/usr/lib/python2.7/dist-packages/cogent/parse/stride.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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | #!/usr/bin/env python
"""Parser for the stride commandline tool.
"""
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Production"
def stride_parser(lines):
"""Parses stride output. Returns a ``full_id:{data}`` dictionary.
The parser does not currently support the following (useful) options:
- hydrogen bond assignments (-h)
- contact order calculation (-k)
The returned data is a dictionary with the following keys:
'STRIDE_SS': secondary structure,
'STRIDE_PHI': phi angle,
'STRIDE_PSI': psi angle,
'STRIDE_ASA': accessible surface area
"""
data = {}
for line in lines:
if line.startswith('ASG'):
res_name = line[5:8] # we use 3
chain_id = line[9]
if chain_id == '-': # stride ' ' -> '-' rename
chain_id = ' '
try:
res_id = int(float(line[10:15]))
res_ic = ' '
except ValueError:
res_id = int(float(line[10:14]))
res_ic = line[14]
ss_code = line[24]
phi = float(line[43:49])
psi = float(line[53:59])
asa = float(line[62:69])
data[(None, None, chain_id, (res_name, res_id, res_ic), None)] = \
{
'STRIDE_SS': ss_code,
'STRIDE_PHI': phi,
'STRIDE_PSI': psi,
'STRIDE_ASA': asa
}
return data
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