dirs = [x for x in os.listdir('.') if os.path.isdir(x)]
dirs.sort()
for d in dirs:
if args.cont:
confiles = [d + '/' + x for x in os.listdir(d) if x.endswith(args.ext)]
else:
confiles = [d +'/' + [x for x in os.listdir(d) if x.endswith(args.ext)][0] ]# side chain dependent info is not used here
pid = d.split('_')[0].lower()
pdb = args.sdir + '/' + pid + '.clean.pdb'
for confile in confiles:
conlst = open(confile)
for con in conlst:
info = con.strip().split()
idx, res1, res2, cond = info[0], info[2], info[3], float(info[6])
if args.cont:
cond = max(float(info[4]), float(info[5]))
seeds = []
if cond > args.cut:
seeds.extend([res1, res2])
else:
continue
outpdb = General.getBase(confile)[:-1] + '_' + res2.replace(',', '') + '.pdb'
if os.path.isfile(outpdb):
continue
fragmade = Fragment.makeFragments(pdb, seeds, outFile = outpdb, flank = args.flank)
if fragmade == -1:
print outpdb, 'not successfully created'
