biopython

v1.71.0

biopython v1.71.0 Bio.PDB.MMCIFParser.FastMMCIFParser

Parse an MMCIF file and return a Structure object.

Link to this section Summary

Functions

__init__()

Create a FastMMCIFParser object

get_structure()

Return the structure

Link to this section Functions

Link to this function __init__()

Create a FastMMCIFParser object.

The mmCIF parser calls a number of standard methods in an aggregated StructureBuilder object. Normally this object is instanciated by the parser object itself, but if the user provides his/her own StructureBuilder object, the latter is used instead.

The main difference between this class and the regular MMCIFParser is that only ‘ATOM’ and ‘HETATM’ lines are parsed here. Use if you are interested only in coordinate information.

Arguments:

  • structure_builder - an optional user implemented StructureBuilder class.
  • QUIET - Evaluated as a Boolean. If true, warnings issued in constructing the SMCRA data will be suppressed. If false (DEFAULT), they will be shown. These warnings might be indicative of problems in the mmCIF file!
Link to this function get_structure()

Return the structure.

Arguments:

  • structure_id - string, the id that will be used for the structure
  • filename - name of the mmCIF file OR an open filehandle