for l in open(args.l):
info = l.strip().split('/')
subdir = info[-2]
name = General.getBase(os.path.basename(info[-1]))
pid, cid = name.split('_')
pdbf = subdir + '/' + pid + '.pdb'
outf = subdir + '/' + name + '.' + args.ext
if (not os.path.isfile(pdbf)) or (os.path.isfile(outf) and os.path.getsize(outf) > 0):
continue
outfs.append(outf)
selstr = '"NAME CA WITHIN 25 OF CHAIN ' + cid + '"'
cmd = ' '.join([PDB.confindPath, '--p', pdbf, '--o', outf, '--rLib', PDB.rotLib, '--pp', '--psel', selstr, '--sel', selstr])
cmds.append(cmd)
count += 1
if count == args.bs:
General.qsub(cmds)
count = 0
outfs = []
cmds = []
if len(outfs) != 0:
General.qsub(cmds)
else: # for batch size > 1, cannot use chain selection
listid = 0
visited = {}
sublist_pdb = open('sl_pdb.'+str(listid), 'w')
sublist_cmap = open('sl_' + args.ext + '.' + str(listid), 'w')
for l in open(args.l):
info = l.strip().split('/')
subdir = info[-2]
name = General.getBase(os.path.basename(info[-1]))
"--p",
pdb,
"--he",
args.he,
"--oh",
args.oh,
],
)
if not args.bbrmsd == None:
cmd.append("--bbrmsd " + args.bbrmsd)
if not args.nohomo == None:
cmd.append("--nohomo " + args.nohomo)
if args.uniq:
cmd.append("--uniq")
if args.nonat:
cmd.append("--nonat")
if args.smart:
cmd.append("--smart")
cmd = " ".join(cmd)
cmds.append(cmd)
if len(cmds) != 0:
General.qsub(cmds)
sleep(0.5)
# print str(count), '/', str(all), ' directories finished...'
os.chdir(odir)
batchsize = 30 # will run 30 command in a single job
count = 0
pdbfs = []
for l in open(args.l):
info = l.strip().split('/')
subdir = info[-2]
name = General.getBase(info[-1])
pdbf = subdir + '/' + name + '.pdb'
outf = subdir + '/' + name + '.' + args.ext
if (not os.path.isfile(pdbf)) or (os.path.isfile(outf)):
continue
pdbfs.append(pdbf)
count += 1
if count == 30:
cmd = ['python', selfbin+'/extractSCcontacts.py', '--ext', args.ext, '--p'] + pdbfs
cmd = ' '.join(cmd)
General.qsub([cmd])
pdbfs = []
count = 0
if len(pdbfs) != 0:
cmd = ['python', selfbin+'/extractSCcontacts.py', '--ext', args.ext, '--p'] + pdbfs
cmd = ' '.join(cmd)
General.qsub([cmd])
