Package Bio :: Package PDB :: Module MMCIFParser' :: Class FastMMCIFParser
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Class FastMMCIFParser

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object --+
         |
        FastMMCIFParser

Parse an MMCIF file and return a Structure object.
Instance Methods [hide private]
 
__init__(self, structure_builder=None, QUIET=False)
Create a FastMMCIFParser object.
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_build_structure(self, structure_id, filehandle) source code
 
get_structure(self, structure_id, filename)
Return the structure.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, structure_builder=None, QUIET=False)
(Constructor)

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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!
Overrides: object.__init__

get_structure(self, structure_id, filename)

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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