Mercurial > repos > bgruening > rdock_rbdock
comparison rbdock.py @ 4:a428230b38f6 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
| author | bgruening |
|---|---|
| date | Fri, 03 Apr 2020 13:32:13 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 3:1709d2c3dc20 | 4:a428230b38f6 |
|---|---|
| 1 import subprocess | |
| 2 import argparse | |
| 3 | |
| 4 def main(): | |
| 5 parser = argparse.ArgumentParser(description='Simple wrapper for rbdock') | |
| 6 parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate') | |
| 7 parser.add_argument('-s', '--seed', type=int, help='Random seed') | |
| 8 args = parser.parse_args() | |
| 9 | |
| 10 cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output'] | |
| 11 if args.seed != None: | |
| 12 cmd += ['-s', str(args.seed)] | |
| 13 | |
| 14 ps = subprocess.Popen(cmd, stdout=subprocess.PIPE) | |
| 15 | |
| 16 error_counter = 0 | |
| 17 for stdout_line in iter(ps.stdout.readline, ''): | |
| 18 if 'RBT_DOCKING_ERROR' in str(stdout_line): | |
| 19 error_counter += 1 | |
| 20 if error_counter == 10: | |
| 21 print(ps.stdout) | |
| 22 exit(23) | |
| 23 if ps.poll() != None: | |
| 24 print(ps.stdout) | |
| 25 exit(int(ps.poll())) | |
| 26 | |
| 27 if __name__ == "__main__": | |
| 28 main() |