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

Classes
class	AtomProperty
	Provides keys for built-in Biomol.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
	A data structure allowing a hierarchical view on biological macromolecules. More...

class	HierarchyViewChain
	HierarchyViewChain. More...

class	HierarchyViewFragment
	HierarchyViewFragment. More...

class	HierarchyViewModel
	HierarchyViewModel. More...

class	HierarchyViewNode
	HierarchyViewNode. More...

class	MMCIFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the MMCIF format. More...

class	MMCIFBZ2MolecularGraphWriter

class	MMCIFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the MMCIF format. More...

class	MMCIFBZ2MoleculeReader

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

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

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

class	MMCIFGZMolecularGraphWriter

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

class	MMCIFGZMoleculeReader

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

class	MMCIFMolecularGraphWriter

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

class	MMCIFMoleculeReader

class	MMTFBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Macromolecular Transmission Format (MMTF) [MMTF]. More...

class	MMTFBZ2MolecularGraphWriter

class	MMTFBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Macromolecular Transmission Format (MMTF) [MMTF] format. More...

class	MMTFBZ2MoleculeReader

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

class	MMTFGZMolecularGraphWriter

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

class	MMTFGZMoleculeReader

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

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

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

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

class	MolecularGraphPointerStringFunctor

class	MolecularGraphProperty
	Provides keys for built-in Biomol.MolecularGraph properties. More...

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

class	PDBBZ2MolecularGraphOutputHandler
	A handler for the output of bzip2-compressed molecular graph data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

class	PDBBZ2MolecularGraphWriter

class	PDBBZ2MoleculeInputHandler
	A handler for the input of bzip2-compressed molecule data in the Brookhaven Protein Data Bank (PDB) [PDB] format. More...

class	PDBBZ2MoleculeReader

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

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

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

class	PDBGZMolecularGraphWriter

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

class	PDBGZMoleculeReader

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

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

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

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

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

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

class	ResidueType

Functions
None	clearChainID (Chem.Atom atom)

bool	hasChainID (Chem.Atom atom)

str	getChainID (Chem.Atom atom)

None	setChainID (Chem.Atom atom, str id)

None	clearAltLocationID (Chem.Atom atom)

bool	hasAltLocationID (Chem.Atom atom)

str	getAltLocationID (Chem.Atom atom)

None	setAltLocationID (Chem.Atom atom, str id)

None	clearEntityID (Chem.Atom atom)

bool	hasEntityID (Chem.Atom atom)

str	getEntityID (Chem.Atom atom)

None	setEntityID (Chem.Atom atom, str id)

None	clearResidueCode (Chem.Atom atom)

bool	hasResidueCode (Chem.Atom atom)

str	getResidueCode (Chem.Atom atom)

None	setResidueCode (Chem.Atom atom, str code)

None	clearResidueInsertionCode (Chem.Atom atom)

bool	hasResidueInsertionCode (Chem.Atom atom)

str	getResidueInsertionCode (Chem.Atom atom)

None	setResidueInsertionCode (Chem.Atom atom, str code)

None	clearResidueAtomName (Chem.Atom atom)

bool	hasResidueAtomName (Chem.Atom atom)

str	getResidueAtomName (Chem.Atom atom)

None	setResidueAtomName (Chem.Atom atom, str name)

None	clearResidueAltAtomName (Chem.Atom atom)

bool	hasResidueAltAtomName (Chem.Atom atom)

str	getResidueAltAtomName (Chem.Atom atom)

None	setResidueAltAtomName (Chem.Atom atom, str name)

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

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

None	clearResidueLinkingAtomFlag (Chem.Atom atom)

bool	hasResidueLinkingAtomFlag (Chem.Atom atom)

bool	getResidueLinkingAtomFlag (Chem.Atom atom)

None	setResidueLinkingAtomFlag (Chem.Atom atom, bool linking)

None	clearResidueLeavingAtomFlag (Chem.Atom atom)

bool	hasResidueLeavingAtomFlag (Chem.Atom atom)

bool	getResidueLeavingAtomFlag (Chem.Atom atom)

None	setResidueLeavingAtomFlag (Chem.Atom atom, bool leaving)

None	clearHeteroAtomFlag (Chem.Atom atom)

bool	hasHeteroAtomFlag (Chem.Atom atom)

bool	getHeteroAtomFlag (Chem.Atom atom)

None	setHeteroAtomFlag (Chem.Atom atom, bool is_het)

bool	isPDBBackboneAtom (Chem.Atom atom)

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)

None	clearResidueSequenceNumber (Chem.Atom atom)

bool	hasResidueSequenceNumber (Chem.Atom atom)

int	getResidueSequenceNumber (Chem.Atom atom)

None	setResidueSequenceNumber (Chem.Atom atom, int seq_no)

None	clearSerialNumber (Chem.Atom atom)

bool	hasSerialNumber (Chem.Atom atom)

int	getSerialNumber (Chem.Atom atom)

None	setSerialNumber (Chem.Atom atom, int serial_no)

None	clearModelNumber (Chem.Atom atom)

bool	hasModelNumber (Chem.Atom atom)

int	getModelNumber (Chem.Atom atom)

None	setModelNumber (Chem.Atom atom, int model_no)

None	clearBFactor (Chem.Atom atom)

bool	hasBFactor (Chem.Atom atom)

float	getBFactor (Chem.Atom atom)

None	setBFactor (Chem.Atom atom, float factor)

None	clearOccupancy (Chem.Atom atom)

bool	hasOccupancy (Chem.Atom atom)

float	getOccupancy (Chem.Atom atom)

None	setOccupancy (Chem.Atom atom, float occupancy)

None	clearPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)

bool	getPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)

None	setPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr, bool ignore)

None	clearPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)

bool	getPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)

None	setPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr, bool evaluate)

None	clearMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)

bool	hasMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)

bool	getMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)

None	setMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)

bool	hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)

bool	getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)

None	setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)

None	clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)

bool	hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)

bool	getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)

None	setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)

None	clearPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)

int	getPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)

None	setPDBFormatVersionParameter (Base.ControlParameterContainer cntnr, int ver)

None	clearMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)

bool	hasMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)

MMCIFDataProcessingFunction	getMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)

None	setMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr, MMCIFDataProcessingFunction func)

None	clearMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)

bool	hasMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)

bool	getMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)

None	setMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr, bool output)

None	clearPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)

bool	getPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)

None	setPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr, bool output)

None	clearPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)

bool	getPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)

None	setPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr, bool output)

None	clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

bool	getPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

None	setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool deduce)

None	clearPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

bool	getPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)

None	setPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool output)

None	clearPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)

bool	getPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)

None	setPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr, bool ignore)

None	clearCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	hasCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	getCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)

None	setCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)

None	clearApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	hasApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	getApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)

None	setApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)

None	setPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output)

None	clearPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)

None	setPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)

None	clearApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)

bool	hasApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)

bool	getApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)

None	setApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)

bool	hasCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)

bool	getCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)

None	setCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr, bool comb)

None	clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

None	setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)

None	setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)

None	setPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	hasPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)

bool	getPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)

None	setPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)

bool	hasPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)

bool	getPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)

None	setPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)

None	clearMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)

bool	hasMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)

bool	getMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)

None	setMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr, bool apply)

None	clearResidueDictionaryParameter (Base.ControlParameterContainer cntnr)

bool	hasResidueDictionaryParameter (Base.ControlParameterContainer cntnr)

ResidueDictionary	getResidueDictionaryParameter (Base.ControlParameterContainer cntnr)

None	setResidueDictionaryParameter (Base.ControlParameterContainer cntnr, ResidueDictionary dict)

None	clearChainID (Chem.MolecularGraph molgraph)

bool	hasChainID (Chem.MolecularGraph molgraph)

str	getChainID (Chem.MolecularGraph molgraph)

None	setChainID (Chem.MolecularGraph molgraph, str id)

None	clearPDBData (Chem.MolecularGraph molgraph)

bool	hasPDBData (Chem.MolecularGraph molgraph)

PDBData	getPDBData (Chem.MolecularGraph molgraph)

None	setPDBData (Chem.MolecularGraph molgraph, PDBData data)

None	clearMMCIFData (Chem.MolecularGraph molgraph)

bool	hasMMCIFData (Chem.MolecularGraph molgraph)

MMCIFData	getMMCIFData (Chem.MolecularGraph molgraph)

None	setMMCIFData (Chem.MolecularGraph molgraph, MMCIFData data)

None	clearResidueCode (Chem.MolecularGraph molgraph)

bool	hasResidueCode (Chem.MolecularGraph molgraph)

str	getResidueCode (Chem.MolecularGraph molgraph)

None	setResidueCode (Chem.MolecularGraph molgraph, str code)

None	clearResidueInsertionCode (Chem.MolecularGraph molgraph)

bool	hasResidueInsertionCode (Chem.MolecularGraph molgraph)

str	getResidueInsertionCode (Chem.MolecularGraph molgraph)

None	setResidueInsertionCode (Chem.MolecularGraph molgraph, str code)

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

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

None	clearResidueSequenceNumber (Chem.MolecularGraph molgraph)

bool	hasResidueSequenceNumber (Chem.MolecularGraph molgraph)

int	getResidueSequenceNumber (Chem.MolecularGraph molgraph)

None	setResidueSequenceNumber (Chem.MolecularGraph molgraph, int seq_no)

None	clearModelNumber (Chem.MolecularGraph molgraph)

bool	hasModelNumber (Chem.MolecularGraph molgraph)

int	getModelNumber (Chem.MolecularGraph molgraph)

None	setModelNumber (Chem.MolecularGraph molgraph, int model_no)

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

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

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

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

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)

bool	combineInterferingResidueCoordinates (Chem.Molecule mol, float max_ctr_dist=1.0)

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)

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)

Variables
int	IGNORE_SEQUENCE_NO = -9223372036854775808

int	IGNORE_SERIAL_NO = -9223372036854775808

Detailed Description

Contains classes and functions related to biological macromolecules.

Function Documentation

◆ clearChainID() [1/2]

None CDPL.Biomol.clearChainID ( Chem.Atom atom )

Parameters

atom

◆ hasChainID() [1/2]

bool CDPL.Biomol.hasChainID ( Chem.Atom atom )

Parameters

atom

Returns

◆ getChainID() [1/2]

str CDPL.Biomol.getChainID ( Chem.Atom atom )

Parameters

atom

Returns

◆ setChainID() [1/2]

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

Parameters

atom
id

◆ clearAltLocationID()

None CDPL.Biomol.clearAltLocationID ( Chem.Atom atom )

Parameters

atom

◆ hasAltLocationID()

bool CDPL.Biomol.hasAltLocationID ( Chem.Atom atom )

Parameters

atom

Returns

◆ getAltLocationID()

str CDPL.Biomol.getAltLocationID ( Chem.Atom atom )

Parameters

atom

Returns

◆ setAltLocationID()

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

Parameters

atom
id

◆ clearEntityID()

None CDPL.Biomol.clearEntityID ( Chem.Atom atom )

Parameters

atom

◆ hasEntityID()

bool CDPL.Biomol.hasEntityID ( Chem.Atom atom )

Parameters

atom

Returns

◆ getEntityID()

str CDPL.Biomol.getEntityID ( Chem.Atom atom )

Parameters

atom

Returns

◆ setEntityID()

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

Parameters

atom
id

◆ clearResidueCode() [1/2]

None CDPL.Biomol.clearResidueCode ( Chem.Atom atom )

Parameters

atom

◆ hasResidueCode() [1/2]

bool CDPL.Biomol.hasResidueCode ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueCode() [1/2]

str CDPL.Biomol.getResidueCode ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueCode() [1/2]

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

Parameters

atom
code

◆ clearResidueInsertionCode() [1/2]

None CDPL.Biomol.clearResidueInsertionCode ( Chem.Atom atom )

Parameters

atom

◆ hasResidueInsertionCode() [1/2]

bool CDPL.Biomol.hasResidueInsertionCode ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueInsertionCode() [1/2]

str CDPL.Biomol.getResidueInsertionCode ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueInsertionCode() [1/2]

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

Parameters

atom
code

◆ clearResidueAtomName()

None CDPL.Biomol.clearResidueAtomName ( Chem.Atom atom )

Parameters

atom

◆ hasResidueAtomName()

bool CDPL.Biomol.hasResidueAtomName ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueAtomName()

str CDPL.Biomol.getResidueAtomName ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueAtomName()

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

Parameters

atom
name

◆ clearResidueAltAtomName()

None CDPL.Biomol.clearResidueAltAtomName ( Chem.Atom atom )

Parameters

atom

◆ hasResidueAltAtomName()

bool CDPL.Biomol.hasResidueAltAtomName ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueAltAtomName()

str CDPL.Biomol.getResidueAltAtomName ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueAltAtomName()

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

Parameters

atom
name

◆ 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`
	)

Parameters

atom
molgraph
res_substruct
cnctd_only
flags
append

◆ areInSameResidue()

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

Parameters

atom1
atom2
flags

Returns

◆ clearResidueLinkingAtomFlag()

None CDPL.Biomol.clearResidueLinkingAtomFlag ( Chem.Atom atom )

Parameters

atom

◆ hasResidueLinkingAtomFlag()

bool CDPL.Biomol.hasResidueLinkingAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueLinkingAtomFlag()

bool CDPL.Biomol.getResidueLinkingAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueLinkingAtomFlag()

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

Parameters

atom
linking

◆ clearResidueLeavingAtomFlag()

None CDPL.Biomol.clearResidueLeavingAtomFlag ( Chem.Atom atom )

Parameters

atom

◆ hasResidueLeavingAtomFlag()

bool CDPL.Biomol.hasResidueLeavingAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueLeavingAtomFlag()

bool CDPL.Biomol.getResidueLeavingAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueLeavingAtomFlag()

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

Parameters

atom
leaving

◆ clearHeteroAtomFlag()

None CDPL.Biomol.clearHeteroAtomFlag ( Chem.Atom atom )

Parameters

atom

◆ hasHeteroAtomFlag()

bool CDPL.Biomol.hasHeteroAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ getHeteroAtomFlag()

bool CDPL.Biomol.getHeteroAtomFlag ( Chem.Atom atom )

Parameters

atom

Returns

◆ setHeteroAtomFlag()

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

Parameters

atom
is_het

◆ isPDBBackboneAtom()

bool CDPL.Biomol.isPDBBackboneAtom ( Chem.Atom atom )

Parameters

atom

Returns

◆ 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`
	)

Parameters

atom
res_code
chain_id
res_seq_no
ins_code
model_no
atom_name
serial_no

Returns

◆ clearResidueSequenceNumber() [1/2]

None CDPL.Biomol.clearResidueSequenceNumber ( Chem.Atom atom )

Parameters

atom

◆ hasResidueSequenceNumber() [1/2]

bool CDPL.Biomol.hasResidueSequenceNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ getResidueSequenceNumber() [1/2]

int CDPL.Biomol.getResidueSequenceNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ setResidueSequenceNumber() [1/2]

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

Parameters

atom
seq_no

◆ clearSerialNumber()

None CDPL.Biomol.clearSerialNumber ( Chem.Atom atom )

Parameters

atom

◆ hasSerialNumber()

bool CDPL.Biomol.hasSerialNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ getSerialNumber()

int CDPL.Biomol.getSerialNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ setSerialNumber()

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

Parameters

atom
serial_no

◆ clearModelNumber() [1/2]

None CDPL.Biomol.clearModelNumber ( Chem.Atom atom )

Parameters

atom

◆ hasModelNumber() [1/2]

bool CDPL.Biomol.hasModelNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ getModelNumber() [1/2]

int CDPL.Biomol.getModelNumber ( Chem.Atom atom )

Parameters

atom

Returns

◆ setModelNumber() [1/2]

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

Parameters

atom
model_no

◆ clearBFactor()

None CDPL.Biomol.clearBFactor ( Chem.Atom atom )

Parameters

atom

◆ hasBFactor()

bool CDPL.Biomol.hasBFactor ( Chem.Atom atom )

Parameters

atom

Returns

◆ getBFactor()

float CDPL.Biomol.getBFactor ( Chem.Atom atom )

Parameters

atom

Returns

◆ setBFactor()

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

Parameters

atom
factor

◆ clearOccupancy()

None CDPL.Biomol.clearOccupancy ( Chem.Atom atom )

Parameters

atom

◆ hasOccupancy()

bool CDPL.Biomol.hasOccupancy ( Chem.Atom atom )

Parameters

atom

Returns

◆ getOccupancy()

float CDPL.Biomol.getOccupancy ( Chem.Atom atom )

Parameters

atom

Returns

◆ setOccupancy()

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

Parameters

atom
occupancy

◆ clearPDBIgnoreFormalChargeFieldParameter()

None CDPL.Biomol.clearPDBIgnoreFormalChargeFieldParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBIgnoreFormalChargeFieldParameter()

bool CDPL.Biomol.hasPDBIgnoreFormalChargeFieldParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBIgnoreFormalChargeFieldParameter()

bool CDPL.Biomol.getPDBIgnoreFormalChargeFieldParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBIgnoreFormalChargeFieldParameter()

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

Parameters

cntnr
ignore

◆ clearPDBEvaluateMASTERRecordParameter()

None CDPL.Biomol.clearPDBEvaluateMASTERRecordParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBEvaluateMASTERRecordParameter()

bool CDPL.Biomol.hasPDBEvaluateMASTERRecordParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBEvaluateMASTERRecordParameter()

bool CDPL.Biomol.getPDBEvaluateMASTERRecordParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBEvaluateMASTERRecordParameter()

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

Parameters

cntnr
evaluate

◆ clearMMCIFApplyDictAtomBondingParameter()

None CDPL.Biomol.clearMMCIFApplyDictAtomBondingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasMMCIFApplyDictAtomBondingParameter()

bool CDPL.Biomol.hasMMCIFApplyDictAtomBondingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getMMCIFApplyDictAtomBondingParameter()

bool CDPL.Biomol.getMMCIFApplyDictAtomBondingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setMMCIFApplyDictAtomBondingParameter()

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

Parameters

cntnr
apply

◆ clearStrictErrorCheckingParameter()

None CDPL.Biomol.clearStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasStrictErrorCheckingParameter()

bool CDPL.Biomol.hasStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getStrictErrorCheckingParameter()

bool CDPL.Biomol.getStrictErrorCheckingParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setStrictErrorCheckingParameter()

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

Parameters

cntnr
strict

◆ clearCheckLineLengthParameter()

None CDPL.Biomol.clearCheckLineLengthParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasCheckLineLengthParameter()

bool CDPL.Biomol.hasCheckLineLengthParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getCheckLineLengthParameter()

bool CDPL.Biomol.getCheckLineLengthParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setCheckLineLengthParameter()

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

Parameters

cntnr
check

◆ clearPDBFormatVersionParameter()

None CDPL.Biomol.clearPDBFormatVersionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBFormatVersionParameter()

bool CDPL.Biomol.hasPDBFormatVersionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBFormatVersionParameter()

int CDPL.Biomol.getPDBFormatVersionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBFormatVersionParameter()

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

Parameters

cntnr
ver

◆ clearMMCIFOutputDataPostprocFunctionParameter()

None CDPL.Biomol.clearMMCIFOutputDataPostprocFunctionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasMMCIFOutputDataPostprocFunctionParameter()

bool CDPL.Biomol.hasMMCIFOutputDataPostprocFunctionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getMMCIFOutputDataPostprocFunctionParameter()

MMCIFDataProcessingFunction CDPL.Biomol.getMMCIFOutputDataPostprocFunctionParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setMMCIFOutputDataPostprocFunctionParameter()

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

Parameters

cntnr
func

◆ clearMMCIFOutputBiopolymersAsChemCompParameter()

None CDPL.Biomol.clearMMCIFOutputBiopolymersAsChemCompParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasMMCIFOutputBiopolymersAsChemCompParameter()

bool CDPL.Biomol.hasMMCIFOutputBiopolymersAsChemCompParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getMMCIFOutputBiopolymersAsChemCompParameter()

bool CDPL.Biomol.getMMCIFOutputBiopolymersAsChemCompParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setMMCIFOutputBiopolymersAsChemCompParameter()

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

Parameters

cntnr
output

◆ clearPDBOutputCONECTRecordsReflectingBondOrderParameter()

None CDPL.Biomol.clearPDBOutputCONECTRecordsReflectingBondOrderParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBOutputCONECTRecordsReflectingBondOrderParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsReflectingBondOrderParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBOutputCONECTRecordsReflectingBondOrderParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsReflectingBondOrderParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

Parameters

cntnr
output

◆ clearPDBOutputCONECTRecordsForAllBondsParameter()

None CDPL.Biomol.clearPDBOutputCONECTRecordsForAllBondsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBOutputCONECTRecordsForAllBondsParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsForAllBondsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBOutputCONECTRecordsForAllBondsParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsForAllBondsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBOutputCONECTRecordsForAllBondsParameter()

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

Parameters

cntnr
output

◆ clearPDBDeduceBondOrdersFromCONECTRecordsParameter()

None CDPL.Biomol.clearPDBDeduceBondOrdersFromCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBDeduceBondOrdersFromCONECTRecordsParameter()

bool CDPL.Biomol.hasPDBDeduceBondOrdersFromCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBDeduceBondOrdersFromCONECTRecordsParameter()

bool CDPL.Biomol.getPDBDeduceBondOrdersFromCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

Parameters

cntnr
deduce

◆ clearPDBOutputCONECTRecordsParameter()

None CDPL.Biomol.clearPDBOutputCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBOutputCONECTRecordsParameter()

bool CDPL.Biomol.hasPDBOutputCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBOutputCONECTRecordsParameter()

bool CDPL.Biomol.getPDBOutputCONECTRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBOutputCONECTRecordsParameter()

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

Parameters

cntnr
output

◆ clearPDBIgnoreConectRecordsParameter()

None CDPL.Biomol.clearPDBIgnoreConectRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBIgnoreConectRecordsParameter()

bool CDPL.Biomol.hasPDBIgnoreConectRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBIgnoreConectRecordsParameter()

bool CDPL.Biomol.getPDBIgnoreConectRecordsParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBIgnoreConectRecordsParameter()

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

Parameters

cntnr
ignore

◆ clearCalcMissingFormalChargesParameter()

None CDPL.Biomol.clearCalcMissingFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasCalcMissingFormalChargesParameter()

bool CDPL.Biomol.hasCalcMissingFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getCalcMissingFormalChargesParameter()

bool CDPL.Biomol.getCalcMissingFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setCalcMissingFormalChargesParameter()

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

Parameters

cntnr
calc

◆ clearApplyDictFormalChargesParameter()

None CDPL.Biomol.clearApplyDictFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasApplyDictFormalChargesParameter()

bool CDPL.Biomol.hasApplyDictFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getApplyDictFormalChargesParameter()

bool CDPL.Biomol.getApplyDictFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setApplyDictFormalChargesParameter()

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

Parameters

cntnr
apply

◆ clearPDBOutputFormalChargesParameter()

None CDPL.Biomol.clearPDBOutputFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBOutputFormalChargesParameter()

bool CDPL.Biomol.hasPDBOutputFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBOutputFormalChargesParameter()

bool CDPL.Biomol.getPDBOutputFormalChargesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBOutputFormalChargesParameter()

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

Parameters

cntnr
output

◆ clearPDBTruncateLinesParameter()

None CDPL.Biomol.clearPDBTruncateLinesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBTruncateLinesParameter()

bool CDPL.Biomol.hasPDBTruncateLinesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBTruncateLinesParameter()

bool CDPL.Biomol.getPDBTruncateLinesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBTruncateLinesParameter()

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

Parameters

cntnr
trunc

◆ clearApplyDictAtomTypesParameter()

None CDPL.Biomol.clearApplyDictAtomTypesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasApplyDictAtomTypesParameter()

bool CDPL.Biomol.hasApplyDictAtomTypesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getApplyDictAtomTypesParameter()

bool CDPL.Biomol.getApplyDictAtomTypesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setApplyDictAtomTypesParameter()

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

Parameters

cntnr
apply

◆ clearCombineInterferingResidueCoordinatesParameter()

None CDPL.Biomol.clearCombineInterferingResidueCoordinatesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasCombineInterferingResidueCoordinatesParameter()

bool CDPL.Biomol.hasCombineInterferingResidueCoordinatesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getCombineInterferingResidueCoordinatesParameter()

bool CDPL.Biomol.getCombineInterferingResidueCoordinatesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setCombineInterferingResidueCoordinatesParameter()

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

Parameters

cntnr
comb

◆ clearPDBApplyDictAtomBondingToNonStdResiduesParameter()

None CDPL.Biomol.clearPDBApplyDictAtomBondingToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBApplyDictAtomBondingToNonStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictAtomBondingToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBApplyDictAtomBondingToNonStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictAtomBondingToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

Parameters

cntnr
apply

◆ clearPDBApplyDictBondOrdersToNonStdResiduesParameter()

None CDPL.Biomol.clearPDBApplyDictBondOrdersToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBApplyDictBondOrdersToNonStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictBondOrdersToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBApplyDictBondOrdersToNonStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictBondOrdersToNonStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

Parameters

cntnr
apply

◆ clearPDBApplyDictAtomBondingToStdResiduesParameter()

None CDPL.Biomol.clearPDBApplyDictAtomBondingToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBApplyDictAtomBondingToStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictAtomBondingToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBApplyDictAtomBondingToStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictAtomBondingToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBApplyDictAtomBondingToStdResiduesParameter()

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

Parameters

cntnr
apply

◆ clearPDBApplyDictBondOrdersToStdResiduesParameter()

None CDPL.Biomol.clearPDBApplyDictBondOrdersToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPDBApplyDictBondOrdersToStdResiduesParameter()

bool CDPL.Biomol.hasPDBApplyDictBondOrdersToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPDBApplyDictBondOrdersToStdResiduesParameter()

bool CDPL.Biomol.getPDBApplyDictBondOrdersToStdResiduesParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPDBApplyDictBondOrdersToStdResiduesParameter()

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

Parameters

cntnr
apply

◆ clearPerceiveMissingBondOrdersParameter()

None CDPL.Biomol.clearPerceiveMissingBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasPerceiveMissingBondOrdersParameter()

bool CDPL.Biomol.hasPerceiveMissingBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getPerceiveMissingBondOrdersParameter()

bool CDPL.Biomol.getPerceiveMissingBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setPerceiveMissingBondOrdersParameter()

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

Parameters

cntnr
perceive

◆ clearMMCIFApplyDictBondOrdersParameter()

None CDPL.Biomol.clearMMCIFApplyDictBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasMMCIFApplyDictBondOrdersParameter()

bool CDPL.Biomol.hasMMCIFApplyDictBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getMMCIFApplyDictBondOrdersParameter()

bool CDPL.Biomol.getMMCIFApplyDictBondOrdersParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setMMCIFApplyDictBondOrdersParameter()

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

Parameters

cntnr
apply

◆ clearResidueDictionaryParameter()

None CDPL.Biomol.clearResidueDictionaryParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

◆ hasResidueDictionaryParameter()

bool CDPL.Biomol.hasResidueDictionaryParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ getResidueDictionaryParameter()

ResidueDictionary CDPL.Biomol.getResidueDictionaryParameter ( Base.ControlParameterContainer cntnr )

Parameters

cntnr

Returns

◆ setResidueDictionaryParameter()

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

Parameters

cntnr
dict

◆ clearChainID() [2/2]

None CDPL.Biomol.clearChainID ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasChainID() [2/2]

bool CDPL.Biomol.hasChainID ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getChainID() [2/2]

str CDPL.Biomol.getChainID ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setChainID() [2/2]

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

Parameters

molgraph
id

◆ clearPDBData()

None CDPL.Biomol.clearPDBData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasPDBData()

bool CDPL.Biomol.hasPDBData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getPDBData()

PDBData CDPL.Biomol.getPDBData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setPDBData()

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

Parameters

molgraph
data

◆ clearMMCIFData()

None CDPL.Biomol.clearMMCIFData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasMMCIFData()

bool CDPL.Biomol.hasMMCIFData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getMMCIFData()

MMCIFData CDPL.Biomol.getMMCIFData ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setMMCIFData()

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

Parameters

molgraph
data

◆ clearResidueCode() [2/2]

None CDPL.Biomol.clearResidueCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasResidueCode() [2/2]

bool CDPL.Biomol.hasResidueCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getResidueCode() [2/2]

str CDPL.Biomol.getResidueCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setResidueCode() [2/2]

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

Parameters

molgraph
code

◆ clearResidueInsertionCode() [2/2]

None CDPL.Biomol.clearResidueInsertionCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasResidueInsertionCode() [2/2]

bool CDPL.Biomol.hasResidueInsertionCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getResidueInsertionCode() [2/2]

str CDPL.Biomol.getResidueInsertionCode ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setResidueInsertionCode() [2/2]

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

Parameters

molgraph
code

◆ setHydrogenResidueSequenceInfo()

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

Parameters

molgraph
overwrite
flags

◆ 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`
	)

Parameters

molgraph
res_code
chain_id
res_seq_no
ins_code
model_no

Returns

◆ clearResidueSequenceNumber() [2/2]

None CDPL.Biomol.clearResidueSequenceNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasResidueSequenceNumber() [2/2]

bool CDPL.Biomol.hasResidueSequenceNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getResidueSequenceNumber() [2/2]

int CDPL.Biomol.getResidueSequenceNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setResidueSequenceNumber() [2/2]

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

Parameters

molgraph
seq_no

◆ clearModelNumber() [2/2]

None CDPL.Biomol.clearModelNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

◆ hasModelNumber() [2/2]

bool CDPL.Biomol.hasModelNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getModelNumber() [2/2]

int CDPL.Biomol.getModelNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ setModelNumber() [2/2]

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

Parameters

molgraph
model_no

◆ 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`
	)

Parameters

molgraph
parent_molgraph
res_substructs
cnctd_only
flags
append

◆ extractEnvironmentResidues() [1/2]

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

Parameters

core
macromol
env_residues
max_dist
append

◆ 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`
	)

Parameters

core
macromol
env_residues
coords_func
max_dist
append

◆ 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`
	)

Parameters

core
macromol
env_atoms
max_dist
inc_core_atoms
append

◆ 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`
	)

Parameters

core
macromol
env_atoms
coords_func
max_dist
inc_core_atoms
append

◆ combineInterferingResidueCoordinates()

bool CDPL.Biomol.combineInterferingResidueCoordinates	(	Chem.Molecule	mol,
		float	max_ctr_dist = `1.0`
	)

Parameters

mol
max_ctr_dist

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

◆ 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

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ clearChainID() [1/2]

◆ hasChainID() [1/2]

◆ getChainID() [1/2]

◆ setChainID() [1/2]

◆ clearAltLocationID()

◆ hasAltLocationID()

◆ getAltLocationID()

◆ setAltLocationID()

◆ clearEntityID()

◆ hasEntityID()

◆ getEntityID()

◆ setEntityID()

◆ clearResidueCode() [1/2]

◆ hasResidueCode() [1/2]

◆ getResidueCode() [1/2]

◆ setResidueCode() [1/2]

◆ clearResidueInsertionCode() [1/2]

◆ hasResidueInsertionCode() [1/2]

◆ getResidueInsertionCode() [1/2]

◆ setResidueInsertionCode() [1/2]

◆ clearResidueAtomName()

◆ hasResidueAtomName()

◆ getResidueAtomName()

◆ setResidueAtomName()

◆ clearResidueAltAtomName()

◆ hasResidueAltAtomName()

◆ getResidueAltAtomName()

◆ setResidueAltAtomName()

◆ extractResidueSubstructure()

◆ areInSameResidue()

◆ clearResidueLinkingAtomFlag()

◆ hasResidueLinkingAtomFlag()

◆ getResidueLinkingAtomFlag()

◆ setResidueLinkingAtomFlag()

◆ clearResidueLeavingAtomFlag()

◆ hasResidueLeavingAtomFlag()

◆ getResidueLeavingAtomFlag()

◆ setResidueLeavingAtomFlag()

◆ clearHeteroAtomFlag()

◆ hasHeteroAtomFlag()

◆ getHeteroAtomFlag()

◆ setHeteroAtomFlag()

◆ isPDBBackboneAtom()

◆ matchesResidueInfo() [1/2]

◆ clearResidueSequenceNumber() [1/2]

◆ hasResidueSequenceNumber() [1/2]

◆ getResidueSequenceNumber() [1/2]

◆ setResidueSequenceNumber() [1/2]

◆ clearSerialNumber()

◆ hasSerialNumber()

◆ getSerialNumber()

◆ setSerialNumber()

◆ clearModelNumber() [1/2]

◆ hasModelNumber() [1/2]

◆ getModelNumber() [1/2]

◆ setModelNumber() [1/2]

◆ clearBFactor()

◆ hasBFactor()

◆ getBFactor()

◆ setBFactor()

◆ clearOccupancy()

◆ hasOccupancy()

◆ getOccupancy()

◆ setOccupancy()

◆ clearPDBIgnoreFormalChargeFieldParameter()

◆ hasPDBIgnoreFormalChargeFieldParameter()

◆ getPDBIgnoreFormalChargeFieldParameter()

◆ setPDBIgnoreFormalChargeFieldParameter()

◆ clearPDBEvaluateMASTERRecordParameter()

◆ hasPDBEvaluateMASTERRecordParameter()

◆ getPDBEvaluateMASTERRecordParameter()

◆ setPDBEvaluateMASTERRecordParameter()

◆ clearMMCIFApplyDictAtomBondingParameter()

◆ hasMMCIFApplyDictAtomBondingParameter()

◆ getMMCIFApplyDictAtomBondingParameter()