def cleanup(*args): if ldir != None and os.path.isdir(ldir): General.destroyLocalSpace(ldir) sys.exit(0)
outfh2.write(resid + '\t' + format(abd, '.3f') + '\n')
outfh3.write(resid + '\t' + format(ssc, '.3f') + '\n')
if args.v:
raw_outstr = [resid + ' :']
sc_components = sorted(score_components[resid], key = lambda x : (x[0], x[1]))
for rawsc in sc_components:
raw_outstr.extend([rawsc[0] + ',' + str(rawsc[1]), rawsc[2], rawsc[3]])
raw_outstr = '\t'.join(raw_outstr) + '\n'
outfhv.write(raw_outstr)
outfh1.close()
outfh2.close()
outfh3.close()
if args.v:
outfhv.close()
print 'Scores calculation done!'
if args.opdb:
opdb1, opdb2, opdb3 = [ x + '.pdb' for x in (outf1, outf2, outf3)]
for x in (outf1, outf2, outf3):
replaceBfactor(args.p, x + '.pdb', x)
if not args.post:
if args.v:
os.system('cp -r ' + ldir + '/' + base + ' ' + outdir)
General.destroyLocalSpace(ldir)
# remove temporary files created
os.remove(list_tmp)
# os.remove(term_support)
args = par.parse_args()
cmd_setup = cmd_setup.replace('dummy.pdb', args.p)
if args.change != None:
assert len(args.change) % 2 == 0
for i in range(0, len(args.change), 2):
cmd_setup.replace(args.change[i], args.change[i+1])
cmd_run = ['/home/grigoryanlab/library/bin/charmrun', '+p'+str(args.nc), '/home/grigoryanlab/library/bin/namd2', 'namdrun_run.ctl >& namdrun_run.out']
cmd_run = ' '.join(cmd_run)
odir = os.getcwd()
# run setup codes
os.system(cmd_setup)
General.destroyLocalSpace(ldir1)
os.chdir(ldir2)
os.system('rm -r vmd*')
# need to have a subprocess with timeout, because wants to stop MD and allow certain time before job terminated
class Command:
def __init__(self, cmd):
self.cmd = cmd
self.process = None
def run(self, timeout):
def target():
print 'Thread started'
self.process = subprocess.Popen(self.cmd, shell=True)
self.process.communicate()
print 'Thread finished'
