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

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object --+
         |
        MMCIFParser

Parse a mmCIF file and return a Structure object.
Instance Methods [hide private]
 
__init__(self, structure_builder=None, QUIET=False)
Create a PDBParser object.
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_build_structure(self, structure_id) 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 PDBParser object.

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

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