Chemical Data Processing Library Python API - Version 1.4.0
Classes | Functions | Variables
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
 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 Chem.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
 Provides constants for the specification of the type of a chemical component (residue). More...
 

Functions

None setAltLocationID (Chem.Atom atom, str id)
 
bool hasAltLocationID (Chem.Atom atom)
 
str getAltLocationID (Chem.Atom atom)
 
None clearAltLocationID (Chem.Atom atom)
 
None setBFactor (Chem.Atom atom, float factor)
 
bool hasBFactor (Chem.Atom atom)
 
float getBFactor (Chem.Atom atom)
 
None clearBFactor (Chem.Atom atom)
 
None setChainID (Chem.Atom atom, str id)
 
bool hasChainID (Chem.Atom atom)
 
str getChainID (Chem.Atom atom)
 
None clearChainID (Chem.Atom atom)
 
None setChainID (Chem.MolecularGraph molgraph, str id)
 
bool hasChainID (Chem.MolecularGraph molgraph)
 
str getChainID (Chem.MolecularGraph molgraph)
 
None clearChainID (Chem.MolecularGraph molgraph)
 
None setEntityID (Chem.Atom atom, str id)
 
bool hasEntityID (Chem.Atom atom)
 
str getEntityID (Chem.Atom atom)
 
None clearEntityID (Chem.Atom atom)
 
None setHeteroAtomFlag (Chem.Atom atom, bool is_het)
 
bool hasHeteroAtomFlag (Chem.Atom atom)
 
bool getHeteroAtomFlag (Chem.Atom atom)
 
None clearHeteroAtomFlag (Chem.Atom atom)
 
None setHydrogenResidueSequenceInfo (Chem.MolecularGraph molgraph, bool overwrite, int flags=2147483648)
 
None setMMCIFData (Chem.MolecularGraph molgraph, MMCIFData data)
 
bool hasMMCIFData (Chem.MolecularGraph molgraph)
 
MMCIFData getMMCIFData (Chem.MolecularGraph molgraph)
 
None clearMMCIFData (Chem.MolecularGraph molgraph)
 
None setModelNumber (Chem.Atom atom, int model_no)
 
bool hasModelNumber (Chem.Atom atom)
 
int getModelNumber (Chem.Atom atom)
 
None clearModelNumber (Chem.Atom atom)
 
None setModelNumber (Chem.MolecularGraph molgraph, int model_no)
 
bool hasModelNumber (Chem.MolecularGraph molgraph)
 
int getModelNumber (Chem.MolecularGraph molgraph)
 
None clearModelNumber (Chem.MolecularGraph molgraph)
 
None setOccupancy (Chem.Atom atom, float occupancy)
 
bool hasOccupancy (Chem.Atom atom)
 
float getOccupancy (Chem.Atom atom)
 
None clearOccupancy (Chem.Atom atom)
 
None setPDBData (Chem.MolecularGraph molgraph, PDBData data)
 
bool hasPDBData (Chem.MolecularGraph molgraph)
 
PDBData getPDBData (Chem.MolecularGraph molgraph)
 
None clearPDBData (Chem.MolecularGraph molgraph)
 
None setResidueAltAtomName (Chem.Atom atom, str name)
 
bool hasResidueAltAtomName (Chem.Atom atom)
 
str getResidueAltAtomName (Chem.Atom atom)
 
None clearResidueAltAtomName (Chem.Atom atom)
 
None setResidueAtomName (Chem.Atom atom, str name)
 
bool hasResidueAtomName (Chem.Atom atom)
 
str getResidueAtomName (Chem.Atom atom)
 
None clearResidueAtomName (Chem.Atom atom)
 
None setResidueCode (Chem.Atom atom, str code)
 
bool hasResidueCode (Chem.Atom atom)
 
str getResidueCode (Chem.Atom atom)
 
None clearResidueCode (Chem.Atom atom)
 
None setResidueCode (Chem.MolecularGraph molgraph, str code)
 
bool hasResidueCode (Chem.MolecularGraph molgraph)
 
str getResidueCode (Chem.MolecularGraph molgraph)
 
None clearResidueCode (Chem.MolecularGraph molgraph)
 
None setResidueInsertionCode (Chem.Atom atom, str code)
 
bool hasResidueInsertionCode (Chem.Atom atom)
 
str getResidueInsertionCode (Chem.Atom atom)
 
None clearResidueInsertionCode (Chem.Atom atom)
 
None setResidueInsertionCode (Chem.MolecularGraph molgraph, str code)
 
bool hasResidueInsertionCode (Chem.MolecularGraph molgraph)
 
str getResidueInsertionCode (Chem.MolecularGraph molgraph)
 
None clearResidueInsertionCode (Chem.MolecularGraph molgraph)
 
None setResidueLeavingAtomFlag (Chem.Atom atom, bool leaving)
 
bool hasResidueLeavingAtomFlag (Chem.Atom atom)
 
bool getResidueLeavingAtomFlag (Chem.Atom atom)
 
None clearResidueLeavingAtomFlag (Chem.Atom atom)
 
None setResidueLinkingAtomFlag (Chem.Atom atom, bool linking)
 
bool hasResidueLinkingAtomFlag (Chem.Atom atom)
 
bool getResidueLinkingAtomFlag (Chem.Atom atom)
 
None clearResidueLinkingAtomFlag (Chem.Atom atom)
 
None setResidueSequenceNumber (Chem.Atom atom, int seq_no)
 
bool hasResidueSequenceNumber (Chem.Atom atom)
 
int getResidueSequenceNumber (Chem.Atom atom)
 
None clearResidueSequenceNumber (Chem.Atom atom)
 
None setResidueSequenceNumber (Chem.MolecularGraph molgraph, int seq_no)
 
bool hasResidueSequenceNumber (Chem.MolecularGraph molgraph)
 
int getResidueSequenceNumber (Chem.MolecularGraph molgraph)
 
None clearResidueSequenceNumber (Chem.MolecularGraph molgraph)
 
None setSerialNumber (Chem.Atom atom, int serial_no)
 
bool hasSerialNumber (Chem.Atom atom)
 
int getSerialNumber (Chem.Atom atom)
 
None clearSerialNumber (Chem.Atom atom)
 
bool areInSameResidue (Chem.Atom atom1, Chem.Atom atom2, int flags=2147483648)
 
bool combineInterferingResidueCoordinates (Chem.Molecule mol, float max_ctr_dist=1.0)
 
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)
 
None extractResidueSubstructure (Chem.Atom atom, Chem.MolecularGraph molgraph, Chem.Fragment res_substruct, bool cnctd_only=False, int flags=2147483648, bool append=False)
 
None extractResidueSubstructures (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent_molgraph, Chem.Fragment res_substructs, bool cnctd_only=False, int flags=2147483648, bool append=False)
 
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)
 
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)
 
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 setApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
bool getApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
None clearApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
None setApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None clearApplyDictFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None setCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
 
bool hasCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None clearCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check)
 
bool hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
 
bool getCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
 
None clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr)
 
None setCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr, bool comb)
 
bool hasCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
 
bool getCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
 
None clearCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr)
 
None setMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
 
bool getMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
 
None clearMMCIFApplyDictAtomBondingParameter (Base.ControlParameterContainer cntnr)
 
None setMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
bool getMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
None clearMMCIFApplyDictBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
None setMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr, bool output)
 
bool hasMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
 
bool getMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
 
None clearMMCIFOutputBiopolymersAsChemCompParameter (Base.ControlParameterContainer cntnr)
 
None setMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr, MMCIFDataProcessingFunction func)
 
bool hasMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
 
MMCIFDataProcessingFunction getMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
 
None clearMMCIFOutputDataPostprocFunctionParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
bool hasPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool deduce)
 
bool hasPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr, bool evaluate)
 
bool hasPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr)
 
None setPDBFormatVersionParameter (Base.ControlParameterContainer cntnr, int ver)
 
bool hasPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
 
int getPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBFormatVersionParameter (Base.ControlParameterContainer cntnr)
 
None setPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool ignore)
 
bool hasPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBIgnoreCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr, bool ignore)
 
bool hasPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr)
 
None setPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr, bool output)
 
bool hasPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBOutputCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool output)
 
bool hasPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBOutputCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr, bool output)
 
bool hasPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBOutputCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
None setPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr, bool output)
 
bool hasPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBOutputFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
 
bool hasPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
None clearPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
None setPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
 
bool hasPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
bool getPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
None clearPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
None setResidueDictionaryParameter (Base.ControlParameterContainer cntnr, ResidueDictionary dict)
 
bool hasResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
ResidueDictionary getResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
None clearResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
None setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict)
 
bool hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
 
bool getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
 
None clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr)
 

Variables

int IGNORE_SEQUENCE_NO = -9223372036854775808
 
int IGNORE_SERIAL_NO = -9223372036854775808
 

Detailed Description

Contains classes and functions related to biological macromolecules.

Function Documentation

◆ setAltLocationID()

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

◆ hasAltLocationID()

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

◆ getAltLocationID()

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

◆ clearAltLocationID()

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

◆ setBFactor()

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

◆ hasBFactor()

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

◆ getBFactor()

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

◆ clearBFactor()

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

◆ setChainID() [1/2]

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

◆ 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

◆ clearChainID() [1/2]

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

◆ setChainID() [2/2]

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

◆ 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

◆ clearChainID() [2/2]

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

◆ setEntityID()

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

◆ hasEntityID()

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

◆ getEntityID()

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

◆ clearEntityID()

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

◆ setHeteroAtomFlag()

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

◆ hasHeteroAtomFlag()

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

◆ getHeteroAtomFlag()

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

◆ clearHeteroAtomFlag()

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

◆ setHydrogenResidueSequenceInfo()

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

◆ setMMCIFData()

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

◆ hasMMCIFData()

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

◆ getMMCIFData()

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

◆ clearMMCIFData()

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

◆ setModelNumber() [1/2]

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

◆ 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

◆ clearModelNumber() [1/2]

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

◆ setModelNumber() [2/2]

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

◆ 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

◆ clearModelNumber() [2/2]

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

◆ setOccupancy()

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

◆ hasOccupancy()

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

◆ getOccupancy()

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

◆ clearOccupancy()

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

◆ setPDBData()

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

◆ hasPDBData()

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

◆ getPDBData()

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

◆ clearPDBData()

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

◆ setResidueAltAtomName()

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

◆ hasResidueAltAtomName()

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

◆ getResidueAltAtomName()

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

◆ clearResidueAltAtomName()

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

◆ setResidueAtomName()

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

◆ hasResidueAtomName()

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

◆ getResidueAtomName()

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

◆ clearResidueAtomName()

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

◆ setResidueCode() [1/2]

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

◆ 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

◆ clearResidueCode() [1/2]

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

◆ setResidueCode() [2/2]

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

◆ 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

◆ clearResidueCode() [2/2]

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

◆ setResidueInsertionCode() [1/2]

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

◆ 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

◆ clearResidueInsertionCode() [1/2]

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

◆ setResidueInsertionCode() [2/2]

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

◆ 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

◆ clearResidueInsertionCode() [2/2]

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

◆ setResidueLeavingAtomFlag()

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

◆ hasResidueLeavingAtomFlag()

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

◆ getResidueLeavingAtomFlag()

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

◆ clearResidueLeavingAtomFlag()

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

◆ setResidueLinkingAtomFlag()

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

◆ hasResidueLinkingAtomFlag()

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

◆ getResidueLinkingAtomFlag()

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

◆ clearResidueLinkingAtomFlag()

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

◆ setResidueSequenceNumber() [1/2]

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

◆ 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

◆ clearResidueSequenceNumber() [1/2]

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

◆ setResidueSequenceNumber() [2/2]

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

◆ 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

◆ clearResidueSequenceNumber() [2/2]

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

◆ setSerialNumber()

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

◆ hasSerialNumber()

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

◆ getSerialNumber()

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

◆ clearSerialNumber()

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

◆ areInSameResidue()

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

◆ combineInterferingResidueCoordinates()

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

◆ 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

◆ 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

◆ 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

◆ 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)
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

◆ 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

◆ setApplyDictAtomTypesParameter()

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

◆ hasApplyDictAtomTypesParameter()

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

◆ getApplyDictAtomTypesParameter()

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

◆ clearApplyDictAtomTypesParameter()

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

◆ setApplyDictFormalChargesParameter()

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

◆ hasApplyDictFormalChargesParameter()

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

◆ getApplyDictFormalChargesParameter()

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

◆ clearApplyDictFormalChargesParameter()

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

◆ setCalcMissingFormalChargesParameter()

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

◆ hasCalcMissingFormalChargesParameter()

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

◆ getCalcMissingFormalChargesParameter()

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

◆ clearCalcMissingFormalChargesParameter()

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

◆ setCheckLineLengthParameter()

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

◆ hasCheckLineLengthParameter()

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

◆ getCheckLineLengthParameter()

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

◆ clearCheckLineLengthParameter()

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

◆ setCombineInterferingResidueCoordinatesParameter()

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

◆ hasCombineInterferingResidueCoordinatesParameter()

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

◆ getCombineInterferingResidueCoordinatesParameter()

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

◆ clearCombineInterferingResidueCoordinatesParameter()

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

◆ setMMCIFApplyDictAtomBondingParameter()

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

◆ hasMMCIFApplyDictAtomBondingParameter()

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

◆ getMMCIFApplyDictAtomBondingParameter()

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

◆ clearMMCIFApplyDictAtomBondingParameter()

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

◆ setMMCIFApplyDictBondOrdersParameter()

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

◆ hasMMCIFApplyDictBondOrdersParameter()

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

◆ getMMCIFApplyDictBondOrdersParameter()

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

◆ clearMMCIFApplyDictBondOrdersParameter()

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

◆ setMMCIFOutputBiopolymersAsChemCompParameter()

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

◆ hasMMCIFOutputBiopolymersAsChemCompParameter()

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

◆ getMMCIFOutputBiopolymersAsChemCompParameter()

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

◆ clearMMCIFOutputBiopolymersAsChemCompParameter()

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

◆ setMMCIFOutputDataPostprocFunctionParameter()

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

◆ hasMMCIFOutputDataPostprocFunctionParameter()

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

◆ getMMCIFOutputDataPostprocFunctionParameter()

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

◆ clearMMCIFOutputDataPostprocFunctionParameter()

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

◆ setPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

◆ hasPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

◆ getPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

◆ clearPDBApplyDictAtomBondingToNonStdResiduesParameter()

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

◆ setPDBApplyDictAtomBondingToStdResiduesParameter()

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

◆ hasPDBApplyDictAtomBondingToStdResiduesParameter()

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

◆ getPDBApplyDictAtomBondingToStdResiduesParameter()

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

◆ clearPDBApplyDictAtomBondingToStdResiduesParameter()

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

◆ setPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

◆ hasPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

◆ getPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

◆ clearPDBApplyDictBondOrdersToNonStdResiduesParameter()

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

◆ setPDBApplyDictBondOrdersToStdResiduesParameter()

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

◆ hasPDBApplyDictBondOrdersToStdResiduesParameter()

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

◆ getPDBApplyDictBondOrdersToStdResiduesParameter()

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

◆ clearPDBApplyDictBondOrdersToStdResiduesParameter()

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

◆ setPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

◆ hasPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

◆ getPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

◆ clearPDBDeduceBondOrdersFromCONECTRecordsParameter()

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

◆ setPDBEvaluateMASTERRecordParameter()

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

◆ hasPDBEvaluateMASTERRecordParameter()

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

◆ getPDBEvaluateMASTERRecordParameter()

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

◆ clearPDBEvaluateMASTERRecordParameter()

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

◆ setPDBFormatVersionParameter()

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

◆ hasPDBFormatVersionParameter()

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

◆ getPDBFormatVersionParameter()

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

◆ clearPDBFormatVersionParameter()

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

◆ setPDBIgnoreCONECTRecordsParameter()

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

◆ hasPDBIgnoreCONECTRecordsParameter()

bool CDPL.Biomol.hasPDBIgnoreCONECTRecordsParameter ( Base.ControlParameterContainer  cntnr)
Parameters
cntnr
Returns

◆ getPDBIgnoreCONECTRecordsParameter()

bool CDPL.Biomol.getPDBIgnoreCONECTRecordsParameter ( Base.ControlParameterContainer  cntnr)
Parameters
cntnr
Returns

◆ clearPDBIgnoreCONECTRecordsParameter()

None CDPL.Biomol.clearPDBIgnoreCONECTRecordsParameter ( Base.ControlParameterContainer  cntnr)
Parameters
cntnr

◆ setPDBIgnoreFormalChargeFieldParameter()

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

◆ hasPDBIgnoreFormalChargeFieldParameter()

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

◆ getPDBIgnoreFormalChargeFieldParameter()

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

◆ clearPDBIgnoreFormalChargeFieldParameter()

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

◆ setPDBOutputCONECTRecordsForAllBondsParameter()

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

◆ hasPDBOutputCONECTRecordsForAllBondsParameter()

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

◆ getPDBOutputCONECTRecordsForAllBondsParameter()

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

◆ clearPDBOutputCONECTRecordsForAllBondsParameter()

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

◆ setPDBOutputCONECTRecordsParameter()

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

◆ hasPDBOutputCONECTRecordsParameter()

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

◆ getPDBOutputCONECTRecordsParameter()

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

◆ clearPDBOutputCONECTRecordsParameter()

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

◆ setPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

◆ hasPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

◆ getPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

◆ clearPDBOutputCONECTRecordsReflectingBondOrderParameter()

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

◆ setPDBOutputFormalChargesParameter()

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

◆ hasPDBOutputFormalChargesParameter()

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

◆ getPDBOutputFormalChargesParameter()

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

◆ clearPDBOutputFormalChargesParameter()

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

◆ setPDBTruncateLinesParameter()

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

◆ hasPDBTruncateLinesParameter()

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

◆ getPDBTruncateLinesParameter()

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

◆ clearPDBTruncateLinesParameter()

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

◆ setPerceiveMissingBondOrdersParameter()

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

◆ hasPerceiveMissingBondOrdersParameter()

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

◆ getPerceiveMissingBondOrdersParameter()

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

◆ clearPerceiveMissingBondOrdersParameter()

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

◆ setResidueDictionaryParameter()

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

◆ hasResidueDictionaryParameter()

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

◆ getResidueDictionaryParameter()

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

◆ clearResidueDictionaryParameter()

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

◆ setStrictErrorCheckingParameter()

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

◆ hasStrictErrorCheckingParameter()

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

◆ getStrictErrorCheckingParameter()

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

◆ clearStrictErrorCheckingParameter()

None CDPL.Biomol.clearStrictErrorCheckingParameter ( Base.ControlParameterContainer  cntnr)
Parameters
cntnr
Generated by doxygen 1.9.1