/usr/lib/python2.7/dist-packages/csb/bio/io/whatif.py is in python-csb 1.2.3+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Simple WhatIf/WhatCheck Summary parser
"""
import re
import os
import shutil
from csb.io import Shell
from csb.io import TempFolder
class WhatCheckParser(object):
"""
Simple WhatIf/WhatCheck Summary parser
"""
def __init__(self, binary='DO_WHATCHECK.COM'):
self.binary = binary
def parse_summary(self, fn):
"""
@param fn: whatif pdbout.txt file to parse
@type fn: str
@return: A dict containing some of the WhatCheck results
@rtype: a dict
"""
f_handler = open(os.path.expanduser(fn))
text = f_handler.read()
info = dict()
re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)')
re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)')
re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)')
info['rama_z_score'] = float(re_ramachandran.search(text).groups(0)[0])
info['bb_z_score'] = float(re_backbone.search(text).groups(0)[0])
info['1st_packing_z_score'] = float(re_1st.search(text).groups(0)[0])
info['2nd_packing_z_score'] = float(re_2nd.search(text).groups(0)[0])
info['rotamer_score'] = float(re_rotamer.search(text).groups(0)[0])
f_handler.close()
return info
parse = parse_summary
def run(self, pdb_file):
"""
Runs WhatCheck for the given pdbfile and parses the output.
Will fail if the WhatCheck binary is not in the path.
@param pdb_file: file to parse
@return: dict of parsed values
"""
wd = os.getcwd()
base = os.path.basename(pdb_file)
with TempFolder() as tmp:
shutil.copy(os.path.expanduser(pdb_file), tmp.name)
os.chdir(tmp.name)
Shell.run('{0} {1}'.format(self.binary,
os.path.join(tmp.name, base)))
out = self.parse_summary(os.path.join(tmp.name, 'pdbout.txt'))
os.chdir(wd)
return out
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