pdb = basename(pdb)
tag = "_trim"
outfn = pdb[:-4] + tag
while exists( outfn+".pdb" ):
outfn += tag
print outfn
outfn = outfn+".pdb"
'''
buf = open( outfn, "w" )
buf.write( outfn_lines )
buf.close()
if __name__=="__main__":
parser = ArgumentParser()
parser.add_argument("pdbs", nargs="+", help="")
parser.add_argument("-r", "--to_trim", nargs="+", required=True, help="format: 123B-134B 156B-167B")
parser.add_argument("--save_hetatm", action="store_true", help="save heteroatoms")
parser.add_argument("--n_processors", type=int, default=20, help="numbers of CPUs you are going to use, default=20")
args = parser.parse_args()
resnum_to_trim_dict = pdb_util.get_resnum_dict( args.to_trim )
joblist = [ (pdb, resnum_to_trim_dict, args.save_hetatm) for pdb in args.pdbs ]
myPool = Pool( processes = args.n_processors )
myResults = myPool.map_async( trim_pdb, joblist )
myResults.get()
print "WARNING:", resnum, "is not present in the pdb"
continue
else:
print "NOT"
return False
outfn_lines += "TER\n" # end of a chain
outfn_lines += "END\n"
assert outfn_lines, "nothing is going to be sliced, check your chain definition while selecting residues"
outfn = pdb_util.get_uniq_outpdbname( pdb, "_sliced")
buf = open( outfn, "w" )
buf.write( outfn_lines )
buf.close()
if __name__=="__main__":
parser = ArgumentParser()
parser.add_argument("pdbs", nargs="+", help="")
parser.add_argument("-r", "--to_slice", nargs="+", required=True, help="format: 123B-134B 156B-167B")
parser.add_argument("--n_processors", type=int, default=20, help="numbers of CPUs you are going to use, default=20")
parser.add_argument("--save_hetatm", action="store_true")
args = parser.parse_args()
resnum_to_slice_dict = pdb_util.get_resnum_dict( args.to_slice )
joblist = [ (pdb, resnum_to_slice_dict, args.save_hetatm) for pdb in args.pdbs ]
myPool = Pool( processes = args.n_processors )
myResults = myPool.map_async( slice_pdb, joblist )
myResults.get()