CDPL.Biomol Package Reference

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

Classes
class	AtomProperty
	Provides keys for built-in biomolecular Chem.Atom properties. More...
class	AtomPropertyDefault
	Provides default values for built-in Chem.Atom properties. More...
class	AtomPropertyFlag
	Provides flags for the specification of basic Chem.Atom properties. More...
class	ControlParameter
	Provides keys for built-in control-parameters. More...
class	ControlParameterDefault
	Provides default values for built-in control-parameters. More...
class	DataFormat
	Provides preinitialized Base.DataFormat objects for all supported biopolymer data formats. More...
class	FileMMCIFBZ2MolecularGraphWriter
class	FileMMCIFBZ2MoleculeReader
class	FileMMCIFGZMolecularGraphWriter
class	FileMMCIFGZMoleculeReader
class	FileMMCIFMolecularGraphWriter
class	FileMMCIFMoleculeReader
class	FileMMTFBZ2MolecularGraphWriter
class	FileMMTFBZ2MoleculeReader
class	FileMMTFGZMolecularGraphWriter
class	FileMMTFGZMoleculeReader
class	FileMMTFMolecularGraphWriter
class	FileMMTFMoleculeReader
class	FilePDBBZ2MolecularGraphWriter
class	FilePDBBZ2MoleculeReader
class	FilePDBGZMolecularGraphWriter
class	FilePDBGZMoleculeReader
class	FilePDBMolecularGraphWriter
class	FilePDBMoleculeReader
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	MMCIFBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFData
	Data structure for the storage of imported MMCIF data (see [MMCIF]). More...
class	MMCIFDataProcessingFunction
	Generic wrapper class used to store a user-defined function for the processing of Biomol.MMCIFData instances. More...
class	MMCIFGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFGZMoleculeReader
	Reader for molecule data in the gzip-compressed Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFMolecularGraphWriter
	Writer for molecular graph data in the Macromolecular Crystallographic Information File (mmCIF) [MMCIF] format. More...
class	MMCIFMoleculeInputHandler
	Handler for the input of molecule 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	MMTFBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...
class	MMTFBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...
class	MMTFGZMoleculeReader
	Reader for molecule data in the gzip-compressed Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...
class	MMTFMolecularGraphWriter
	Writer for molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFMoleculeInputHandler
	Handler for the input of molecule data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MMTFMoleculeReader
	Reader for molecule data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...
class	MolecularGraphPointerStringFunctor
class	MolecularGraphProperty
	Provides keys for built-in Chem.MolecularGraph properties. More...
class	MolecularGraphPropertyDefault
	Provides default values for built-in Chem.MolecularGraph properties. More...
class	PDBBZ2MolecularGraphOutputHandler
	Handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBBZ2MolecularGraphWriter
	Writer for molecular graph data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBBZ2MoleculeInputHandler
	Handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBBZ2MoleculeReader
	Reader for molecule data in the bzip2-compressed Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBData
	Data structure for the storage of data records found in PDB formatted data [PDB]. More...
class	PDBFormatVersion
	Provides constants for the specification of the Brookhaven Protein Data Bank (PDB) [PDB] format version. More...
class	PDBGZMolecularGraphOutputHandler
	Handler for the output of gzip-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBGZMolecularGraphWriter
	Writer for molecular graph data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBGZMoleculeInputHandler
	Handler for the input of gzip-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBGZMoleculeReader
	Reader for molecule data in the gzip-compressed Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBMolecularGraphOutputHandler
	Handler for the output of molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBMolecularGraphWriter
	Writer for molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...
class	PDBMoleculeInputHandler
	Handler for the input of molecule 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...
class	ResidueType
	Provides constants for the specification of the type of a chemical component (residue). More...

Functions
None	setAltLocationID (Chem.Atom atom, str id)
	Sets the value of the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom to id. More...
bool	hasAltLocationID (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom is set. More...
str	getAltLocationID (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom. More...
None	clearAltLocationID (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom. More...
None	setBFactor (Chem.Atom atom, float factor)
	Sets the value of the Biomol.AtomProperty.B_FACTOR property of the atom atom to factor. More...
bool	hasBFactor (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.B_FACTOR property of the atom atom is set. More...
float	getBFactor (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.B_FACTOR property of the atom atom. More...
None	clearBFactor (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.B_FACTOR property of the atom atom. More...
None	setChainID (Chem.Atom atom, str id)
	Sets the value of the Biomol.AtomProperty.CHAIN_ID property of the atom atom to id. More...
bool	hasChainID (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.CHAIN_ID property of the atom atom is set. More...
str	getChainID (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.CHAIN_ID property of the atom atom. More...
None	clearChainID (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.CHAIN_ID property of the atom atom. More...
None	setChainID (Chem.MolecularGraph molgraph, str id)
	Sets the value of the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph to id. More...
bool	hasChainID (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph is set. More...
str	getChainID (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph. More...
None	clearChainID (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph. More...
None	setEntityID (Chem.Atom atom, str id)
	Sets the value of the Biomol.AtomProperty.ENTITY_ID property of the atom atom to id. More...
bool	hasEntityID (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.ENTITY_ID property of the atom atom is set. More...
str	getEntityID (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.ENTITY_ID property of the atom atom. More...
None	clearEntityID (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.ENTITY_ID property of the atom atom. More...
None	setHeteroAtomFlag (Chem.Atom atom, bool is_het)
	Sets the value of the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom to is_het. More...
bool	hasHeteroAtomFlag (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom is set. More...
bool	getHeteroAtomFlag (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom. More...
None	clearHeteroAtomFlag (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom. More...
None	setHydrogenResidueSequenceInfo (Chem.MolecularGraph molgraph, bool overwrite, int flags=2147483648)
	Copies residue identifying properties from heavy atoms to their attached hydrogen atoms in the molecular graph molgraph. More...
None	setMMCIFData (Chem.MolecularGraph molgraph, MMCIFData data)
	Sets the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph to data. More...
bool	hasMMCIFData (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph is set. More...
MMCIFData	getMMCIFData (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph. More...
None	clearMMCIFData (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph. More...
None	setModelNumber (Chem.Atom atom, int model_no)
	Sets the value of the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom to model_no. More...
bool	hasModelNumber (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom is set. More...
int	getModelNumber (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom. More...
None	clearModelNumber (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom. More...
None	setModelNumber (Chem.MolecularGraph molgraph, int model_no)
	Sets the value of the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph to model_no. More...
bool	hasModelNumber (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph is set. More...
int	getModelNumber (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph. More...
None	clearModelNumber (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph. More...
None	setOccupancy (Chem.Atom atom, float occupancy)
	Sets the value of the Biomol.AtomProperty.OCCUPANCY property of the atom atom to occupancy. More...
bool	hasOccupancy (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.OCCUPANCY property of the atom atom is set. More...
float	getOccupancy (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.OCCUPANCY property of the atom atom. More...
None	clearOccupancy (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.OCCUPANCY property of the atom atom. More...
None	setPDBData (Chem.MolecularGraph molgraph, PDBData data)
	Sets the value of the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph to data. More...
bool	hasPDBData (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph is set. More...
PDBData	getPDBData (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph. More...
None	clearPDBData (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph. More...
None	setResidueAltAtomName (Chem.Atom atom, str name)
	Sets the value of the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom to name. More...
bool	hasResidueAltAtomName (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom is set. More...
str	getResidueAltAtomName (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom. More...
None	clearResidueAltAtomName (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom. More...
None	setResidueAtomName (Chem.Atom atom, str name)
	Sets the value of the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom to name. More...
bool	hasResidueAtomName (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom is set. More...
str	getResidueAtomName (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom. More...
None	clearResidueAtomName (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom. More...
None	setResidueCode (Chem.Atom atom, str code)
	Sets the value of the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom to code. More...
bool	hasResidueCode (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom is set. More...
str	getResidueCode (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom. More...
None	clearResidueCode (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom. More...
None	setResidueCode (Chem.MolecularGraph molgraph, str code)
	Sets the value of the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph to code. More...
bool	hasResidueCode (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph is set. More...
str	getResidueCode (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph. More...
None	clearResidueCode (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph. More...
None	setResidueInsertionCode (Chem.Atom atom, str code)
	Sets the value of the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom to code. More...
bool	hasResidueInsertionCode (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom is set. More...
str	getResidueInsertionCode (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom. More...
None	clearResidueInsertionCode (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom. More...
None	setResidueInsertionCode (Chem.MolecularGraph molgraph, str code)
	Sets the value of the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph to code. More...
bool	hasResidueInsertionCode (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph is set. More...
str	getResidueInsertionCode (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph. More...
None	clearResidueInsertionCode (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph. More...
None	setResidueLeavingAtomFlag (Chem.Atom atom, bool leaving)
	Sets the value of the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom to leaving. More...
bool	hasResidueLeavingAtomFlag (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom is set. More...
bool	getResidueLeavingAtomFlag (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom. More...
None	clearResidueLeavingAtomFlag (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom. More...
None	setResidueLinkingAtomFlag (Chem.Atom atom, bool linking)
	Sets the value of the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom to linking. More...
bool	hasResidueLinkingAtomFlag (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom is set. More...
bool	getResidueLinkingAtomFlag (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom. More...
None	clearResidueLinkingAtomFlag (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom. More...
None	setResidueSequenceNumber (Chem.Atom atom, int seq_no)
	Sets the value of the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom to seq_no. More...
bool	hasResidueSequenceNumber (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom is set. More...
int	getResidueSequenceNumber (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom. More...
None	clearResidueSequenceNumber (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom. More...
None	setResidueSequenceNumber (Chem.MolecularGraph molgraph, int seq_no)
	Sets the value of the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph to seq_no. More...
bool	hasResidueSequenceNumber (Chem.MolecularGraph molgraph)
	Tells whether the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph is set. More...
int	getResidueSequenceNumber (Chem.MolecularGraph molgraph)
	Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph. More...
None	clearResidueSequenceNumber (Chem.MolecularGraph molgraph)
	Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph. More...
None	setSerialNumber (Chem.Atom atom, int serial_no)
	Sets the value of the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom to serial_no. More...
bool	hasSerialNumber (Chem.Atom atom)
	Tells whether the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom is set. More...
int	getSerialNumber (Chem.Atom atom)
	Returns the value of the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom. More...
None	clearSerialNumber (Chem.Atom atom)
	Clears the value of the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom. More...
bool	areInSameResidue (Chem.Atom atom1, Chem.Atom atom2, int flags=2147483648)
	Tells whether the atoms atom1 and atom2 belong to the same residue, comparing the atom properties selected by flags. More...
bool	combineInterferingResidueCoordinates (Chem.Molecule mol, float max_ctr_dist=1.0)
	Merges alternative residue conformers in mol whose residue centers lie within max_ctr_dist of one another. More...
None	extractEnvironmentResidues (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_residues, float max_dist, bool append=False)
	Extracts the residues of the molecular graph macromol that contain at least one atom within max_dist of any atom of core. More...
None	extractEnvironmentResidues (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_residues, Chem.Atom3DCoordinatesFunction coords_func, float max_dist, bool append=False)
	Extracts the residues of the molecular graph macromol that contain at least one atom within max_dist of any atom of core, using coords_func to obtain atom positions. More...
None	extractProximalAtoms (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_atoms, float max_dist, bool inc_core_atoms=False, bool append=False)
	Extracts the atoms of the molecular graph macromol that lie within max_dist of any atom of core. More...
None	extractProximalAtoms (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_atoms, Chem.Atom3DCoordinatesFunction coords_func, float max_dist, bool inc_core_atoms=False, bool append=False)
	Extracts the atoms of the molecular graph macromol that lie within max_dist of any atom of core, using coords_func to obtain atom positions. More...
None	extractResidueSubstructure (Chem.Atom atom, Chem.MolecularGraph molgraph, Chem.Fragment res_substruct, bool cnctd_only=False, int flags=2147483648, bool append=False)
	Extracts the substructure of the residue the atom atom belongs to into res_substruct. More...
None	extractResidueSubstructures (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent_molgraph, Chem.Fragment res_substructs, bool cnctd_only=False, int flags=2147483648, bool append=False)
	Extracts the substructures of all residues that are specified by atoms in the molecular graph molgraph from the parent molecular graph parent_molgraph. More...
int	findResidueAtom (object cntnr, int idx, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808)
int	findResidue (object cntnr, int idx, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808)
bool	isPDBBackboneAtom (Chem.Atom atom)
	Tells whether the atom atom is a backbone atom of an amino acid or nucleotide residue. More...
bool	matchesResidueInfo (Chem.Atom atom, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808)
	Tells whether the residue attributes of the atom atom match the given filter values. More...
bool	matchesResidueInfo (Chem.MolecularGraph molgraph, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0)
	Tells whether the residue identity attributes of the molecular graph molgraph match the given filter values. More...
None	setApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter of cntnr to apply. More...
bool	hasApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter of cntnr is set. More...
bool	getApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter stored in cntnr. More...
None	clearApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter from cntnr. More...
None	setApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter of cntnr to apply. More...
bool	hasApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter from cntnr. More...
None	setCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
	Sets the value of the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter of cntnr to calc. More...
bool	hasCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter from cntnr. More...
None	setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)
	Sets the value of the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr to check. More...
bool	hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set. More...
bool	getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr. More...
None	clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr. More...
None	setCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr, bool comb)
	Sets the value of the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr to comb. More...
bool	hasCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr is set. More...
bool	getCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter stored in cntnr. More...
None	clearCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter from cntnr. More...
None	setMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr to apply. More...
bool	hasMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr is set. More...
bool	getMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter stored in cntnr. More...
None	clearMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter from cntnr. More...
None	setMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr to apply. More...
bool	hasMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr is set. More...
bool	getMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter stored in cntnr. More...
None	clearMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter from cntnr. More...
None	setMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr to output. More...
bool	hasMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr is set. More...
bool	getMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter stored in cntnr. More...
None	clearMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter from cntnr. More...
None	setMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr, MMCIFDataProcessingFunction func)
	Sets the value of the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr to func. More...
bool	hasMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr is set. More...
MMCIFDataProcessingFunction	getMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter stored in cntnr. More...
None	clearMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter from cntnr. More...
None	setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr to apply. More...
bool	hasPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr is set. More...
bool	getPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter stored in cntnr. More...
None	clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter from cntnr. More...
None	setPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr to apply. More...
bool	hasPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr is set. More...
bool	getPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter stored in cntnr. More...
None	clearPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter from cntnr. More...
None	setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr to apply. More...
bool	hasPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr is set. More...
bool	getPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter stored in cntnr. More...
None	clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter from cntnr. More...
None	setPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
	Sets the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr to apply. More...
bool	hasPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr is set. More...
bool	getPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter stored in cntnr. More...
None	clearPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter from cntnr. More...
None	setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool deduce)
	Sets the value of the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr to deduce. More...
bool	hasPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr is set. More...
bool	getPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter stored in cntnr. More...
None	clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter from cntnr. More...
None	setPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr, bool evaluate)
bool	hasPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter of cntnr is set. More...
bool	getPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter stored in cntnr. More...
None	clearPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter from cntnr. More...
None	setPDBFormatVersionParameter (Base.ControlParameterContainer cntnr, int ver)
	Sets the value of the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter of cntnr to ver. More...
bool	hasPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter of cntnr is set. More...
int	getPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter stored in cntnr. More...
None	clearPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter from cntnr. More...
None	setPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool ignore)
	Sets the value of the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter of cntnr to ignore. More...
bool	hasPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter of cntnr is set. More...
bool	getPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter stored in cntnr. More...
None	clearPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter from cntnr. More...
None	setPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr, bool ignore)
	Sets the value of the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr to ignore. More...
bool	hasPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr is set. More...
bool	getPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter stored in cntnr. More...
None	clearPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter from cntnr. More...
None	setPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr to output. More...
bool	hasPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr is set. More...
bool	getPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter stored in cntnr. More...
None	clearPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter from cntnr. More...
None	setPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter of cntnr to output. More...
bool	hasPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter of cntnr is set. More...
bool	getPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter stored in cntnr. More...
None	clearPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter from cntnr. More...
None	setPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr to output. More...
bool	hasPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr is set. More...
bool	getPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter stored in cntnr. More...
None	clearPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter from cntnr. More...
None	setPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output)
	Sets the value of the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr to output. More...
bool	hasPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr is set. More...
bool	getPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter stored in cntnr. More...
None	clearPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter from cntnr. More...
None	setPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
	Sets the value of the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter of cntnr to trunc. More...
bool	hasPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter of cntnr is set. More...
bool	getPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter stored in cntnr. More...
None	clearPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter from cntnr. More...
None	setPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
	Sets the value of the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr to perceive. More...
bool	hasPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr is set. More...
bool	getPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter stored in cntnr. More...
None	clearPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter from cntnr. More...
None	setResidueDictionaryParameter (Base.ControlParameterContainer cntnr, ResidueDictionary dict)
	Sets the value of the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter of cntnr to dict. More...
bool	hasResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter of cntnr is set. More...
ResidueDictionary	getResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter stored in cntnr. More...
None	clearResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter from cntnr. More...
None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
	Sets the value of the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr to strict. More...
bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Tells whether the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set. More...
bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Returns the value of the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr. More...
None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
	Removes the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr. More...

Variables
int	IGNORE_SEQUENCE_NO = -9223372036854775808
	Sentinel value indicating that the residue sequence number should be ignored.
int	IGNORE_SERIAL_NO = -9223372036854775808
	Sentinel value indicating that the atom serial number should be ignored.

Detailed Description

Contains classes and functions related to biological macromolecules.

Function Documentation

setAltLocationID()

None CDPL.Biomol.setAltLocationID	(	Chem.Atom	atom,
		str	id
	)

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

Parameters

atom	The atom for which to set the property value.
id	The new alternate location identifier.

hasAltLocationID()

bool CDPL.Biomol.hasAltLocationID

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the alternate location identifier is set, and False otherwise.

getAltLocationID()

str CDPL.Biomol.getAltLocationID

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The alternate location identifier.

clearAltLocationID()

None CDPL.Biomol.clearAltLocationID

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.ALT_LOCATION_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setBFactor()

None CDPL.Biomol.setBFactor	(	Chem.Atom	atom,
		float	factor
	)

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

Parameters

atom	The atom for which to set the property value.
factor	The new temperature (B) factor.

hasBFactor()

bool CDPL.Biomol.hasBFactor

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.B_FACTOR property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the temperature factor is set, and False otherwise.

getBFactor()

float CDPL.Biomol.getBFactor

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The temperature (B) factor.

clearBFactor()

None CDPL.Biomol.clearBFactor

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.B_FACTOR property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setChainID() [1/2]

None CDPL.Biomol.setChainID	(	Chem.Atom	atom,
		str	id
	)

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

Parameters

atom	The atom for which to set the property value.
id	The new chain ID.

hasChainID() [1/2]

bool CDPL.Biomol.hasChainID

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.CHAIN_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the chain ID is set, and False otherwise.

getChainID() [1/2]

str CDPL.Biomol.getChainID

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

A reference to the chain ID.

clearChainID() [1/2]

None CDPL.Biomol.clearChainID

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.CHAIN_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setChainID() [2/2]

None CDPL.Biomol.setChainID	(	Chem.MolecularGraph	molgraph,
		str	id
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
id	The new chain ID.

hasChainID() [2/2]

bool CDPL.Biomol.hasChainID

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the chain ID is set, and False otherwise.

getChainID() [2/2]

str CDPL.Biomol.getChainID

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

A reference to the chain ID.

clearChainID() [2/2]

None CDPL.Biomol.clearChainID

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.CHAIN_ID property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setEntityID()

None CDPL.Biomol.setEntityID	(	Chem.Atom	atom,
		str	id
	)

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

Parameters

atom	The atom for which to set the property value.
id	The new entity ID.

hasEntityID()

bool CDPL.Biomol.hasEntityID

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.ENTITY_ID property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the entity ID is set, and False otherwise.

getEntityID()

str CDPL.Biomol.getEntityID

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

A reference to the entity ID.

Since

1.2

clearEntityID()

None CDPL.Biomol.clearEntityID

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.ENTITY_ID property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setHeteroAtomFlag()

None CDPL.Biomol.setHeteroAtomFlag	(	Chem.Atom	atom,
		bool	is_het
	)

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

Parameters

atom	The atom for which to set the property value.
is_het	True to mark the atom as a heteroatom, and False otherwise.

hasHeteroAtomFlag()

bool CDPL.Biomol.hasHeteroAtomFlag

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the heteroatom flag is set, and False otherwise.

getHeteroAtomFlag()

bool CDPL.Biomol.getHeteroAtomFlag

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is flagged as a heteroatom (PDB HETATM record), and False otherwise.

clearHeteroAtomFlag()

None CDPL.Biomol.clearHeteroAtomFlag

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.HETERO_ATOM_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setHydrogenResidueSequenceInfo()

None CDPL.Biomol.setHydrogenResidueSequenceInfo	(	Chem.MolecularGraph	molgraph,
		bool	overwrite,
		int	flags = 2147483648
	)

Copies residue identifying properties from heavy atoms to their attached hydrogen atoms in the molecular graph 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.

setMMCIFData()

None CDPL.Biomol.setMMCIFData	(	Chem.MolecularGraph	molgraph,
		MMCIFData	data
	)

Sets the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph to data.

Parameters

molgraph	The molecular graph for which to set the property value.
data	The new mmCIF data record.

hasMMCIFData()

bool CDPL.Biomol.hasMMCIFData

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the mmCIF data record is set, and False otherwise.

getMMCIFData()

MMCIFData CDPL.Biomol.getMMCIFData

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

A reference to the mmCIF data record shared reference.

Since

1.2

clearMMCIFData()

None CDPL.Biomol.clearMMCIFData

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.MMCIF_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setModelNumber() [1/2]

None CDPL.Biomol.setModelNumber	(	Chem.Atom	atom,
		int	model_no
	)

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

Parameters

atom	The atom for which to set the property value.
model_no	The new model number.

hasModelNumber() [1/2]

bool CDPL.Biomol.hasModelNumber

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the model number is set, and False otherwise.

getModelNumber() [1/2]

int CDPL.Biomol.getModelNumber

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The model number.

clearModelNumber() [1/2]

None CDPL.Biomol.clearModelNumber

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.MODEL_NUMBER property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setModelNumber() [2/2]

None CDPL.Biomol.setModelNumber	(	Chem.MolecularGraph	molgraph,
		int	model_no
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
model_no	The new model number.

hasModelNumber() [2/2]

bool CDPL.Biomol.hasModelNumber

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the model number is set, and False otherwise.

getModelNumber() [2/2]

int CDPL.Biomol.getModelNumber

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The model number.

clearModelNumber() [2/2]

None CDPL.Biomol.clearModelNumber

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.MODEL_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setOccupancy()

None CDPL.Biomol.setOccupancy	(	Chem.Atom	atom,
		float	occupancy
	)

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

Parameters

atom	The atom for which to set the property value.
occupancy	The new occupancy value.

hasOccupancy()

bool CDPL.Biomol.hasOccupancy

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.OCCUPANCY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the occupancy is set, and False otherwise.

getOccupancy()

float CDPL.Biomol.getOccupancy

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The occupancy value.

clearOccupancy()

None CDPL.Biomol.clearOccupancy

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.OCCUPANCY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setPDBData()

None CDPL.Biomol.setPDBData	(	Chem.MolecularGraph	molgraph,
		PDBData	data
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
data	The new PDB data record.

hasPDBData()

bool CDPL.Biomol.hasPDBData

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the PDB data record is set, and False otherwise.

getPDBData()

PDBData CDPL.Biomol.getPDBData

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

A reference to the PDB data record shared reference.

clearPDBData()

None CDPL.Biomol.clearPDBData

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.PDB_DATA property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setResidueAltAtomName()

None CDPL.Biomol.setResidueAltAtomName	(	Chem.Atom	atom,
		str	name
	)

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

Parameters

atom	The atom for which to set the property value.
name	The new alternative residue atom name.

hasResidueAltAtomName()

bool CDPL.Biomol.hasResidueAltAtomName

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the alternative residue atom name is set, and False otherwise.

getResidueAltAtomName()

str CDPL.Biomol.getResidueAltAtomName

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

A reference to the alternative residue atom name.

clearResidueAltAtomName()

None CDPL.Biomol.clearResidueAltAtomName

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_ALT_ATOM_NAME property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueAtomName()

None CDPL.Biomol.setResidueAtomName	(	Chem.Atom	atom,
		str	name
	)

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

Parameters

atom	The atom for which to set the property value.
name	The new residuel atom name.

hasResidueAtomName()

bool CDPL.Biomol.hasResidueAtomName

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the residue atom name is set, and False otherwise.

getResidueAtomName()

str CDPL.Biomol.getResidueAtomName

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

A reference to the residue atom name.

clearResidueAtomName()

None CDPL.Biomol.clearResidueAtomName

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_ATOM_NAME property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueCode() [1/2]

None CDPL.Biomol.setResidueCode	(	Chem.Atom	atom,
		str	code
	)

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

Parameters

atom	The atom for which to set the property value.
code	The new residue three-letter code.

hasResidueCode() [1/2]

bool CDPL.Biomol.hasResidueCode

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the residue code is set, and False otherwise.

getResidueCode() [1/2]

str CDPL.Biomol.getResidueCode

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

A reference to the residue three-letter code.

clearResidueCode() [1/2]

None CDPL.Biomol.clearResidueCode

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_CODE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueCode() [2/2]

None CDPL.Biomol.setResidueCode	(	Chem.MolecularGraph	molgraph,
		str	code
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
code	The new residue three-letter code.

hasResidueCode() [2/2]

bool CDPL.Biomol.hasResidueCode

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the residue code is set, and False otherwise.

getResidueCode() [2/2]

str CDPL.Biomol.getResidueCode

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

A reference to the residue three-letter code.

clearResidueCode() [2/2]

None CDPL.Biomol.clearResidueCode

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setResidueInsertionCode() [1/2]

None CDPL.Biomol.setResidueInsertionCode	(	Chem.Atom	atom,
		str	code
	)

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

Parameters

atom	The atom for which to set the property value.
code	The new residue insertion code.

hasResidueInsertionCode() [1/2]

bool CDPL.Biomol.hasResidueInsertionCode

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the residue insertion code is set, and False otherwise.

getResidueInsertionCode() [1/2]

str CDPL.Biomol.getResidueInsertionCode

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The residue insertion code.

clearResidueInsertionCode() [1/2]

None CDPL.Biomol.clearResidueInsertionCode

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_INSERTION_CODE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueInsertionCode() [2/2]

None CDPL.Biomol.setResidueInsertionCode	(	Chem.MolecularGraph	molgraph,
		str	code
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
code	The new residue insertion code.

hasResidueInsertionCode() [2/2]

bool CDPL.Biomol.hasResidueInsertionCode

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the residue insertion code is set, and False otherwise.

getResidueInsertionCode() [2/2]

str CDPL.Biomol.getResidueInsertionCode

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The residue insertion code.

clearResidueInsertionCode() [2/2]

None CDPL.Biomol.clearResidueInsertionCode

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_INSERTION_CODE property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setResidueLeavingAtomFlag()

None CDPL.Biomol.setResidueLeavingAtomFlag	(	Chem.Atom	atom,
		bool	leaving
	)

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

Parameters

atom	The atom for which to set the property value.
leaving	True to mark the atom as a leaving atom, and False otherwise.

hasResidueLeavingAtomFlag()

bool CDPL.Biomol.hasResidueLeavingAtomFlag

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the leaving atom flag is set, and False otherwise.

getResidueLeavingAtomFlag()

bool CDPL.Biomol.getResidueLeavingAtomFlag

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is a leaving atom in its parent residue, and False otherwise.

clearResidueLeavingAtomFlag()

None CDPL.Biomol.clearResidueLeavingAtomFlag

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_LEAVING_ATOM_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueLinkingAtomFlag()

None CDPL.Biomol.setResidueLinkingAtomFlag	(	Chem.Atom	atom,
		bool	linking
	)

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

Parameters

atom	The atom for which to set the property value.
linking	True to mark the atom as a linking atom, and False otherwise.

hasResidueLinkingAtomFlag()

bool CDPL.Biomol.hasResidueLinkingAtomFlag

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the linking-atom flag is set, and False otherwise.

getResidueLinkingAtomFlag()

bool CDPL.Biomol.getResidueLinkingAtomFlag

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

True if the atom is a linking atom between residues, and False otherwise.

clearResidueLinkingAtomFlag()

None CDPL.Biomol.clearResidueLinkingAtomFlag

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_LINKING_ATOM_FLAG property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueSequenceNumber() [1/2]

None CDPL.Biomol.setResidueSequenceNumber	(	Chem.Atom	atom,
		int	seq_no
	)

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

Parameters

atom	The atom for which to set the property value.
seq_no	The new residue sequence number.

hasResidueSequenceNumber() [1/2]

bool CDPL.Biomol.hasResidueSequenceNumber

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the residue sequence number is set, and False otherwise.

getResidueSequenceNumber() [1/2]

int CDPL.Biomol.getResidueSequenceNumber

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The residue sequence number.

clearResidueSequenceNumber() [1/2]

None CDPL.Biomol.clearResidueSequenceNumber

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.RESIDUE_SEQUENCE_NUMBER property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

setResidueSequenceNumber() [2/2]

None CDPL.Biomol.setResidueSequenceNumber	(	Chem.MolecularGraph	molgraph,
		int	seq_no
	)

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

Parameters

molgraph	The molecular graph for which to set the property value.
seq_no	The new residue sequence number.

hasResidueSequenceNumber() [2/2]

bool CDPL.Biomol.hasResidueSequenceNumber

(

Chem.MolecularGraph

molgraph

)

Tells whether the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph is set.

Parameters

molgraph

The molecular graph for which to query the property value.

Returns

True if the residue sequence number is set, and False otherwise.

getResidueSequenceNumber() [2/2]

int CDPL.Biomol.getResidueSequenceNumber

(

Chem.MolecularGraph

molgraph

)

Returns the value of the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to return the property value.

Returns

The residue sequence number.

clearResidueSequenceNumber() [2/2]

None CDPL.Biomol.clearResidueSequenceNumber

(

Chem.MolecularGraph

molgraph

)

Clears the value of the Biomol.MolecularGraphProperty.RESIDUE_SEQUENCE_NUMBER property of the molecular graph molgraph.

Parameters

molgraph

The molecular graph for which to clear the property value.

setSerialNumber()

None CDPL.Biomol.setSerialNumber	(	Chem.Atom	atom,
		int	serial_no
	)

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

Parameters

atom	The atom for which to set the property value.
serial_no	The new atom serial number.

hasSerialNumber()

bool CDPL.Biomol.hasSerialNumber

(

Chem.Atom

atom

)

Tells whether the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns

True if the atom serial number is set, and False otherwise.

getSerialNumber()

int CDPL.Biomol.getSerialNumber

(

Chem.Atom

atom

)

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

Parameters

atom	The atom for which to return the property value.

Returns

The atom serial number.

clearSerialNumber()

None CDPL.Biomol.clearSerialNumber

(

Chem.Atom

atom

)

Clears the value of the Biomol.AtomProperty.SERIAL_NUMBER property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

areInSameResidue()

bool CDPL.Biomol.areInSameResidue	(	Chem.Atom	atom1,
		Chem.Atom	atom2,
		int	flags = 2147483648
	)

Tells whether the atoms 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.

combineInterferingResidueCoordinates()

bool CDPL.Biomol.combineInterferingResidueCoordinates	(	Chem.Molecule	mol,
		float	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.

extractEnvironmentResidues() [1/2]

None CDPL.Biomol.extractEnvironmentResidues	(	Chem.MolecularGraph	core,
		Chem.MolecularGraph	macromol,
		Chem.Fragment	env_residues,
		float	max_dist,
		bool	append = False
	)

Extracts the residues of the molecular graph 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 environment residues.
env_residues	The output fragment receiving the extracted environment residues.
max_dist	The maximum allowed minimal distance between the environment residue and the core atoms.
append	If True, the extracted residue atoms and bonds are appended to env_residues. If False, env_residues is cleared first.

extractEnvironmentResidues() [2/2]

None CDPL.Biomol.extractEnvironmentResidues	(	Chem.MolecularGraph	core,
		Chem.MolecularGraph	macromol,
		Chem.Fragment	env_residues,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	max_dist,
		bool	append = False
	)

Extracts the residues of the molecular graph 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 minimal distance between the environment residue and the core atoms.
append	If True, the extracted residue atoms and bonds are appended to env_residues. If False, env_residues is cleared first.

extractProximalAtoms() [1/2]

None CDPL.Biomol.extractProximalAtoms	(	Chem.MolecularGraph	core,
		Chem.MolecularGraph	macromol,
		Chem.Fragment	env_atoms,
		float	max_dist,
		bool	inc_core_atoms = False,
		bool	append = False
	)

Extracts the atoms of the molecular graph macromol that lie within max_dist of any atom of core.

Parameters

core	The core molecular graph defining the reference atom positions.
macromol	The molecular graph providing the environment 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]

None CDPL.Biomol.extractProximalAtoms	(	Chem.MolecularGraph	core,
		Chem.MolecularGraph	macromol,
		Chem.Fragment	env_atoms,
		Chem.Atom3DCoordinatesFunction	coords_func,
		float	max_dist,
		bool	inc_core_atoms = False,
		bool	append = False
	)

Extracts the atoms of the molecular graph 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 environment 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.

extractResidueSubstructure()

None CDPL.Biomol.extractResidueSubstructure	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		Chem.Fragment	res_substruct,
		bool	cnctd_only = False,
		int	flags = 2147483648,
		bool	append = False
	)

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

Parameters

atom	The query atom whose residue substructure is to be extracted.
molgraph	The molecular graph providing the structural context.
res_substruct	The output fragment receiving the extracted residue substructure.
cnctd_only	If True, only atoms in the connected component of the atom 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.

extractResidueSubstructures()

None CDPL.Biomol.extractResidueSubstructures	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	parent_molgraph,
		Chem.Fragment	res_substructs,
		bool	cnctd_only = False,
		int	flags = 2147483648,
		bool	append = False
	)

Extracts the substructures of all residues that are specified by atoms in the molecular graph molgraph from the parent molecular graph parent_molgraph.

Parameters

molgraph	The molecular graph whose atoms specify the residues to extract.
parent_molgraph	The parent molecular 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.

findResidueAtom()

int CDPL.Biomol.findResidueAtom	(	object	cntnr,
		int	idx,
		str	res_code = '',
		str	chain_id = '',
		int	res_seq_no = -9223372036854775808,
		str	ins_code = '\x00',
		int	model_no = 0,
		str	atom_name = '',
		int	serial_no = -9223372036854775808
	)

Parameters

cntnr
idx
res_code
chain_id
res_seq_no
ins_code
model_no
atom_name
serial_no

Returns

findResidue()

int CDPL.Biomol.findResidue	(	object	cntnr,
		int	idx,
		str	res_code = '',
		str	chain_id = '',
		int	res_seq_no = -9223372036854775808,
		str	ins_code = '\x00',
		int	model_no = 0,
		str	atom_name = '',
		int	serial_no = -9223372036854775808
	)

Parameters

cntnr
idx
res_code
chain_id
res_seq_no
ins_code
model_no
atom_name
serial_no

Returns

isPDBBackboneAtom()

bool CDPL.Biomol.isPDBBackboneAtom

(

Chem.Atom

atom

)

Tells whether the atom atom is a backbone atom of an amino acid or nucleotide residue.

Parameters

atom	The atom to test.

Returns

True if the atom is a backbone atom, and False otherwise.

matchesResidueInfo() [1/2]

bool CDPL.Biomol.matchesResidueInfo	(	Chem.Atom	atom,
		str	res_code = '',
		str	chain_id = '',
		int	res_seq_no = -9223372036854775808,
		str	ins_code = '\x00',
		int	model_no = 0,
		str	atom_name = '',
		int	serial_no = -9223372036854775808
	)

Tells whether the residue attributes of the atom 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.

matchesResidueInfo() [2/2]

bool CDPL.Biomol.matchesResidueInfo	(	Chem.MolecularGraph	molgraph,
		str	res_code = '',
		str	chain_id = '',
		int	res_seq_no = -9223372036854775808,
		str	ins_code = '\x00',
		int	model_no = 0
	)

Tells whether the residue identity attributes of the molecular graph 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.

setApplyDictAtomTypesParameter()

None CDPL.Biomol.setApplyDictAtomTypesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 if not.

Since

1.2

hasApplyDictAtomTypesParameter()

bool CDPL.Biomol.hasApplyDictAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getApplyDictAtomTypesParameter()

bool CDPL.Biomol.getApplyDictAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearApplyDictAtomTypesParameter()

None CDPL.Biomol.clearApplyDictAtomTypesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.APPLY_DICT_ATOM_TYPES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setApplyDictFormalChargesParameter()

None CDPL.Biomol.setApplyDictFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 if not.

Since

1.2

hasApplyDictFormalChargesParameter()

bool CDPL.Biomol.hasApplyDictFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getApplyDictFormalChargesParameter()

bool CDPL.Biomol.getApplyDictFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearApplyDictFormalChargesParameter()

None CDPL.Biomol.clearApplyDictFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.APPLY_DICT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCalcMissingFormalChargesParameter()

None CDPL.Biomol.setCalcMissingFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	calc
	)

Sets the value of 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.

Since

1.2

hasCalcMissingFormalChargesParameter()

bool CDPL.Biomol.hasCalcMissingFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getCalcMissingFormalChargesParameter()

bool CDPL.Biomol.getCalcMissingFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearCalcMissingFormalChargesParameter()

None CDPL.Biomol.clearCalcMissingFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.CALC_MISSING_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setCheckLineLengthParameter()

None CDPL.Biomol.setCheckLineLengthParameter	(	Base.ControlParameterContainer	cntnr,
		bool	check
	)

Sets the value of 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()

bool CDPL.Biomol.hasCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getCheckLineLengthParameter()

bool CDPL.Biomol.getCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearCheckLineLengthParameter()

None CDPL.Biomol.clearCheckLineLengthParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.CHECK_LINE_LENGTH parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setCombineInterferingResidueCoordinatesParameter()

None CDPL.Biomol.setCombineInterferingResidueCoordinatesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	comb
	)

Sets the value of 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()

bool CDPL.Biomol.hasCombineInterferingResidueCoordinatesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getCombineInterferingResidueCoordinatesParameter()

bool CDPL.Biomol.getCombineInterferingResidueCoordinatesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearCombineInterferingResidueCoordinatesParameter()

None CDPL.Biomol.clearCombineInterferingResidueCoordinatesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.COMBINE_INTERFERING_RESIDUE_COORDINATES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setMMCIFApplyDictAtomBondingParameter()

None CDPL.Biomol.setMMCIFApplyDictAtomBondingParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 information during mmCIF input, and False if not.

Since

1.2

hasMMCIFApplyDictAtomBondingParameter()

bool CDPL.Biomol.hasMMCIFApplyDictAtomBondingParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getMMCIFApplyDictAtomBondingParameter()

bool CDPL.Biomol.getMMCIFApplyDictAtomBondingParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearMMCIFApplyDictAtomBondingParameter()

None CDPL.Biomol.clearMMCIFApplyDictAtomBondingParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.MMCIF_APPLY_DICT_ATOM_BONDING parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setMMCIFApplyDictBondOrdersParameter()

None CDPL.Biomol.setMMCIFApplyDictBondOrdersParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 order information during mmCIF input, and False if not.

Since

1.2

hasMMCIFApplyDictBondOrdersParameter()

bool CDPL.Biomol.hasMMCIFApplyDictBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getMMCIFApplyDictBondOrdersParameter()

bool CDPL.Biomol.getMMCIFApplyDictBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearMMCIFApplyDictBondOrdersParameter()

None CDPL.Biomol.clearMMCIFApplyDictBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.MMCIF_APPLY_DICT_BOND_ORDERS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setMMCIFOutputBiopolymersAsChemCompParameter()

None CDPL.Biomol.setMMCIFOutputBiopolymersAsChemCompParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

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

Parameters

cntnr	The control-parameter container.
output	True if explicit residue structures shall be emitted as chem_comp category data, and False if not.

Since

1.2

hasMMCIFOutputBiopolymersAsChemCompParameter()

bool CDPL.Biomol.hasMMCIFOutputBiopolymersAsChemCompParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getMMCIFOutputBiopolymersAsChemCompParameter()

bool CDPL.Biomol.getMMCIFOutputBiopolymersAsChemCompParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearMMCIFOutputBiopolymersAsChemCompParameter()

None 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.

Since

1.2

setMMCIFOutputDataPostprocFunctionParameter()

None CDPL.Biomol.setMMCIFOutputDataPostprocFunctionParameter	(	Base.ControlParameterContainer	cntnr,
		MMCIFDataProcessingFunction	func
	)

Sets the value of 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.

Since

1.2

hasMMCIFOutputDataPostprocFunctionParameter()

bool CDPL.Biomol.hasMMCIFOutputDataPostprocFunctionParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getMMCIFOutputDataPostprocFunctionParameter()

MMCIFDataProcessingFunction CDPL.Biomol.getMMCIFOutputDataPostprocFunctionParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

A reference to the mmCIF output data postprocessing function.

Since

1.2

clearMMCIFOutputDataPostprocFunctionParameter()

None CDPL.Biomol.clearMMCIFOutputDataPostprocFunctionParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setPDBApplyDictAtomBondingToNonStdResiduesParameter()

None CDPL.Biomol.setPDBApplyDictAtomBondingToNonStdResiduesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 information to non-standard residues, and False if not.

hasPDBApplyDictAtomBondingToNonStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictAtomBondingToNonStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBApplyDictAtomBondingToNonStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictAtomBondingToNonStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBApplyDictAtomBondingToNonStdResiduesParameter()

None 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.

setPDBApplyDictAtomBondingToStdResiduesParameter()

None CDPL.Biomol.setPDBApplyDictAtomBondingToStdResiduesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 information to standard residues, and False if not.

hasPDBApplyDictAtomBondingToStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictAtomBondingToStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBApplyDictAtomBondingToStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictAtomBondingToStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBApplyDictAtomBondingToStdResiduesParameter()

None 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.

setPDBApplyDictBondOrdersToNonStdResiduesParameter()

None CDPL.Biomol.setPDBApplyDictBondOrdersToNonStdResiduesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 order information to non-standard residues, and False if not.

hasPDBApplyDictBondOrdersToNonStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictBondOrdersToNonStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBApplyDictBondOrdersToNonStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictBondOrdersToNonStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBApplyDictBondOrdersToNonStdResiduesParameter()

None 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.

setPDBApplyDictBondOrdersToStdResiduesParameter()

None CDPL.Biomol.setPDBApplyDictBondOrdersToStdResiduesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	apply
	)

Sets the value of 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 order information to standard residues, and False if not.

hasPDBApplyDictBondOrdersToStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictBondOrdersToStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBApplyDictBondOrdersToStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictBondOrdersToStdResiduesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBApplyDictBondOrdersToStdResiduesParameter()

None 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.

setPDBDeduceBondOrdersFromCONECTRecordsParameter()

None CDPL.Biomol.setPDBDeduceBondOrdersFromCONECTRecordsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	deduce
	)

Sets the value of 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()

bool CDPL.Biomol.hasPDBDeduceBondOrdersFromCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBDeduceBondOrdersFromCONECTRecordsParameter()

bool CDPL.Biomol.getPDBDeduceBondOrdersFromCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBDeduceBondOrdersFromCONECTRecordsParameter()

None 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.

setPDBEvaluateMASTERRecordParameter()

None CDPL.Biomol.setPDBEvaluateMASTERRecordParameter	(	Base.ControlParameterContainer	cntnr,
		bool	evaluate
	)

Parameters

cntnr
evaluate

hasPDBEvaluateMASTERRecordParameter()

bool CDPL.Biomol.hasPDBEvaluateMASTERRecordParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBEvaluateMASTERRecordParameter()

bool CDPL.Biomol.getPDBEvaluateMASTERRecordParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBEvaluateMASTERRecordParameter()

None CDPL.Biomol.clearPDBEvaluateMASTERRecordParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_EVALUATE_MASTER_RECORD parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setPDBFormatVersionParameter()

None CDPL.Biomol.setPDBFormatVersionParameter	(	Base.ControlParameterContainer	cntnr,
		int	ver
	)

Sets the value of 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()

bool CDPL.Biomol.hasPDBFormatVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBFormatVersionParameter()

int CDPL.Biomol.getPDBFormatVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The PDB format version (see Biomol.PDBFormatVersion).

clearPDBFormatVersionParameter()

None CDPL.Biomol.clearPDBFormatVersionParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_FORMAT_VERSION parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setPDBIgnoreCONECTRecordsParameter()

None CDPL.Biomol.setPDBIgnoreCONECTRecordsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	ignore
	)

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

Parameters

cntnr	The control-parameter container.
ignore	True to ignore CONECT records during PDB data input, and False to process them.

Since

1.3

hasPDBIgnoreCONECTRecordsParameter()

bool CDPL.Biomol.hasPDBIgnoreCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.3

getPDBIgnoreCONECTRecordsParameter()

bool CDPL.Biomol.getPDBIgnoreCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.3

clearPDBIgnoreCONECTRecordsParameter()

None CDPL.Biomol.clearPDBIgnoreCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_IGNORE_CONECT_RECORDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.3

setPDBIgnoreFormalChargeFieldParameter()

None CDPL.Biomol.setPDBIgnoreFormalChargeFieldParameter	(	Base.ControlParameterContainer	cntnr,
		bool	ignore
	)

Sets the value of 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()

bool CDPL.Biomol.hasPDBIgnoreFormalChargeFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBIgnoreFormalChargeFieldParameter()

bool CDPL.Biomol.getPDBIgnoreFormalChargeFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBIgnoreFormalChargeFieldParameter()

None CDPL.Biomol.clearPDBIgnoreFormalChargeFieldParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_IGNORE_FORMAL_CHARGE_FIELD parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setPDBOutputCONECTRecordsForAllBondsParameter()

None CDPL.Biomol.setPDBOutputCONECTRecordsForAllBondsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Sets the value of 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 residue ones), and False to write them only for non-standard residue bonds.

Since

1.2

hasPDBOutputCONECTRecordsForAllBondsParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsForAllBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getPDBOutputCONECTRecordsForAllBondsParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsForAllBondsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearPDBOutputCONECTRecordsForAllBondsParameter()

None 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.

Since

1.2

setPDBOutputCONECTRecordsParameter()

None CDPL.Biomol.setPDBOutputCONECTRecordsParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Sets the value of 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 if not.

Since

1.2

hasPDBOutputCONECTRecordsParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getPDBOutputCONECTRecordsParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearPDBOutputCONECTRecordsParameter()

None CDPL.Biomol.clearPDBOutputCONECTRecordsParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setPDBOutputCONECTRecordsReflectingBondOrderParameter()

None CDPL.Biomol.setPDBOutputCONECTRecordsReflectingBondOrderParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Sets the value of 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.

Since

1.2

hasPDBOutputCONECTRecordsReflectingBondOrderParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsReflectingBondOrderParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getPDBOutputCONECTRecordsReflectingBondOrderParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsReflectingBondOrderParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearPDBOutputCONECTRecordsReflectingBondOrderParameter()

None 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.

Since

1.2

setPDBOutputFormalChargesParameter()

None CDPL.Biomol.setPDBOutputFormalChargesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	output
	)

Sets the value of 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.

Since

1.2

hasPDBOutputFormalChargesParameter()

bool CDPL.Biomol.hasPDBOutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getPDBOutputFormalChargesParameter()

bool CDPL.Biomol.getPDBOutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearPDBOutputFormalChargesParameter()

None CDPL.Biomol.clearPDBOutputFormalChargesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_OUTPUT_FORMAL_CHARGES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setPDBTruncateLinesParameter()

None CDPL.Biomol.setPDBTruncateLinesParameter	(	Base.ControlParameterContainer	cntnr,
		bool	trunc
	)

Sets the value of 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 not truncate them.

hasPDBTruncateLinesParameter()

bool CDPL.Biomol.hasPDBTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getPDBTruncateLinesParameter()

bool CDPL.Biomol.getPDBTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearPDBTruncateLinesParameter()

None CDPL.Biomol.clearPDBTruncateLinesParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PDB_TRUNCATE_LINES parameter from cntnr.

Parameters

cntnr

The control-parameter container.

setPerceiveMissingBondOrdersParameter()

None CDPL.Biomol.setPerceiveMissingBondOrdersParameter	(	Base.ControlParameterContainer	cntnr,
		bool	perceive
	)

Sets the value of 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.

Since

1.2

hasPerceiveMissingBondOrdersParameter()

bool CDPL.Biomol.hasPerceiveMissingBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getPerceiveMissingBondOrdersParameter()

bool CDPL.Biomol.getPerceiveMissingBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

Since

1.2

clearPerceiveMissingBondOrdersParameter()

None CDPL.Biomol.clearPerceiveMissingBondOrdersParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.PERCEIVE_MISSING_BOND_ORDERS parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setResidueDictionaryParameter()

None CDPL.Biomol.setResidueDictionaryParameter	(	Base.ControlParameterContainer	cntnr,
		ResidueDictionary	dict
	)

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

Parameters

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

Since

1.2

hasResidueDictionaryParameter()

bool CDPL.Biomol.hasResidueDictionaryParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

Since

1.2

getResidueDictionaryParameter()

ResidueDictionary CDPL.Biomol.getResidueDictionaryParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

A shared reference to the residue dictionary.

Since

1.2

clearResidueDictionaryParameter()

None CDPL.Biomol.clearResidueDictionaryParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.RESIDUE_DICTIONARY parameter from cntnr.

Parameters

cntnr

The control-parameter container.

Since

1.2

setStrictErrorCheckingParameter()

None CDPL.Biomol.setStrictErrorCheckingParameter	(	Base.ControlParameterContainer	cntnr,
		bool	strict
	)

Sets the value of 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()

bool CDPL.Biomol.hasStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Tells whether the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter of cntnr is set.

Parameters

cntnr

The control-parameter container.

Returns

True if the parameter is set, and False otherwise.

getStrictErrorCheckingParameter()

bool CDPL.Biomol.getStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Returns the value of the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter stored in cntnr.

Parameters

cntnr

The control-parameter container.

Returns

The value of the parameter.

clearStrictErrorCheckingParameter()

None CDPL.Biomol.clearStrictErrorCheckingParameter

(

Base.ControlParameterContainer

cntnr

)

Removes the Biomol.ControlParameter.STRICT_ERROR_CHECKING parameter from cntnr.

Parameters

cntnr

The control-parameter container.