Mercurial > repos > bgruening > rdock_rbcavity
changeset 2:d52d6ee95cf2 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
| author | bgruening |
|---|---|
| date | Fri, 03 Apr 2020 13:32:38 -0400 |
| parents | 5f73eb32ddbf |
| children | 2f218be61685 |
| files | rbdock.py test-data/broken_ligand.sdf |
| diffstat | 2 files changed, 187 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.py Fri Apr 03 13:32:38 2020 -0400 @@ -0,0 +1,28 @@ +import subprocess +import argparse + +def main(): + parser = argparse.ArgumentParser(description='Simple wrapper for rbdock') + parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate') + parser.add_argument('-s', '--seed', type=int, help='Random seed') + args = parser.parse_args() + + cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output'] + if args.seed != None: + cmd += ['-s', str(args.seed)] + + ps = subprocess.Popen(cmd, stdout=subprocess.PIPE) + + error_counter = 0 + for stdout_line in iter(ps.stdout.readline, ''): + if 'RBT_DOCKING_ERROR' in str(stdout_line): + error_counter += 1 + if error_counter == 10: + print(ps.stdout) + exit(23) + if ps.poll() != None: + print(ps.stdout) + exit(int(ps.poll())) + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken_ligand.sdf Fri Apr 03 13:32:38 2020 -0400 @@ -0,0 +1,159 @@ +Cc1ccsc1C1(O)CCOC1 + OpenBabel03262013053D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 2.6244 -0.3204 0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1487 -0.0653 -0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5577 1.2199 0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7851 1.2166 -0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4005 -0.3714 0.0020 S 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1829 -0.9540 -0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7593 -3.2703 1.1063 C 0 0 3 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7298 -2.3113 -0.2964 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 3.1460 0.6144 0.0045 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8955 -0.8785 -0.8702 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8896 -0.8781 0.8782 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1148 2.0915 0.0058 H 0 0 0 0 0 0 0 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