/usr/lib/python2.7/dist-packages/chempy/bmin/__init__.py is in pymol 1.8.4.0+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 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | from __future__ import print_function
import os
import shutil
import glob
import re
import string
import sys
import time
import socket # for gethostname()
import getpass # for getuser()
import re
from chempy import feedback
# "do" is the preferred command for running tinker
def do(run_prefix):
if feedback['bmin']:
print(" "+str(__name__)+': launching %s...'%bmin_path)
if hasattr(sys.stdout,"flush"):
sys.stdout.flush()
for a in [ ".m1", ".m2", ".log", ".out" ]:
if os.path.exists(run_prefix + a):
os.unlink(run_prefix + a)
pth = "."
# pth = os.getcwd()
# pth = re.sub(r".*\/"+getpass.getuser()+"\/",'',pth)
# cmd = "rsh "+socket.gethostname()+" "+bmin_path+" "+pth+"/"+run_prefix
cmd = bmin_path+" "+pth+"/"+run_prefix
print(cmd)
os.system(cmd)
while 1:
if os.path.exists(run_prefix+".out"): break
time.sleep(0.1)
if feedback['bmin']:
os.system("cat bmintmp.log")
print(" "+str(__name__)+': bmin job complete. ')
if hasattr(sys.stdout,"flush"):
sys.stdout.flush()
if 'SCHRODINGER' in os.environ:
base = os.environ['SCHRODINGER']
bmin_path = base + '/bmin'
# os.environ['MMSHARE_EXEC'] = '/apps/schrodinger/mmshare-v10028/bin/Linux-x86'
# os.environ['MMOD_EXEC'] = '/apps/schrodinger/macromodel-v71008/bin/Linux-x86'
# bmin_path = os.environ['MMOD_EXEC']+"/bmin"
else:
bmin_path = "bmin"
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