/usr/share/pdb2pqr/extensions/summary.py is in pdb2pqr 1.9.0+dfsg-1.
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 | """
Summary extension
Print protein summary file.
Currently prints a list of all residue in protein.
"""
__date__ = "21 October 2011"
__author__ = "Kyle Monson"
import extensions
def usage():
"""
Returns usage text for summary.
"""
return 'Print protein summary information to {output-path}.summary.'
def create_summary_output(routines, outfile):
"""
Output the interaction energy between each possible residue pair.
"""
routines.write("Printing protein summary...\n")
output = extensions.extOutputHelper(routines, outfile)
output.write(routines.protein.getSummary() + '\n')
for residue in routines.protein.getResidues():
output.write(str(residue)+'\n')
def run_extension(routines, outroot, options):
outname = outroot + ".summary"
with open(outname, "w") as outfile:
create_summary_output(routines, outfile)
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