/usr/lib/python2.7/dist-packages/cogent/db/pdb.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | #!/usr/bin/env python
"""Retrieves records by id from PDB, the Protein Data Bank."""
from cogent.db.util import UrlGetter
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
pdb_base='http://www.rcsb.org/pdb/files/'
class Pdb(UrlGetter):
"""Returns a pdb file."""
BaseUrl = pdb_base
Suffix='.pdb'
Key=None
def __str__(self):
return self.BaseUrl + str(self.Key) + self.Suffix
def __getitem__(self, item):
"""Returns handle to file containing specified PDB id."""
orig_key = self.Key
self.Key = item.lower()
result = self.open()
self.Key = orig_key
return result
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