIFApplyDictBondOrdersParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	apply
	)

◆ hasMMCIFApplyDictBondOrdersParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasMMCIFApplyDictBondOrdersParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearMMCIFApplyDictBondOrdersParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearMMCIFApplyDictBondOrdersParameter ( Base::ControlParameterContainer & cntnr )

◆ getMMCIFOutputBiopolymersAsChemCompParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::getMMCIFOutputBiopolymersAsChemCompParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setMMCIFOutputBiopolymersAsChemCompParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setMMCIFOutputBiopolymersAsChemCompParameter	(	Base::ControlParameterContainer &	cntnr,
		bool	output
	)

◆ hasMMCIFOutputBiopolymersAsChemCompParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasMMCIFOutputBiopolymersAsChemCompParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearMMCIFOutputBiopolymersAsChemCompParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearMMCIFOutputBiopolymersAsChemCompParameter ( Base::ControlParameterContainer & cntnr )

◆ getMMCIFOutputDataPostprocFunctionParameter()

CDPL_BIOMOL_API const MMCIFDataProcessingFunction& CDPL::Biomol::getMMCIFOutputDataPostprocFunctionParameter ( const Base::ControlParameterContainer & cntnr )

Since: 1.2

◆ setMMCIFOutputDataPostprocFunctionParameter()

CDPL_BIOMOL_API void CDPL::Biomol::setMMCIFOutputDataPostprocFunctionParameter	(	Base::ControlParameterContainer &	cntnr,
		const MMCIFDataProcessingFunction &	func
	)

◆ hasMMCIFOutputDataPostprocFunctionParameter()

CDPL_BIOMOL_API bool CDPL::Biomol::hasMMCIFOutputDataPostprocFunctionParameter ( const Base::ControlParameterContainer & cntnr )

◆ clearMMCIFOutputDataPostprocFunctionParameter()

CDPL_BIOMOL_API void CDPL::Biomol::clearMMCIFOutputDataPostprocFunctionParameter ( Base::ControlParameterContainer & cntnr )

◆ operator<<() [1/2]

CDPL_BIOMOL_API std::ostream& CDPL::Biomol::operator<<	(	std::ostream &	os,
		const MMCIFData &	data
	)

Since: 1.2

◆ operator<<() [2/2]

CDPL_BIOMOL_API std::ostream& CDPL::Biomol::operator<<	(	std::ostream &	os,
		const MMCIFData::Category &	cat
	)

Since: 1.2

◆ getResidueCode() [2/2]

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getResidueCode ( const Chem::MolecularGraph & molgraph )

◆ setResidueCode() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueCode	(	Chem::MolecularGraph &	molgraph,
		const std::string &	code
	)

◆ clearResidueCode() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueCode ( Chem::MolecularGraph & molgraph )

◆ hasResidueCode() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueCode ( const Chem::MolecularGraph & molgraph )

◆ getResidueSequenceNumber() [2/2]

CDPL_BIOMOL_API long CDPL::Biomol::getResidueSequenceNumber ( const Chem::MolecularGraph & molgraph )

◆ setResidueSequenceNumber() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueSequenceNumber	(	Chem::MolecularGraph &	molgraph,
		long	seq_no
	)

◆ clearResidueSequenceNumber() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueSequenceNumber ( Chem::MolecularGraph & molgraph )

◆ hasResidueSequenceNumber() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueSequenceNumber ( const Chem::MolecularGraph & molgraph )

◆ getResidueInsertionCode() [2/2]

CDPL_BIOMOL_API char CDPL::Biomol::getResidueInsertionCode ( const Chem::MolecularGraph & molgraph )

◆ setResidueInsertionCode() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::setResidueInsertionCode	(	Chem::MolecularGraph &	molgraph,
		char	code
	)

◆ clearResidueInsertionCode() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearResidueInsertionCode ( Chem::MolecularGraph & molgraph )

◆ hasResidueInsertionCode() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasResidueInsertionCode ( const Chem::MolecularGraph & molgraph )

◆ getChainID() [2/2]

CDPL_BIOMOL_API const std::string& CDPL::Biomol::getChainID ( const Chem::MolecularGraph & molgraph )

◆ setChainID() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::setChainID	(	Chem::MolecularGraph &	molgraph,
		const std::string &	id
	)

◆ clearChainID() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearChainID ( Chem::MolecularGraph & molgraph )

◆ hasChainID() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasChainID ( const Chem::MolecularGraph & molgraph )

◆ getModelNumber() [2/2]

CDPL_BIOMOL_API std::size_t CDPL::Biomol::getModelNumber ( const Chem::MolecularGraph & molgraph )

◆ setModelNumber() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::setModelNumber	(	Chem::MolecularGraph &	molgraph,
		std::size_t	model_no
	)

◆ clearModelNumber() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::clearModelNumber ( Chem::MolecularGraph & molgraph )

◆ hasModelNumber() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::hasModelNumber ( const Chem::MolecularGraph & molgraph )

◆ getPDBData()

CDPL_BIOMOL_API const PDBData::SharedPointer& CDPL::Biomol::getPDBData ( const Chem::MolecularGraph & molgraph )

◆ setPDBData()

CDPL_BIOMOL_API void CDPL::Biomol::setPDBData	(	Chem::MolecularGraph &	molgraph,
		const PDBData::SharedPointer &	data
	)

◆ clearPDBData()

CDPL_BIOMOL_API void CDPL::Biomol::clearPDBData ( Chem::MolecularGraph & molgraph )

◆ hasPDBData()

CDPL_BIOMOL_API bool CDPL::Biomol::hasPDBData ( const Chem::MolecularGraph & molgraph )

◆ getMMCIFData()

CDPL_BIOMOL_API const MMCIFData::SharedPointer& CDPL::Biomol::getMMCIFData ( const Chem::MolecularGraph & molgraph )

Since: 1.2

◆ setMMCIFData()

CDPL_BIOMOL_API void CDPL::Biomol::setMMCIFData	(	Chem::MolecularGraph &	molgraph,
		const MMCIFData::SharedPointer &	data
	)

◆ clearMMCIFData()

CDPL_BIOMOL_API void CDPL::Biomol::clearMMCIFData ( Chem::MolecularGraph & molgraph )

◆ hasMMCIFData()

CDPL_BIOMOL_API bool CDPL::Biomol::hasMMCIFData ( const Chem::MolecularGraph & molgraph )

◆ extractResidueSubstructures()

CDPL_BIOMOL_API void CDPL::Biomol::extractResidueSubstructures	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	parent_molgraph,
		Chem::Fragment &	res_substructs,
		bool	cnctd_only = `false`,
		unsigned int	flags = `AtomPropertyFlag::DEFAULT`,
		bool	append = `false`
	)

◆ extractProximalAtoms() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::extractProximalAtoms	(	const Chem::MolecularGraph &	core,
		const Chem::MolecularGraph &	macromol,
		Chem::Fragment &	env_atoms,
		double	max_dist,
		bool	inc_core_atoms = `false`,
		bool	append = `false`
	)

◆ extractProximalAtoms() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::extractProximalAtoms	(	const Chem::MolecularGraph &	core,
		const Chem::MolecularGraph &	macromol,
		Chem::Fragment &	env_atoms,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		double	max_dist,
		bool	inc_core_atoms = `false`,
		bool	append = `false`
	)

◆ extractEnvironmentResidues() [1/2]

CDPL_BIOMOL_API void CDPL::Biomol::extractEnvironmentResidues	(	const Chem::MolecularGraph &	core,
		const Chem::MolecularGraph &	macromol,
		Chem::Fragment &	env_residues,
		double	max_dist,
		bool	append = `false`
	)

◆ extractEnvironmentResidues() [2/2]

CDPL_BIOMOL_API void CDPL::Biomol::extractEnvironmentResidues	(	const Chem::MolecularGraph &	core,
		const Chem::MolecularGraph &	macromol,
		Chem::Fragment &	env_residues,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		double	max_dist,
		bool	append = `false`
	)

◆ setHydrogenResidueSequenceInfo()

CDPL_BIOMOL_API void CDPL::Biomol::setHydrogenResidueSequenceInfo	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite,
		unsigned int	flags = `AtomPropertyFlag::DEFAULT`
	)

◆ matchesResidueInfo() [2/2]

CDPL_BIOMOL_API bool CDPL::Biomol::matchesResidueInfo	(	const Chem::MolecularGraph &	molgraph,
		const char *	res_code = `0`,
		const char *	chain_id = `0`,
		long	res_seq_no = `IGNORE_SEQUENCE_NO`,
		char	ins_code = `0`,
		std::size_t	model_no = `0`
	)

◆ combineInterferingResidueCoordinates()

CDPL_BIOMOL_API bool CDPL::Biomol::combineInterferingResidueCoordinates	(	Chem::Molecule &	mol,
		double	max_ctr_dist = `1.0`
	)

◆ findResidueAtom()

template<typename Iter >

Iter CDPL::Biomol::findResidueAtom	(	Iter	it,
		Iter	end,
		const char *	res_code = `0`,
		const char *	chain_id = `0`,
		long	res_seq_no = `IGNORE_SEQUENCE_NO`,
		char	ins_code = `0`,
		std::size_t	model_no = `0`,
		const char *	atom_name = `0`,
		long	serial_no = `IGNORE_SERIAL_NO`
	)

◆ findResidue()