Chemical Data Processing Library Python API - Version 1.1.1
Classes | Functions | Variables
CDPL.Biomol Package Reference

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  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 datastructure 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  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 datastructure 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 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 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 clearPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr)
 
None setPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr, bool write)
 
None clearPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr, bool write)
 
None clearPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool write)
 
None clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool deduce)
 
None clearPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr)
 
None setPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr, bool ignore)
 
None clearPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr, bool write)
 
None clearPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc)
 
None clearPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr, bool apply)
 
None clearPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc)
 
None clearPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr)
 
None setPDBApplyDictAtomTypesParameter (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 clearPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
bool getPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr)
 
None setPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive)
 
None clearPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
bool hasPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
ResidueDictionary getPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr)
 
None setPDBResidueDictionaryParameter (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 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)
 
None convertMOL2ToPDBResidueInfo (Chem.MolecularGraph molgraph, bool override)
 
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

◆ 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

◆ 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

◆ clearPDBWriteCONECTRecordsReflectingBondOrderParameter()

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

◆ hasPDBWriteCONECTRecordsReflectingBondOrderParameter()

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

◆ getPDBWriteCONECTRecordsReflectingBondOrderParameter()

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

◆ setPDBWriteCONECTRecordsReflectingBondOrderParameter()

None CDPL.Biomol.setPDBWriteCONECTRecordsReflectingBondOrderParameter ( Base.ControlParameterContainer  cntnr,
bool  write 
)
Parameters
cntnr
write

◆ clearPDBWriteCONECTRecordsForAllBondsParameter()

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

◆ hasPDBWriteCONECTRecordsForAllBondsParameter()

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

◆ getPDBWriteCONECTRecordsForAllBondsParameter()

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

◆ setPDBWriteCONECTRecordsForAllBondsParameter()

None CDPL.Biomol.setPDBWriteCONECTRecordsForAllBondsParameter ( Base.ControlParameterContainer  cntnr,
bool  write 
)
Parameters
cntnr
write

◆ clearPDBWriteCONECTRecordsParameter()

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

◆ hasPDBWriteCONECTRecordsParameter()

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

◆ getPDBWriteCONECTRecordsParameter()

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

◆ setPDBWriteCONECTRecordsParameter()

None CDPL.Biomol.setPDBWriteCONECTRecordsParameter ( Base.ControlParameterContainer  cntnr,
bool  write 
)
Parameters
cntnr
write

◆ 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

◆ 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

◆ clearPDBWriteFormalChargesParameter()

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

◆ hasPDBWriteFormalChargesParameter()

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

◆ getPDBWriteFormalChargesParameter()

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

◆ setPDBWriteFormalChargesParameter()

None CDPL.Biomol.setPDBWriteFormalChargesParameter ( Base.ControlParameterContainer  cntnr,
bool  write 
)
Parameters
cntnr
write

◆ clearPDBCalcMissingFormalChargesParameter()

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

◆ hasPDBCalcMissingFormalChargesParameter()

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

◆ getPDBCalcMissingFormalChargesParameter()

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

◆ setPDBCalcMissingFormalChargesParameter()

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

◆ clearPDBApplyDictFormalAtomChargesParameter()

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

◆ hasPDBApplyDictFormalAtomChargesParameter()

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

◆ getPDBApplyDictFormalAtomChargesParameter()

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

◆ setPDBApplyDictFormalAtomChargesParameter()

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

◆ 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

◆ clearPDBApplyDictAtomTypesParameter()

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

◆ hasPDBApplyDictAtomTypesParameter()

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

◆ getPDBApplyDictAtomTypesParameter()

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

◆ setPDBApplyDictAtomTypesParameter()

None CDPL.Biomol.setPDBApplyDictAtomTypesParameter ( 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

◆ clearPDBPerceiveMissingBondOrdersParameter()

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

◆ hasPDBPerceiveMissingBondOrdersParameter()

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

◆ getPDBPerceiveMissingBondOrdersParameter()

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

◆ setPDBPerceiveMissingBondOrdersParameter()

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

◆ clearPDBResidueDictionaryParameter()

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

◆ hasPDBResidueDictionaryParameter()

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

◆ getPDBResidueDictionaryParameter()

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

◆ setPDBResidueDictionaryParameter()

None CDPL.Biomol.setPDBResidueDictionaryParameter ( 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

◆ 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

◆ convertMOL2ToPDBResidueInfo()

None CDPL.Biomol.convertMOL2ToPDBResidueInfo ( Chem.MolecularGraph  molgraph,
bool  override 
)
Parameters
molgraph
override

◆ 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