import os, sys, argparse, glob
import General, PDB
selfbin = General.selfbin(sys.argv[0])
par = argparse.ArgumentParser()
par.add_argument('--head', required = True, help = 'head of files')
par.add_argument('--id', default = '0.4', help = 'identity cutoff')
par.add_argument('--db', help = 'database, if not specified, use default')
par.add_argument('--conR', action = 'store_true', help = 'whether this is for a pair of contact')
par.add_argument('--env', help = 'if not None, also modify an .env file')
args = par.parse_args()
dirs = [x for x in os.listdir('.') if os.path.isdir(x)]
dirs.sort()
odir = os.getcwd()
for d in dirs:
os.chdir(odir)
os.chdir(d)
pdbs = glob.glob('*.pdb')
cmds = []
resn = int(d.split('_')[1][2:])
for pdb in pdbs:
matchf = args.head + '_' + General.changeExt(pdb, 'match')
if not os.path.isfile(matchf):
continue
pos = PDB.findPositionInPDB(pdb, resn)
# if output file is already there, skip the job
if os.path.isfile('nr'+args.id +'_'+matchf):
continue
