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# Copyright 2016 Anthony Bradley. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Support for loading 3D structures stored in MMTF files."""
try:
from mmtf import fetch, parse
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError("Install mmtf to use Bio.PDB.mmtf "
"(e.g. pip install mmtf-python)")
from Bio.PDB.mmtf.DefaultParser import StructureDecoder
def get_from_decoded(decoder):
"""Return structure from decoder."""
structure_decoder = StructureDecoder()
decoder.pass_data_on(structure_decoder)
return structure_decoder.structure_bulder.get_structure()
class MMTFParser(object):
"""Class to get a Biopython structure from a URL or a filename."""
@staticmethod
def get_structure_from_url(pdb_id):
"""Get a structure from a URL - given a PDB id.
:param pdb_id: the input PDB id
:return: the structure
"""
decoder = fetch(pdb_id)
return get_from_decoded(decoder)
@staticmethod
def get_structure(file_path):
"""Get a structure from a file - given a file path.
:param file_path: the input file path
:return: the structure
"""
decoder = parse(file_path)
return get_from_decoded(decoder)
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