Bio.PDB.PDBParser'.PDBParser

Class PDBParser

object --+ | PDBParser

Parse a PDB file and return a Structure object.

Instance Methods

__init__(self, PERMISSIVE=True, get_header=False, structure_builder=None, QUIET=False)
The PDB parser call a number of standard methods in an aggregated StructureBuilder object.

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_get_header(self, header_coords_trailer)
Get the header of the PDB file, return the rest.

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_handle_PDB_exception(self, message, line_counter)
This method catches an exception that occurs in the StructureBuilder object (if PERMISSIVE), or raises it again, this time adding the PDB line number to the error message.

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_parse(self, header_coords_trailer)
Parse the PDB file.

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_parse_coordinates(self, coords_trailer)
Parse the atomic data in the PDB file.

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get_header(self)
Return the header.

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get_structure(self, id, file)
Return the structure.

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get_trailer(self)
Return the trailer.

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

init(self, PERMISSIVE=True, get_header=False, structure_builder=None, QUIET=False)
(Constructor)

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

Arguments:

o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT),
the exceptions are caught, but some residues or atoms will be missing.
THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.

o structure_builder - an optional user implemented StructureBuilder class.

o 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 PDB file!

Overrides: object.__init__

get_structure(self, id, file)

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Return the structure.

Arguments:
o id - string, the id that will be used for the structure
o file - name of the PDB file OR an open filehandle

Class PDBParser

__init__(self, PERMISSIVE=True, get_header=False, structure_builder=None, QUIET=False) (Constructor)

get_structure(self, id, file)

init(self, PERMISSIVE=True, get_header=False, structure_builder=None, QUIET=False)
(Constructor)