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

Namespaces
	AtomProperty
	Provides keys for built-in biomolecular Chem::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 Chem::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
	Provides constants for the specification of the type of a chemical component (residue).

Classes
class	HierarchyView
	Data structure providing a hierarchical view on biological macromolecules. More...

class	HierarchyViewChain
	Data structure for the representation of biological macromolecule chains. More...

class	HierarchyViewFragment
	Data structure for the representation of a single contiguous fragment of a biological macromolecule chain. More...

class	HierarchyViewModel
	Data structure for the representation of individual biological macromolecule models. More...

class	HierarchyViewNode
	Abstract base class for nodes of the Biomol::HierarchyView tree (models, chains, residues). More...

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

class	MMCIFMolecularGraphWriter
	Writer for molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

class	MMCIFMoleculeReader
	Reader for molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

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

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

class	PDBData
	Data structure for the storage of data records found in PDB formatted data [PDB]. More...

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

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

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

class	ResidueList
	Data structure for the storage of residues extracted from biological macromolecules. More...

Typedefs
typedef Util::DefaultDataOutputHandler< MMCIFBZ2MolecularGraphWriter, DataFormat::MMCIF_BZ2 >	MMCIFBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::CompressedDataWriter< MMCIFMolecularGraphWriter, Util::BZip2OStream >	MMCIFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::DefaultDataInputHandler< MMCIFBZ2MoleculeReader, DataFormat::MMCIF_BZ2 >	MMCIFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::CompressedDataReader< MMCIFMoleculeReader, Util::BZip2IStream >	MMCIFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef std::function< void(Biomol::MMCIFData &, const Chem::MolecularGraph &)>	MMCIFDataProcessingFunction
	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
	Handler for the output of gzip-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::CompressedDataWriter< MMCIFMolecularGraphWriter, Util::GZipOStream >	MMCIFGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::DefaultDataInputHandler< MMCIFGZMoleculeReader, DataFormat::MMCIF_GZ >	MMCIFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::CompressedDataReader< MMCIFMoleculeReader, Util::GZipIStream >	MMCIFGZMoleculeReader
	Reader for molecule data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::DefaultDataOutputHandler< MMCIFMolecularGraphWriter, DataFormat::MMCIF >	MMCIFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

typedef Util::DefaultDataInputHandler< MMCIFMoleculeReader, DataFormat::MMCIF >	MMCIFMoleculeInputHandler
	Handler for the input of molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...

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

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

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

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

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

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

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

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

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

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

typedef Util::DefaultDataOutputHandler< PDBMolecularGraphWriter, DataFormat::PDB >	PDBMolecularGraphOutputHandler
	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
	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)
	Returns the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of atom. More...

CDPL_BIOMOL_API void	setResidueAtomName (Chem::Atom &atom, const std::string &name)
	Sets the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of atom to name. More...

CDPL_BIOMOL_API void	clearResidueAtomName (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_ATOM_NAME property from atom. More...

CDPL_BIOMOL_API bool	hasResidueAtomName (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ATOM_NAME property. More...

CDPL_BIOMOL_API const std::string &	getResidueAltAtomName (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of atom. More...

CDPL_BIOMOL_API void	setResidueAltAtomName (Chem::Atom &atom, const std::string &name)
	Sets the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of atom to name. More...

CDPL_BIOMOL_API void	clearResidueAltAtomName (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property from atom. More...

CDPL_BIOMOL_API bool	hasResidueAltAtomName (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property. More...

CDPL_BIOMOL_API bool	getResidueLeavingAtomFlag (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of atom. More...

CDPL_BIOMOL_API void	setResidueLeavingAtomFlag (Chem::Atom &atom, bool leaving)
	Sets the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of atom to leaving. More...

CDPL_BIOMOL_API void	clearResidueLeavingAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property from atom. More...

CDPL_BIOMOL_API bool	hasResidueLeavingAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property. More...

CDPL_BIOMOL_API bool	getResidueLinkingAtomFlag (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of atom. More...

CDPL_BIOMOL_API void	setResidueLinkingAtomFlag (Chem::Atom &atom, bool linking)
	Sets the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of atom to linking. More...

CDPL_BIOMOL_API void	clearResidueLinkingAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property from atom. More...

CDPL_BIOMOL_API bool	hasResidueLinkingAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property. More...

CDPL_BIOMOL_API const std::string &	getResidueCode (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_CODE property of atom. More...

CDPL_BIOMOL_API void	setResidueCode (Chem::Atom &atom, const std::string &code)
	Sets the value of the Biomol::AtomProperty::RESIDUE_CODE property of atom to code. More...

CDPL_BIOMOL_API void	clearResidueCode (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_CODE property from atom. More...

CDPL_BIOMOL_API bool	hasResidueCode (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_CODE property. More...

CDPL_BIOMOL_API long	getResidueSequenceNumber (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of atom. More...

CDPL_BIOMOL_API void	setResidueSequenceNumber (Chem::Atom &atom, long seq_no)
	Sets the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of atom to seq_no. More...

CDPL_BIOMOL_API void	clearResidueSequenceNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property from atom. More...

CDPL_BIOMOL_API bool	hasResidueSequenceNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property. More...

CDPL_BIOMOL_API char	getResidueInsertionCode (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of atom. More...

CDPL_BIOMOL_API void	setResidueInsertionCode (Chem::Atom &atom, char code)
	Sets the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of atom to code. More...

CDPL_BIOMOL_API void	clearResidueInsertionCode (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property from atom. More...

CDPL_BIOMOL_API bool	hasResidueInsertionCode (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_INSERTION_CODE property. More...

CDPL_BIOMOL_API bool	getHeteroAtomFlag (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of atom. More...

CDPL_BIOMOL_API void	setHeteroAtomFlag (Chem::Atom &atom, bool is_het)
	Sets the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of atom to is_het. More...

CDPL_BIOMOL_API void	clearHeteroAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::HETERO_ATOM_FLAG property from atom. More...

CDPL_BIOMOL_API bool	hasHeteroAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::HETERO_ATOM_FLAG property. More...

CDPL_BIOMOL_API const std::string &	getChainID (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::CHAIN_ID property of atom. More...

CDPL_BIOMOL_API void	setChainID (Chem::Atom &atom, const std::string &id)
	Sets the value of the Biomol::AtomProperty::CHAIN_ID property of atom to id. More...

CDPL_BIOMOL_API void	clearChainID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::CHAIN_ID property from atom. More...

CDPL_BIOMOL_API bool	hasChainID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::CHAIN_ID property. More...

CDPL_BIOMOL_API char	getAltLocationID (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of atom. More...

CDPL_BIOMOL_API void	setAltLocationID (Chem::Atom &atom, char id)
	Sets the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of atom to id. More...

CDPL_BIOMOL_API void	clearAltLocationID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::ALT_LOCATION_ID property from atom. More...

CDPL_BIOMOL_API bool	hasAltLocationID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::ALT_LOCATION_ID property. More...

CDPL_BIOMOL_API const std::string &	getEntityID (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::ENTITY_ID property of atom. More...

CDPL_BIOMOL_API void	setEntityID (Chem::Atom &atom, const std::string &id)
	Sets the value of the Biomol::AtomProperty::ENTITY_ID property of atom to id. More...

CDPL_BIOMOL_API void	clearEntityID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::ENTITY_ID property from atom. More...

CDPL_BIOMOL_API bool	hasEntityID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::ENTITY_ID property. More...

CDPL_BIOMOL_API std::size_t	getModelNumber (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::MODEL_NUMBER property of atom. More...

CDPL_BIOMOL_API void	setModelNumber (Chem::Atom &atom, std::size_t model_no)
	Sets the value of the Biomol::AtomProperty::MODEL_NUMBER property of atom to model_no. More...

CDPL_BIOMOL_API void	clearModelNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::MODEL_NUMBER property from atom. More...

CDPL_BIOMOL_API bool	hasModelNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::MODEL_NUMBER property. More...

CDPL_BIOMOL_API long	getSerialNumber (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::SERIAL_NUMBER property of atom. More...

CDPL_BIOMOL_API void	setSerialNumber (Chem::Atom &atom, long serial_no)
	Sets the value of the Biomol::AtomProperty::SERIAL_NUMBER property of atom to serial_no. More...

CDPL_BIOMOL_API void	clearSerialNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::SERIAL_NUMBER property from atom. More...

CDPL_BIOMOL_API bool	hasSerialNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::SERIAL_NUMBER property. More...

CDPL_BIOMOL_API double	getOccupancy (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::OCCUPANCY property of atom. More...

CDPL_BIOMOL_API void	setOccupancy (Chem::Atom &atom, double occupancy)
	Sets the value of the Biomol::AtomProperty::OCCUPANCY property of atom to occupancy. More...

CDPL_BIOMOL_API void	clearOccupancy (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::OCCUPANCY property from atom. More...

CDPL_BIOMOL_API bool	hasOccupancy (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::OCCUPANCY property. More...

CDPL_BIOMOL_API double	getBFactor (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::B_FACTOR property of atom. More...

CDPL_BIOMOL_API void	setBFactor (Chem::Atom &atom, double factor)
	Sets the value of the Biomol::AtomProperty::B_FACTOR property of atom to factor. More...

CDPL_BIOMOL_API void	clearBFactor (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::B_FACTOR property from atom. More...

CDPL_BIOMOL_API bool	hasBFactor (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::B_FACTOR property. More...

CDPL_BIOMOL_API bool	isPDBBackboneAtom (const Chem::Atom &atom)
	Tells whether atom is a backbone atom of a PDB-style amino-acid or nucleotide residue. More...

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)
	Tells whether the residue-identity attributes of atom match the given filter values. More...

CDPL_BIOMOL_API bool	areInSameResidue (const Chem::Atom &atom1, const Chem::Atom &atom2, unsigned int flags=AtomPropertyFlag::DEFAULT)
	Tells whether atom1 and atom2 belong to the same residue, comparing the atom properties selected by flags. More...

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)
	Extracts the substructure of the residue atom belongs to into res_substruct. More...

CDPL_BIOMOL_API bool	getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr. More...

CDPL_BIOMOL_API void	setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict)
	Sets the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict. More...

CDPL_BIOMOL_API bool	hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter. More...

CDPL_BIOMOL_API void	clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr. More...

CDPL_BIOMOL_API bool	getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr. More...

CDPL_BIOMOL_API void	setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check)
	Sets the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr to check. More...

CDPL_BIOMOL_API bool	hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::CHECK_LINE_LENGTH parameter. More...

CDPL_BIOMOL_API void	clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter from cntnr. More...

CDPL_BIOMOL_API const ResidueDictionary::SharedPointer &	getResidueDictionaryParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter of cntnr. More...

CDPL_BIOMOL_API void	setResidueDictionaryParameter (Base::ControlParameterContainer &cntnr, const ResidueDictionary::SharedPointer &dict)
	Sets the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter of cntnr to dict. More...

CDPL_BIOMOL_API bool	hasResidueDictionaryParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::RESIDUE_DICTIONARY parameter. More...

CDPL_BIOMOL_API void	clearResidueDictionaryParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter from cntnr. More...

CDPL_BIOMOL_API bool	getApplyDictFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter of cntnr. More...

CDPL_BIOMOL_API void	setApplyDictFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasApplyDictFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter. More...

CDPL_BIOMOL_API void	clearApplyDictFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getApplyDictAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter of cntnr. More...

CDPL_BIOMOL_API void	setApplyDictAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasApplyDictAtomTypesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter. More...

CDPL_BIOMOL_API void	clearApplyDictAtomTypesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getCalcMissingFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter of cntnr. More...

CDPL_BIOMOL_API void	setCalcMissingFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc)
	Sets the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter of cntnr to calc. More...

CDPL_BIOMOL_API bool	hasCalcMissingFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter. More...

CDPL_BIOMOL_API void	clearCalcMissingFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPerceiveMissingBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr. More...

CDPL_BIOMOL_API void	setPerceiveMissingBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive)
	Sets the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr to perceive. More...

CDPL_BIOMOL_API bool	hasPerceiveMissingBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter. More...

CDPL_BIOMOL_API void	clearPerceiveMissingBondOrdersParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getCombineInterferingResidueCoordinatesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr. More...

CDPL_BIOMOL_API void	setCombineInterferingResidueCoordinatesParameter (Base::ControlParameterContainer &cntnr, bool comb)
	Sets the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr to comb. More...

CDPL_BIOMOL_API bool	hasCombineInterferingResidueCoordinatesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter. More...

CDPL_BIOMOL_API void	clearCombineInterferingResidueCoordinatesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBApplyDictAtomBondingToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBApplyDictAtomBondingToStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasPDBApplyDictAtomBondingToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter. More...

CDPL_BIOMOL_API void	clearPDBApplyDictAtomBondingToStdResiduesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBApplyDictAtomBondingToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasPDBApplyDictAtomBondingToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter. More...

CDPL_BIOMOL_API void	clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBApplyDictBondOrdersToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBApplyDictBondOrdersToStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasPDBApplyDictBondOrdersToStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter. More...

CDPL_BIOMOL_API void	clearPDBApplyDictBondOrdersToStdResiduesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBApplyDictBondOrdersToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasPDBApplyDictBondOrdersToNonStdResiduesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter. More...

CDPL_BIOMOL_API void	clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBIgnoreCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBIgnoreCONECTRecordsParameter (Base::ControlParameterContainer &cntnr, bool ignore)
	Sets the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter of cntnr to ignore. More...

CDPL_BIOMOL_API bool	hasPDBIgnoreCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter. More...

CDPL_BIOMOL_API void	clearPDBIgnoreCONECTRecordsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBDeduceBondOrdersFromCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base::ControlParameterContainer &cntnr, bool deduce)
	Sets the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr to deduce. More...

CDPL_BIOMOL_API bool	hasPDBDeduceBondOrdersFromCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter. More...

CDPL_BIOMOL_API void	clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBIgnoreFormalChargeFieldParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBIgnoreFormalChargeFieldParameter (Base::ControlParameterContainer &cntnr, bool ignore)
	Sets the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr to ignore. More...

CDPL_BIOMOL_API bool	hasPDBIgnoreFormalChargeFieldParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter. More...

CDPL_BIOMOL_API void	clearPDBIgnoreFormalChargeFieldParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBEvaluateMASTERRecordParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBEvaluateMASTERRecordParameter (Base::ControlParameterContainer &cntnr, bool eval)
	Sets the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter of cntnr to eval. More...

CDPL_BIOMOL_API bool	hasPDBEvaluateMASTERRecordParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter. More...

CDPL_BIOMOL_API void	clearPDBEvaluateMASTERRecordParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc)
	Sets the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter of cntnr to trunc. More...

CDPL_BIOMOL_API bool	hasPDBTruncateLinesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter. More...

CDPL_BIOMOL_API void	clearPDBTruncateLinesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBOutputFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBOutputFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr to output. More...

CDPL_BIOMOL_API bool	hasPDBOutputFormalChargesParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter. More...

CDPL_BIOMOL_API void	clearPDBOutputFormalChargesParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBOutputCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBOutputCONECTRecordsParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter of cntnr to output. More...

CDPL_BIOMOL_API bool	hasPDBOutputCONECTRecordsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter. More...

CDPL_BIOMOL_API void	clearPDBOutputCONECTRecordsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBOutputCONECTRecordsForAllBondsParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBOutputCONECTRecordsForAllBondsParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr to output. More...

CDPL_BIOMOL_API bool	hasPDBOutputCONECTRecordsForAllBondsParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter. More...

CDPL_BIOMOL_API void	clearPDBOutputCONECTRecordsForAllBondsParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getPDBOutputCONECTRecordsReflectingBondOrderParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBOutputCONECTRecordsReflectingBondOrderParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr to output. More...

CDPL_BIOMOL_API bool	hasPDBOutputCONECTRecordsReflectingBondOrderParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter. More...

CDPL_BIOMOL_API void	clearPDBOutputCONECTRecordsReflectingBondOrderParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter from cntnr. More...

CDPL_BIOMOL_API unsigned int	getPDBFormatVersionParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter of cntnr. More...

CDPL_BIOMOL_API void	setPDBFormatVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int ver)
	Sets the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter of cntnr to ver. More...

CDPL_BIOMOL_API bool	hasPDBFormatVersionParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_FORMAT_VERSION parameter. More...

CDPL_BIOMOL_API void	clearPDBFormatVersionParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter from cntnr. More...

CDPL_BIOMOL_API bool	getMMCIFApplyDictAtomBondingParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr. More...

CDPL_BIOMOL_API void	setMMCIFApplyDictAtomBondingParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasMMCIFApplyDictAtomBondingParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter. More...

CDPL_BIOMOL_API void	clearMMCIFApplyDictAtomBondingParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter from cntnr. More...

CDPL_BIOMOL_API bool	getMMCIFApplyDictBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr. More...

CDPL_BIOMOL_API void	setMMCIFApplyDictBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool apply)
	Sets the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr to apply. More...

CDPL_BIOMOL_API bool	hasMMCIFApplyDictBondOrdersParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter. More...

CDPL_BIOMOL_API void	clearMMCIFApplyDictBondOrdersParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter from cntnr. More...

CDPL_BIOMOL_API bool	getMMCIFOutputBiopolymersAsChemCompParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr. More...

CDPL_BIOMOL_API void	setMMCIFOutputBiopolymersAsChemCompParameter (Base::ControlParameterContainer &cntnr, bool output)
	Sets the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr to output. More...

CDPL_BIOMOL_API bool	hasMMCIFOutputBiopolymersAsChemCompParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter. More...

CDPL_BIOMOL_API void	clearMMCIFOutputBiopolymersAsChemCompParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter from cntnr. More...

CDPL_BIOMOL_API const MMCIFDataProcessingFunction &	getMMCIFOutputDataPostprocFunctionParameter (const Base::ControlParameterContainer &cntnr)
	Returns the value of the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr. More...

CDPL_BIOMOL_API void	setMMCIFOutputDataPostprocFunctionParameter (Base::ControlParameterContainer &cntnr, const MMCIFDataProcessingFunction &func)
	Sets the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr to func. More...

CDPL_BIOMOL_API bool	hasMMCIFOutputDataPostprocFunctionParameter (const Base::ControlParameterContainer &cntnr)
	Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter. More...

CDPL_BIOMOL_API void	clearMMCIFOutputDataPostprocFunctionParameter (Base::ControlParameterContainer &cntnr)
	Removes the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter from cntnr. More...

CDPL_BIOMOL_API std::ostream &	operator<< (std::ostream &os, const MMCIFData &data)
	Writes the mmCIF data record data in textual mmCIF format to the output stream os. More...

CDPL_BIOMOL_API std::ostream &	operator<< (std::ostream &os, const MMCIFData::Category &cat)
	Writes the mmCIF category cat in textual mmCIF format to the output stream os. More...

CDPL_BIOMOL_API const std::string &	getResidueCode (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_CODE property of molgraph. More...

CDPL_BIOMOL_API void	setResidueCode (Chem::MolecularGraph &molgraph, const std::string &code)
	Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_CODE property of molgraph to code. More...

CDPL_BIOMOL_API void	clearResidueCode (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::RESIDUE_CODE property from molgraph. More...

CDPL_BIOMOL_API bool	hasResidueCode (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_CODE property. More...

CDPL_BIOMOL_API long	getResidueSequenceNumber (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property of molgraph. More...

CDPL_BIOMOL_API void	setResidueSequenceNumber (Chem::MolecularGraph &molgraph, long seq_no)
	Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property of molgraph to seq_no. More...

CDPL_BIOMOL_API void	clearResidueSequenceNumber (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property from molgraph. More...

CDPL_BIOMOL_API bool	hasResidueSequenceNumber (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property. More...

CDPL_BIOMOL_API char	getResidueInsertionCode (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property of molgraph. More...

CDPL_BIOMOL_API void	setResidueInsertionCode (Chem::MolecularGraph &molgraph, char code)
	Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property of molgraph to code. More...

CDPL_BIOMOL_API void	clearResidueInsertionCode (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property from molgraph. More...

CDPL_BIOMOL_API bool	hasResidueInsertionCode (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property. More...

CDPL_BIOMOL_API const std::string &	getChainID (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::CHAIN_ID property of molgraph. More...

CDPL_BIOMOL_API void	setChainID (Chem::MolecularGraph &molgraph, const std::string &id)
	Sets the value of the Biomol::MolecularGraphProperty::CHAIN_ID property of molgraph to id. More...

CDPL_BIOMOL_API void	clearChainID (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::CHAIN_ID property from molgraph. More...

CDPL_BIOMOL_API bool	hasChainID (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::CHAIN_ID property. More...

CDPL_BIOMOL_API std::size_t	getModelNumber (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::MODEL_NUMBER property of molgraph. More...

CDPL_BIOMOL_API void	setModelNumber (Chem::MolecularGraph &molgraph, std::size_t model_no)
	Sets the value of the Biomol::MolecularGraphProperty::MODEL_NUMBER property of molgraph to model_no. More...

CDPL_BIOMOL_API void	clearModelNumber (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::MODEL_NUMBER property from molgraph. More...

CDPL_BIOMOL_API bool	hasModelNumber (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::MODEL_NUMBER property. More...

CDPL_BIOMOL_API const PDBData::SharedPointer &	getPDBData (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::PDB_DATA property of molgraph. More...

CDPL_BIOMOL_API void	setPDBData (Chem::MolecularGraph &molgraph, const PDBData::SharedPointer &data)
	Sets the value of the Biomol::MolecularGraphProperty::PDB_DATA property of molgraph to data. More...

CDPL_BIOMOL_API void	clearPDBData (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::PDB_DATA property from molgraph. More...

CDPL_BIOMOL_API bool	hasPDBData (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::PDB_DATA property. More...

CDPL_BIOMOL_API const MMCIFData::SharedPointer &	getMMCIFData (const Chem::MolecularGraph &molgraph)
	Returns the value of the Biomol::MolecularGraphProperty::MMCIF_DATA property of molgraph. More...

CDPL_BIOMOL_API void	setMMCIFData (Chem::MolecularGraph &molgraph, const MMCIFData::SharedPointer &data)
	Sets the value of the Biomol::MolecularGraphProperty::MMCIF_DATA property of molgraph to data. More...

CDPL_BIOMOL_API void	clearMMCIFData (Chem::MolecularGraph &molgraph)
	Removes the Biomol::MolecularGraphProperty::MMCIF_DATA property from molgraph. More...

CDPL_BIOMOL_API bool	hasMMCIFData (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::MMCIF_DATA property. More...

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)
	Extracts the substructures of all residues represented in molgraph from the parent macromolecular graph parent_molgraph. More...

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)
	Extracts the atoms of macromol that lie within max_dist of any atom of core. More...

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)
	Extracts the atoms of macromol that lie within max_dist of any atom of core, using coords_func to obtain atom positions. More...

CDPL_BIOMOL_API void	extractEnvironmentResidues (const Chem::MolecularGraph &core, const Chem::MolecularGraph &macromol, Chem::Fragment &env_residues, double max_dist, bool append=false)
	Extracts the residues of macromol that contain at least one atom within max_dist of any atom of core. More...

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)
	Extracts the residues of macromol that contain at least one atom within max_dist of any atom of core, using coords_func to obtain atom positions. More...

CDPL_BIOMOL_API void	setHydrogenResidueSequenceInfo (Chem::MolecularGraph &molgraph, bool overwrite, unsigned int flags=AtomPropertyFlag::DEFAULT)
	Copies residue-identifying properties from heavy atoms to their attached hydrogen atoms in molgraph. More...

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)
	Tells whether the residue-identity attributes of molgraph match the given filter values. More...

CDPL_BIOMOL_API bool	combineInterferingResidueCoordinates (Chem::Molecule &mol, double max_ctr_dist=1.0)
	Merges alternative residue conformers in mol whose residue centers lie within max_ctr_dist of one another. More...

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)
	Searches the iterator range [it, end) for the first atom whose PDB-style residue identity attributes match the given filter values. More...

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)
	Searches the iterator range [it, end) for the first residue (molecular graph) whose PDB-style identity attributes match the given filter values, optionally requiring a matching atom. More...

Variables
const long	IGNORE_SEQUENCE_NO = std::numeric_limits<long>::min()
	Sentinel value indicating that the residue sequence number should be ignored when matching residues. More...

const long	IGNORE_SERIAL_NO = std::numeric_limits<long>::min()
	Sentinel value indicating that the atom serial number should be ignored when matching atoms. More...

Detailed Description

Contains classes and functions related to biological macromolecules.

Typedef Documentation

◆ MMCIFBZ2MolecularGraphOutputHandler

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

Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFBZ2MolecularGraphWriter

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

Writer for molecular graph data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFBZ2MoleculeInputHandler

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

Handler for the input of bzip2-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFBZ2MoleculeReader

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

Reader for molecule data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFDataProcessingFunction

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

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

Handler for the output of gzip-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFGZMolecularGraphWriter

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

Writer for molecular graph data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFGZMoleculeInputHandler

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

Handler for the input of gzip-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFGZMoleculeReader

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

Reader for molecule data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFMolecularGraphOutputHandler

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

Handler for the output of molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMCIFMoleculeInputHandler

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

Handler for the input of molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format.

Since: 1.2

◆ MMTFBZ2MolecularGraphOutputHandler

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

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

Writer for molecular graph data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFBZ2MoleculeInputHandler

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

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

Reader for molecule data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFGZMolecularGraphOutputHandler

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

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

Writer for molecular graph data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFGZMoleculeInputHandler

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

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

Reader for molecule data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF].

◆ MMTFMolecularGraphOutputHandler

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

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

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

◆ PDBBZ2MolecularGraphOutputHandler

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

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

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

◆ PDBBZ2MoleculeInputHandler

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

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

Reader for molecule data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBGZMolecularGraphOutputHandler

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

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

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

◆ PDBGZMoleculeInputHandler

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

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

Reader for molecule data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format.

◆ PDBMolecularGraphOutputHandler

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

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

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 )

Returns the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of atom.

Parameters

atom The atom.

Returns: A const reference to the residue-local atom name.

◆ setResidueAtomName()

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

Sets the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of atom to name.

Parameters

atom	The atom.
name	The new residue-local atom name.

◆ clearResidueAtomName()

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

Removes the Biomol::AtomProperty::RESIDUE_ATOM_NAME property from atom.

Parameters

atom The atom.

◆ hasResidueAtomName()

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ATOM_NAME property.

Parameters

atom The atom.

Returns: true if the residue-local atom name is set, and false otherwise.

◆ getResidueAltAtomName()

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

Returns the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of atom.

Parameters

atom The atom.

Returns: A const reference to the alternative residue-local atom name.

◆ setResidueAltAtomName()

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

Sets the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of atom to name.

Parameters

atom	The atom.
name	The new alternative residue-local atom name.

◆ clearResidueAltAtomName()

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

Removes the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property from atom.

Parameters

atom The atom.

◆ hasResidueAltAtomName()

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property.

Parameters

atom The atom.

Returns: true if the alternative residue-local atom name is set, and false otherwise.

◆ getResidueLeavingAtomFlag()

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

Returns the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of atom.

Parameters

atom The atom.

Returns: true if the atom is a leaving atom in its parent residue, and false otherwise.

◆ setResidueLeavingAtomFlag()

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

Sets the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of atom to leaving.

Parameters

atom	The atom.
leaving	`true` to mark the atom as a leaving atom, and `false` otherwise.

◆ clearResidueLeavingAtomFlag()

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

Removes the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property from atom.

Parameters

atom The atom.

◆ hasResidueLeavingAtomFlag()

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property.

Parameters

atom The atom.

Returns: true if the leaving-atom flag is set, and false otherwise.

◆ getResidueLinkingAtomFlag()

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

Returns the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of atom.

Parameters

atom The atom.

Returns: true if the atom is a linking atom between residues, and false otherwise.

◆ setResidueLinkingAtomFlag()

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

Sets the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of atom to linking.

Parameters

atom	The atom.
linking	`true` to mark the atom as a linking atom, and `false` otherwise.

◆ clearResidueLinkingAtomFlag()

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

Removes the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property from atom.

Parameters

atom The atom.

◆ hasResidueLinkingAtomFlag()

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property.

Parameters

atom The atom.

Returns: true if the linking-atom flag is set, and false otherwise.

◆ getResidueCode() [1/2]

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

Returns the value of the Biomol::AtomProperty::RESIDUE_CODE property of atom.

Parameters

atom The atom.

Returns: A const reference to the residue three-letter code.

◆ setResidueCode() [1/2]

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

Sets the value of the Biomol::AtomProperty::RESIDUE_CODE property of atom to code.

Parameters

atom	The atom.
code	The new residue three-letter code.

◆ clearResidueCode() [1/2]

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

Removes the Biomol::AtomProperty::RESIDUE_CODE property from atom.

Parameters

atom The atom.

◆ hasResidueCode() [1/2]

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_CODE property.

Parameters

atom The atom.

Returns: true if the residue code is set, and false otherwise.

◆ getResidueSequenceNumber() [1/2]

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

Returns the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of atom.

Parameters

atom The atom.

Returns: The residue sequence number.

◆ setResidueSequenceNumber() [1/2]

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

Sets the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of atom to seq_no.

Parameters

atom	The atom.
seq_no	The new residue sequence number.

◆ clearResidueSequenceNumber() [1/2]

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

Removes the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property from atom.

Parameters

atom The atom.

◆ hasResidueSequenceNumber() [1/2]

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property.

Parameters

atom The atom.

Returns: true if the residue sequence number is set, and false otherwise.

◆ getResidueInsertionCode() [1/2]

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

Returns the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of atom.

Parameters

atom The atom.

Returns: The residue insertion code.

◆ setResidueInsertionCode() [1/2]

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

Sets the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of atom to code.

Parameters

atom	The atom.
code	The new residue insertion code.

◆ clearResidueInsertionCode() [1/2]

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

Removes the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property from atom.

Parameters

atom The atom.

◆ hasResidueInsertionCode() [1/2]

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

Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_INSERTION_CODE property.

Parameters

atom The atom.

Returns: true if the residue insertion code is set, and false otherwise.

◆ getHeteroAtomFlag()

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

Returns the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of atom.

Parameters

atom The atom.

Returns: true if the atom is flagged as a heteroatom (PDB HETATM record), and false otherwise.

◆ setHeteroAtomFlag()

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

Sets the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of atom to is_het.

Parameters

atom	The atom.
is_het	`true` to mark the atom as a heteroatom, and `false` otherwise.

◆ clearHeteroAtomFlag()

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

Removes the Biomol::AtomProperty::HETERO_ATOM_FLAG property from atom.

Parameters

atom The atom.

◆ hasHeteroAtomFlag()

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

Tells whether atom carries an explicit Biomol::AtomProperty::HETERO_ATOM_FLAG property.

Parameters

atom The atom.

Returns: true if the heteroatom flag is set, and false otherwise.

◆ getChainID() [1/2]

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

Returns the value of the Biomol::AtomProperty::CHAIN_ID property of atom.

Parameters

atom The atom.

Returns: A const reference to the chain ID.

◆ setChainID() [1/2]

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

Sets the value of the Biomol::AtomProperty::CHAIN_ID property of atom to id.

Parameters

atom	The atom.
id	The new chain ID.

◆ clearChainID() [1/2]

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

Removes the Biomol::AtomProperty::CHAIN_ID property from atom.

Parameters

atom The atom.

◆ hasChainID() [1/2]

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

Tells whether atom carries an explicit Biomol::AtomProperty::CHAIN_ID property.

Parameters

atom The atom.

Returns: true if the chain ID is set, and false otherwise.

◆ getAltLocationID()

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

Returns the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of atom.

Parameters

atom The atom.

Returns: The alternate-location identifier.

◆ setAltLocationID()

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

Sets the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of atom to id.

Parameters

atom	The atom.
id	The new alternate-location identifier.

◆ clearAltLocationID()

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

Removes the Biomol::AtomProperty::ALT_LOCATION_ID property from atom.

Parameters

atom The atom.

◆ hasAltLocationID()

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

Tells whether atom carries an explicit Biomol::AtomProperty::ALT_LOCATION_ID property.

Parameters

atom The atom.

Returns: true if the alternate-location identifier is set, and false otherwise.

◆ getEntityID()

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

Returns the value of the Biomol::AtomProperty::ENTITY_ID property of atom.

Parameters

atom The atom.

Returns: A const reference to the entity ID.

Since: 1.2

◆ setEntityID()

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

Sets the value of the Biomol::AtomProperty::ENTITY_ID property of atom to id.

Parameters

atom	The atom.
id	The new entity ID.

◆ clearEntityID()

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

Removes the Biomol::AtomProperty::ENTITY_ID property from atom.

Parameters

atom The atom.

◆ hasEntityID()

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

Tells whether atom carries an explicit Biomol::AtomProperty::ENTITY_ID property.

Parameters

atom The atom.

Returns: true if the entity ID is set, and false otherwise.

◆ getModelNumber() [1/2]

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

Returns the value of the Biomol::AtomProperty::MODEL_NUMBER property of atom.

Parameters

atom The atom.

Returns: The model number.

◆ setModelNumber() [1/2]

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

Sets the value of the Biomol::AtomProperty::MODEL_NUMBER property of atom to model_no.

Parameters

atom	The atom.
model_no	The new model number.

◆ clearModelNumber() [1/2]

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

Removes the Biomol::AtomProperty::MODEL_NUMBER property from atom.

Parameters

atom The atom.

◆ hasModelNumber() [1/2]

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

Tells whether atom carries an explicit Biomol::AtomProperty::MODEL_NUMBER property.

Parameters

atom The atom.

Returns: true if the model number is set, and false otherwise.

◆ getSerialNumber()

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

Returns the value of the Biomol::AtomProperty::SERIAL_NUMBER property of atom.

Parameters

atom The atom.

Returns: The atom serial number.

◆ setSerialNumber()

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

Sets the value of the Biomol::AtomProperty::SERIAL_NUMBER property of atom to serial_no.

Parameters

atom	The atom.
serial_no	The new atom serial number.

◆ clearSerialNumber()

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

Removes the Biomol::AtomProperty::SERIAL_NUMBER property from atom.

Parameters

atom The atom.

◆ hasSerialNumber()

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

Tells whether atom carries an explicit Biomol::AtomProperty::SERIAL_NUMBER property.

Parameters

atom The atom.

Returns: true if the atom serial number is set, and false otherwise.

◆ getOccupancy()

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

Returns the value of the Biomol::AtomProperty::OCCUPANCY property of atom.

Parameters

atom The atom.

Returns: The occupancy value.

◆ setOccupancy()

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

Sets the value of the Biomol::AtomProperty::OCCUPANCY property of atom to occupancy.

Parameters

atom	The atom.
occupancy	The new occupancy value.

◆ clearOccupancy()

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

Removes the Biomol::AtomProperty::OCCUPANCY property from atom.

Parameters

atom The atom.

◆ hasOccupancy()

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

Tells whether atom carries an explicit Biomol::AtomProperty::OCCUPANCY property.

Parameters

atom The atom.

Returns: true if the occupancy is set, and false otherwise.

◆ getBFactor()

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

Returns the value of the Biomol::AtomProperty::B_FACTOR property of atom.

Parameters

atom The atom.

Returns: The temperature (B) factor.

◆ setBFactor()

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

Sets the value of the Biomol::AtomProperty::B_FACTOR property of atom to factor.

Parameters

atom	The atom.
factor	The new temperature (B) factor.

◆ clearBFactor()

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

Removes the Biomol::AtomProperty::B_FACTOR property from atom.

Parameters

atom The atom.

◆ hasBFactor()

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

Tells whether atom carries an explicit Biomol::AtomProperty::B_FACTOR property.

Parameters

atom The atom.

Returns: true if the temperature factor is set, and false otherwise.

◆ isPDBBackboneAtom()

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

Tells whether atom is a backbone atom of a PDB-style amino-acid or nucleotide residue.

Parameters

atom The atom.

Returns: true if the atom's residue-local name identifies it as a backbone atom, and false otherwise.

◆ 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`
	)

Tells whether the residue-identity attributes of atom match the given filter values.

Each filter argument is ignored when set to its sentinel value (nullptr / 0 / IGNORE_SEQUENCE_NO / IGNORE_SERIAL_NO). All supplied filters must match for the function to return true.

Parameters

atom	The atom to test.
res_code	The PDB three-letter residue code to match (or `nullptr` to ignore).
chain_id	The PDB chain ID to match (or `nullptr` to ignore).
res_seq_no	The PDB residue sequence number to match (or IGNORE_SEQUENCE_NO to ignore).
ins_code	The PDB insertion code to match (or `0` to ignore).
model_no	The PDB model number to match (or `0` to ignore).
atom_name	The PDB atom name to match (or `nullptr` to ignore).
serial_no	The PDB atom serial number to match (or IGNORE_SERIAL_NO to ignore).

Returns: true if all supplied filters match, and false otherwise.

◆ areInSameResidue()

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

Tells whether atom1 and atom2 belong to the same residue, comparing the atom properties selected by flags.

Parameters

atom1	The first atom.
atom2	The second atom.
flags	The bitwise-OR combination of Biomol::AtomPropertyFlag values selecting the residue-identifying properties to compare.

Returns: true if both atoms agree on all selected properties, and false otherwise.

◆ 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`
	)

Extracts the substructure of the residue atom belongs to into res_substruct.

Parameters

atom	The query atom whose residue substructure is to be extracted.
molgraph	The molecular graph providing the residue context.
res_substruct	The output fragment receiving the extracted residue substructure.
cnctd_only	If `true`, only atoms in the connected component of atom within the residue are extracted.
flags	The bitwise-OR combination of Biomol::AtomPropertyFlag values selecting the residue-identifying properties.
append	If `true`, the extracted atoms and bonds are appended to res_substruct; if `false`, res_substruct is cleared first.

◆ getStrictErrorCheckingParameter()

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

Returns the value of the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The strict-error-checking flag.

◆ setStrictErrorCheckingParameter()

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

Sets the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter of cntnr to strict.

Parameters

cntnr	The control-parameter container.
strict	`true` to enable strict error checking, and `false` to disable it.

◆ hasStrictErrorCheckingParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearStrictErrorCheckingParameter()

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

Removes the Biomol::ControlParameter::STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getCheckLineLengthParameter()

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

Returns the value of the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The check-line-length flag.

◆ setCheckLineLengthParameter()

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

Sets the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter of cntnr to check.

Parameters

cntnr	The control-parameter container.
check	`true` to enable line-length checking, and `false` to disable it.

◆ hasCheckLineLengthParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::CHECK_LINE_LENGTH parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearCheckLineLengthParameter()

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

Removes the Biomol::ControlParameter::CHECK_LINE_LENGTH parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getResidueDictionaryParameter()

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

Returns the value of the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: A const reference to the residue-dictionary shared pointer.

Since: 1.2

◆ setResidueDictionaryParameter()

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

Sets the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter of cntnr to dict.

Parameters

cntnr	The control-parameter container.
dict	The new residue dictionary.

◆ hasResidueDictionaryParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::RESIDUE_DICTIONARY parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearResidueDictionaryParameter()

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

Removes the Biomol::ControlParameter::RESIDUE_DICTIONARY parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getApplyDictFormalChargesParameter()

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

Returns the value of the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The apply-dictionary-formal-charges flag.

Since: 1.2

◆ setApplyDictFormalChargesParameter()

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

Sets the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived formal charges, and `false` to skip them.

◆ hasApplyDictFormalChargesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearApplyDictFormalChargesParameter()

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

Removes the Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getApplyDictAtomTypesParameter()

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

Returns the value of the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The apply-dictionary-atom-types flag.

Since: 1.2

◆ setApplyDictAtomTypesParameter()

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

Sets the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived atom types, and `false` to skip them.

◆ hasApplyDictAtomTypesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearApplyDictAtomTypesParameter()

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

Removes the Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getCalcMissingFormalChargesParameter()

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

Returns the value of the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The calc-missing-formal-charges flag.

Since: 1.2

◆ setCalcMissingFormalChargesParameter()

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

Sets the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter of cntnr to calc.

Parameters

cntnr	The control-parameter container.
calc	`true` to calculate missing formal charges, and `false` to leave them unset.

◆ hasCalcMissingFormalChargesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearCalcMissingFormalChargesParameter()

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

Removes the Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPerceiveMissingBondOrdersParameter()

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

Returns the value of the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The perceive-missing-bond-orders flag.

Since: 1.2

◆ setPerceiveMissingBondOrdersParameter()

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

Sets the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr to perceive.

Parameters

cntnr	The control-parameter container.
perceive	`true` to perceive missing bond orders, and `false` to leave them unset.

◆ hasPerceiveMissingBondOrdersParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPerceiveMissingBondOrdersParameter()

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

Removes the Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getCombineInterferingResidueCoordinatesParameter()

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

Returns the value of the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The combine-interfering-residue-coordinates flag.

◆ setCombineInterferingResidueCoordinatesParameter()

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

Sets the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr to comb.

Parameters

cntnr	The control-parameter container.
comb	`true` to merge interfering residue conformers, and `false` to keep them separate.

◆ hasCombineInterferingResidueCoordinatesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearCombineInterferingResidueCoordinatesParameter()

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

Removes the Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBApplyDictAtomBondingToStdResiduesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-apply-dict-atom-bonding-to-std-residues flag.

◆ setPDBApplyDictAtomBondingToStdResiduesParameter()

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

Sets the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived atom-bonding to standard residues, and `false` to skip it.

◆ hasPDBApplyDictAtomBondingToStdResiduesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBApplyDictAtomBondingToStdResiduesParameter()

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

Removes the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-apply-dict-atom-bonding-to-non-std-residues flag.

◆ setPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

Sets the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived atom-bonding to non-standard residues, and `false` to skip it.

◆ hasPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

Removes the Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBApplyDictBondOrdersToStdResiduesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-apply-dict-bond-orders-to-std-residues flag.

◆ setPDBApplyDictBondOrdersToStdResiduesParameter()

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

Sets the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived bond orders to standard residues, and `false` to skip it.

◆ hasPDBApplyDictBondOrdersToStdResiduesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBApplyDictBondOrdersToStdResiduesParameter()

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

Removes the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-apply-dict-bond-orders-to-non-std-residues flag.

◆ setPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

Sets the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived bond orders to non-standard residues, and `false` to skip it.

◆ hasPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

Removes the Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBIgnoreCONECTRecordsParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-ignore-CONECT-records flag.

Since: 1.3

◆ setPDBIgnoreCONECTRecordsParameter()

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

Sets the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter of cntnr to ignore.

Parameters

cntnr	The control-parameter container.
ignore	`true` to skip `CONECT` records during PDB data input, and `false` to process them.

◆ hasPDBIgnoreCONECTRecordsParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBIgnoreCONECTRecordsParameter()

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

Removes the Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-deduce-bond-orders-from-CONECT-records flag.

◆ setPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

Sets the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr to deduce.

Parameters

cntnr	The control-parameter container.
deduce	`true` to deduce bond orders from the duplication pattern of bonded atom pairs in `CONECT` records, and `false` to skip the deduction.

◆ hasPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

Removes the Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBIgnoreFormalChargeFieldParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-ignore-formal-charge-field flag.

◆ setPDBIgnoreFormalChargeFieldParameter()

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

Sets the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr to ignore.

Parameters

cntnr	The control-parameter container.
ignore	`true` to ignore the formal-charge field of `ATOM/HETATM records`, and `false` to honor it.

◆ hasPDBIgnoreFormalChargeFieldParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBIgnoreFormalChargeFieldParameter()

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

Removes the Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBEvaluateMASTERRecordParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-evaluate-MASTER-record flag.

◆ setPDBEvaluateMASTERRecordParameter()

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

Sets the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter of cntnr to eval.

Parameters

cntnr	The control-parameter container.
eval	`true` to verify record counts against the PDB `MASTER` record, and `false` to skip the verification.

◆ hasPDBEvaluateMASTERRecordParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBEvaluateMASTERRecordParameter()

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

Removes the Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBTruncateLinesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-truncate-lines flag.

◆ setPDBTruncateLinesParameter()

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

Sets the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter of cntnr to trunc.

Parameters

cntnr	The control-parameter container.
trunc	`true` to truncate output PDB data lines exceeding the maximum allowed line length, and `false` to fail the write operation instead.

◆ hasPDBTruncateLinesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBTruncateLinesParameter()

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

Removes the Biomol::ControlParameter::PDB_TRUNCATE_LINES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBOutputFormalChargesParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-output-formal-charges flag.

Since: 1.2

◆ setPDBOutputFormalChargesParameter()

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

Sets the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	`true` to write the formal-charge field of `ATOM/HETATM records`, and `false` to leave it blank.

◆ hasPDBOutputFormalChargesParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBOutputFormalChargesParameter()

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

Removes the Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBOutputCONECTRecordsParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-output-CONECT-records flag.

Since: 1.2

◆ setPDBOutputCONECTRecordsParameter()

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

Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	`true` to write `CONECT` records, and `false` to skip them.

◆ hasPDBOutputCONECTRecordsParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBOutputCONECTRecordsParameter()

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

Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBOutputCONECTRecordsForAllBondsParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-output-CONECT-records-for-all-bonds flag.

Since: 1.2

◆ setPDBOutputCONECTRecordsForAllBondsParameter()

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

Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	`true` to write `CONECT` records for all bonds (and not only for non-standard ones), and `false` to write them only for non-standard bonds.

◆ hasPDBOutputCONECTRecordsForAllBondsParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBOutputCONECTRecordsForAllBondsParameter()

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

Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB-output-CONECT-records-reflecting-bond-order flag.

Since: 1.2

◆ setPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

Sets the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	`true` to encode the bond order via the duplication count of bonded atom pairs in `CONECT` records, and `false` to emit each pair only once.

◆ hasPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

Removes the Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getPDBFormatVersionParameter()

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

Returns the value of the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The PDB format version (see Biomol::PDBFormatVersion).

◆ setPDBFormatVersionParameter()

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

Sets the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter of cntnr to ver.

Parameters

cntnr	The control-parameter container.
ver	The new PDB format version (see Biomol::PDBFormatVersion).

◆ hasPDBFormatVersionParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::PDB_FORMAT_VERSION parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearPDBFormatVersionParameter()

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

Removes the Biomol::ControlParameter::PDB_FORMAT_VERSION parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getMMCIFApplyDictAtomBondingParameter()

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

Returns the value of the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The mmCIF-apply-dict-atom-bonding flag.

Since: 1.2

◆ setMMCIFApplyDictAtomBondingParameter()

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

Sets the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived atom-bonding during mmCIF input, and `false` to skip it.

◆ hasMMCIFApplyDictAtomBondingParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearMMCIFApplyDictAtomBondingParameter()

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

Removes the Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getMMCIFApplyDictBondOrdersParameter()

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

Returns the value of the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The mmCIF-apply-dict-bond-orders flag.

Since: 1.2

◆ setMMCIFApplyDictBondOrdersParameter()

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

Sets the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr to apply.

Parameters

cntnr	The control-parameter container.
apply	`true` to apply dictionary-derived bond orders during mmCIF input, and `false` to skip them.

◆ hasMMCIFApplyDictBondOrdersParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearMMCIFApplyDictBondOrdersParameter()

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

Removes the Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getMMCIFOutputBiopolymersAsChemCompParameter()

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

Returns the value of the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: The mmCIF-output-biopolymers-as-chem-comp flag.

Since: 1.2

◆ setMMCIFOutputBiopolymersAsChemCompParameter()

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

Sets the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr to output.

Parameters

cntnr	The control-parameter container.
output	`true` to emit biopolymer residues using the `chem_comp` data category, and `false` to use the regular polymer-residue encoding.

◆ hasMMCIFOutputBiopolymersAsChemCompParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearMMCIFOutputBiopolymersAsChemCompParameter()

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

Removes the Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ getMMCIFOutputDataPostprocFunctionParameter()

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

Returns the value of the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr.

Parameters

cntnr The control-parameter container.

Returns: A const reference to the mmCIF-output data-postprocessing function.

Since: 1.2

◆ setMMCIFOutputDataPostprocFunctionParameter()

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

Sets the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr to func.

Parameters

cntnr	The control-parameter container.
func	The new mmCIF-output data-postprocessing function.

◆ hasMMCIFOutputDataPostprocFunctionParameter()

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

Tells whether cntnr carries an explicit Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter.

Parameters

cntnr The control-parameter container.

Returns: true if the parameter is set, and false otherwise.

◆ clearMMCIFOutputDataPostprocFunctionParameter()

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

Removes the Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter from cntnr.

Parameters

cntnr The control-parameter container.

◆ operator<<() [1/2]

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

Writes the mmCIF data record data in textual mmCIF format to the output stream os.

Parameters

os	The output stream to write to.
data	The mmCIF data record to write.

Returns: A reference to os.

Since: 1.2

◆ operator<<() [2/2]

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

Writes the mmCIF category cat in textual mmCIF format to the output stream os.

Parameters

os	The output stream to write to.
cat	The mmCIF category to write.

Returns: A reference to os.

Since: 1.2

◆ getResidueCode() [2/2]

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

Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_CODE property of molgraph.

Parameters

molgraph The molecular graph.

Returns: A const reference to the residue three-letter code.

◆ setResidueCode() [2/2]

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

Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_CODE property of molgraph to code.

Parameters

molgraph	The molecular graph.
code	The new residue three-letter code.

◆ clearResidueCode() [2/2]

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

Removes the Biomol::MolecularGraphProperty::RESIDUE_CODE property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasResidueCode() [2/2]

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_CODE property.

Parameters

molgraph The molecular graph.

Returns: true if the residue code is set, and false otherwise.

◆ getResidueSequenceNumber() [2/2]

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

Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property of molgraph.

Parameters

molgraph The molecular graph.

Returns: The residue sequence number.

◆ setResidueSequenceNumber() [2/2]

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

Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property of molgraph to seq_no.

Parameters

molgraph	The molecular graph.
seq_no	The new residue sequence number.

◆ clearResidueSequenceNumber() [2/2]

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

Removes the Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasResidueSequenceNumber() [2/2]

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_SEQUENCE_NUMBER property.

Parameters

molgraph The molecular graph.

Returns: true if the residue sequence number is set, and false otherwise.

◆ getResidueInsertionCode() [2/2]

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

Returns the value of the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property of molgraph.

Parameters

molgraph The molecular graph.

Returns: The residue insertion code.

◆ setResidueInsertionCode() [2/2]

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

Sets the value of the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property of molgraph to code.

Parameters

molgraph	The molecular graph.
code	The new residue insertion code.

◆ clearResidueInsertionCode() [2/2]

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

Removes the Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasResidueInsertionCode() [2/2]

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::RESIDUE_INSERTION_CODE property.

Parameters

molgraph The molecular graph.

Returns: true if the residue insertion code is set, and false otherwise.

◆ getChainID() [2/2]

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

Returns the value of the Biomol::MolecularGraphProperty::CHAIN_ID property of molgraph.

Parameters

molgraph The molecular graph.

Returns: A const reference to the chain ID.

◆ setChainID() [2/2]

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

Sets the value of the Biomol::MolecularGraphProperty::CHAIN_ID property of molgraph to id.

Parameters

molgraph	The molecular graph.
id	The new chain ID.

◆ clearChainID() [2/2]

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

Removes the Biomol::MolecularGraphProperty::CHAIN_ID property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasChainID() [2/2]

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::CHAIN_ID property.

Parameters

molgraph The molecular graph.

Returns: true if the chain ID is set, and false otherwise.

◆ getModelNumber() [2/2]

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

Returns the value of the Biomol::MolecularGraphProperty::MODEL_NUMBER property of molgraph.

Parameters

molgraph The molecular graph.

Returns: The model number.

◆ setModelNumber() [2/2]

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

Sets the value of the Biomol::MolecularGraphProperty::MODEL_NUMBER property of molgraph to model_no.

Parameters

molgraph	The molecular graph.
model_no	The new model number.

◆ clearModelNumber() [2/2]

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

Removes the Biomol::MolecularGraphProperty::MODEL_NUMBER property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasModelNumber() [2/2]

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::MODEL_NUMBER property.

Parameters

molgraph The molecular graph.

Returns: true if the model number is set, and false otherwise.

◆ getPDBData()

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

Returns the value of the Biomol::MolecularGraphProperty::PDB_DATA property of molgraph.

Parameters

molgraph The molecular graph.

Returns: A const reference to the PDB data record shared pointer.

◆ setPDBData()

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

Sets the value of the Biomol::MolecularGraphProperty::PDB_DATA property of molgraph to data.

Parameters

molgraph	The molecular graph.
data	The new PDB data record.

◆ clearPDBData()

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

Removes the Biomol::MolecularGraphProperty::PDB_DATA property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasPDBData()

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::PDB_DATA property.

Parameters

molgraph The molecular graph.

Returns: true if the PDB data record is set, and false otherwise.

◆ getMMCIFData()

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

Returns the value of the Biomol::MolecularGraphProperty::MMCIF_DATA property of molgraph.

Parameters

molgraph The molecular graph.

Returns: A const reference to the mmCIF data record shared pointer.

Since: 1.2

◆ setMMCIFData()

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

Sets the value of the Biomol::MolecularGraphProperty::MMCIF_DATA property of molgraph to data.

Parameters

molgraph	The molecular graph.
data	The new mmCIF data record.

◆ clearMMCIFData()

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

Removes the Biomol::MolecularGraphProperty::MMCIF_DATA property from molgraph.

Parameters

molgraph The molecular graph.

◆ hasMMCIFData()

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

Tells whether molgraph carries an explicit Biomol::MolecularGraphProperty::MMCIF_DATA property.

Parameters

molgraph The molecular graph.

Returns: true if the mmCIF data record is set, and false otherwise.

◆ 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`
	)

Extracts the substructures of all residues represented in molgraph from the parent macromolecular graph parent_molgraph.

Parameters

molgraph	The molecular graph providing the residue selection.
parent_molgraph	The macromolecular graph from which to extract the residue substructures.
res_substructs	The output fragment receiving the extracted residue substructures.
cnctd_only	If `true`, only atoms in the connected component of each residue's representative atom are extracted.
flags	The bitwise-OR combination of Biomol::AtomPropertyFlag values selecting the residue-identifying properties.
append	If `true`, the extracted atoms and bonds are appended to res_substructs; if `false`, res_substructs is cleared first.

◆ 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`
	)

Extracts the atoms of macromol that lie within max_dist of any atom of core.

Parameters

core	The core molecular graph defining the reference atom positions.
macromol	The macromolecular graph providing the candidate atoms.
env_atoms	The output fragment receiving the extracted environment atoms.
max_dist	The maximum allowed distance between an environment atom and the nearest core atom.
inc_core_atoms	If `true`, the atoms of core are also added to env_atoms.
append	If `true`, the extracted atoms are appended to env_atoms; if `false`, env_atoms is cleared first.

◆ 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`
	)

Extracts the atoms of macromol that lie within max_dist of any atom of core, using coords_func to obtain atom positions.

Parameters

core	The core molecular graph defining the reference atom positions.
macromol	The macromolecular graph providing the candidate atoms.
env_atoms	The output fragment receiving the extracted environment atoms.
coords_func	The function used to retrieve the 3D coordinates of an atom.
max_dist	The maximum allowed distance between an environment atom and the nearest core atom.
inc_core_atoms	If `true`, the atoms of core are also added to env_atoms.
append	If `true`, the extracted atoms are appended to env_atoms; if `false`, env_atoms is cleared first.

◆ 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`
	)

Extracts the residues of macromol that contain at least one atom within max_dist of any atom of core.

Parameters

core	The core molecular graph defining the reference atom positions.
macromol	The macromolecular graph providing the candidate residues.
env_residues	The output fragment receiving the extracted environment residues.
max_dist	The maximum allowed distance between any atom of the environment residue and the nearest core atom.
append	If `true`, the extracted residue atoms and bonds are appended to env_residues; if `false`, env_residues is cleared first.

◆ 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`
	)

Extracts the residues of macromol that contain at least one atom within max_dist of any atom of core, using coords_func to obtain atom positions.

Parameters

core	The core molecular graph defining the reference atom positions.
macromol	The macromolecular graph providing the candidate residues.
env_residues	The output fragment receiving the extracted environment residues.
coords_func	The function used to retrieve the 3D coordinates of an atom.
max_dist	The maximum allowed distance between any atom of the environment residue and the nearest core atom.
append	If `true`, the extracted residue atoms and bonds are appended to env_residues; if `false`, env_residues is cleared first.

◆ setHydrogenResidueSequenceInfo()

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

Copies residue-identifying properties from heavy atoms to their attached hydrogen atoms in molgraph.

Parameters

molgraph	The molecular graph whose hydrogen atoms shall receive residue-identifying properties.
overwrite	If `true`, existing residue-identifying properties of hydrogen atoms are overwritten.
flags	The bitwise-OR combination of Biomol::AtomPropertyFlag values selecting the residue-identifying properties to propagate.

◆ 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`
	)

Tells whether the residue-identity attributes of molgraph match the given filter values.

Each filter argument is ignored when set to its sentinel value (nullptr / 0 / IGNORE_SEQUENCE_NO). All supplied filters must match for the function to return true.

Parameters

molgraph	The molecular graph to test.
res_code	The PDB three-letter residue code to match (or `nullptr` to ignore).
chain_id	The PDB chain ID to match (or `nullptr` to ignore).
res_seq_no	The PDB residue sequence number to match (or IGNORE_SEQUENCE_NO to ignore).
ins_code	The PDB insertion code to match (or `0` to ignore).
model_no	The PDB model number to match (or `0` to ignore).

Returns: true if all supplied filters match, and false otherwise.

◆ combineInterferingResidueCoordinates()

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

Merges alternative residue conformers in mol whose residue centers lie within max_ctr_dist of one another.

Many PDB and mmCIF structures encode alternative conformations of a residue as multiple residues with distinct alternate-location identifiers but mostly overlapping atom positions. This function detects such interfering residue copies (residues whose geometric centers are closer than max_ctr_dist) and combines them into a single residue with all observed atom positions, leaving the molecule's topology and residue ordering otherwise unchanged.

Parameters

mol	The molecule whose interfering residues are to be combined.
max_ctr_dist	The maximum distance between residue centers that still qualifies them as interfering copies of one another.

Returns: true if at least one residue group was combined, and false if no interfering residues were found.

◆ 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`
	)

Searches the iterator range [it, end) for the first atom whose PDB-style residue identity attributes match the given filter values.

Each filter argument is ignored when set to its sentinel value (nullptr / 0 / IGNORE_SEQUENCE_NO / IGNORE_SERIAL_NO). All supplied filters must match for an atom to be considered a hit.

Template Parameters

Iter	The (forward) iterator type whose value type is `Chem::Atom`.

Parameters

it	Iterator pointing to the first atom of the range.
end	Iterator pointing one past the last atom of the range.
res_code	The PDB three-letter residue code to match (or `nullptr` to ignore).
chain_id	The PDB chain ID to match (or `nullptr` to ignore).
res_seq_no	The PDB residue sequence number to match (or IGNORE_SEQUENCE_NO to ignore).
ins_code	The PDB insertion code to match (or 0 to ignore).
model_no	The PDB model number to match (or 0 to ignore).
atom_name	The PDB atom name to match (or `nullptr` to ignore).
serial_no	The PDB atom serial number to match (or IGNORE_SERIAL_NO to ignore).

Returns: An iterator pointing to the first matching atom, or end if no match was found.

◆ findResidue()

template<typename Iter >

Iter CDPL::Biomol::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`
	)

Searches the iterator range [it, end) for the first residue (molecular graph) whose PDB-style identity attributes match the given filter values, optionally requiring a matching atom.

Each filter argument is ignored when set to its sentinel value. If both atom_name and serial_no are sentinels, the search returns the first residue matching the residue-level filters. Otherwise, a residue is only returned if it additionally contains an atom matching atom_name / serial_no.

Template Parameters

Iter	The (forward) iterator type whose value type is convertible to `Chem::MolecularGraph`.

Parameters

it	Iterator pointing to the first residue of the range.
end	Iterator pointing one past the last residue of the range.
res_code	The PDB three-letter residue code to match (or `nullptr` to ignore).
chain_id	The PDB chain ID to match (or `nullptr` to ignore).
res_seq_no	The PDB residue sequence number to match (or IGNORE_SEQUENCE_NO to ignore).
ins_code	The PDB insertion code to match (or 0 to ignore).
model_no	The PDB model number to match (or 0 to ignore).
atom_name	The PDB atom name an atom of the residue must match (or `nullptr` to ignore).
serial_no	The PDB atom serial number an atom of the residue must match (or IGNORE_SERIAL_NO to ignore).

Returns: An iterator pointing to the first matching residue, or end if no match was found.

Variable Documentation

◆ IGNORE_SEQUENCE_NO

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

Sentinel value indicating that the residue sequence number should be ignored when matching residues.

◆ IGNORE_SERIAL_NO

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

Sentinel value indicating that the atom serial number should be ignored when matching atoms.

Namespaces

Classes

Typedefs

Functions

Variables

Detailed Description

Typedef Documentation

◆ MMCIFBZ2MolecularGraphOutputHandler

◆ MMCIFBZ2MolecularGraphWriter

◆ MMCIFBZ2MoleculeInputHandler

◆ MMCIFBZ2MoleculeReader

◆ MMCIFDataProcessingFunction

◆ MMCIFGZMolecularGraphOutputHandler

◆ MMCIFGZMolecularGraphWriter

◆ MMCIFGZMoleculeInputHandler

◆ MMCIFGZMoleculeReader

◆ MMCIFMolecularGraphOutputHandler

◆ MMCIFMoleculeInputHandler

◆ MMTFBZ2MolecularGraphOutputHandler

◆ MMTFBZ2MolecularGraphWriter

◆ MMTFBZ2MoleculeInputHandler

◆ MMTFBZ2MoleculeReader

◆ MMTFGZMolecularGraphOutputHandler

◆ MMTFGZMolecularGraphWriter

◆ MMTFGZMoleculeInputHandler

◆ MMTFGZMoleculeReader

◆ MMTFMolecularGraphOutputHandler

◆ MMTFMoleculeInputHandler

◆ PDBBZ2MolecularGraphOutputHandler

◆ PDBBZ2MolecularGraphWriter

◆ PDBBZ2MoleculeInputHandler

◆ PDBBZ2MoleculeReader

◆ PDBGZMolecularGraphOutputHandler

◆ PDBGZMolecularGraphWriter

◆ PDBGZMoleculeInputHandler

◆ PDBGZMoleculeReader

◆ PDBMolecularGraphOutputHandler

◆ PDBMoleculeInputHandler

Function Documentation

◆ getResidueAtomName()

◆ setResidueAtomName()

◆ clearResidueAtomName()

◆ hasResidueAtomName()

◆ getResidueAltAtomName()

◆ setResidueAltAtomName()

◆ clearResidueAltAtomName()

◆ hasResidueAltAtomName()

◆ getResidueLeavingAtomFlag()

◆ setResidueLeavingAtomFlag()

◆ clearResidueLeavingAtomFlag()

◆ hasResidueLeavingAtomFlag()

◆ getResidueLinkingAtomFlag()

◆ setResidueLinkingAtomFlag()

◆ clearResidueLinkingAtomFlag()

◆ hasResidueLinkingAtomFlag()

◆ getResidueCode() [1/2]

◆ setResidueCode() [1/2]

◆ clearResidueCode() [1/2]

◆ hasResidueCode() [1/2]

◆ getResidueSequenceNumber() [1/2]

◆ setResidueSequenceNumber() [1/2]

◆ clearResidueSequenceNumber() [1/2]

◆ hasResidueSequenceNumber() [1/2]

◆ getResidueInsertionCode() [1/2]

◆ setResidueInsertionCode() [1/2]

◆ clearResidueInsertionCode() [1/2]

◆ hasResidueInsertionCode() [1/2]

◆ getHeteroAtomFlag()

◆ setHeteroAtomFlag()

◆ clearHeteroAtomFlag()

◆ hasHeteroAtomFlag()

◆ getChainID() [1/2]

◆ setChainID() [1/2]

◆ clearChainID() [1/2]

◆ hasChainID() [1/2]

◆ getAltLocationID()

◆ setAltLocationID()

◆ clearAltLocationID()

◆ hasAltLocationID()

◆ getEntityID()