| Previous changeset 1:5f73eb32ddbf (2020-03-17) Next changeset 3:2f218be61685 (2020-04-14) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad" |
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added:
rbdock.py test-data/broken_ligand.sdf |
| b |
| diff -r 5f73eb32ddbf -r d52d6ee95cf2 rbdock.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.py Fri Apr 03 13:32:38 2020 -0400 |
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| @@ -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() |
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| diff -r 5f73eb32ddbf -r d52d6ee95cf2 test-data/broken_ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken_ligand.sdf Fri Apr 03 13:32:38 2020 -0400 |
| b |
| @@ -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 0 0 0 0 0 + -1.3714 2.0694 -0.0084 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6424 -1.9351 0.5862 H 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 0 + -7.0120 23.8848 3.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6611 23.8468 4.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5581 22.0928 3.4830 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7132 24.7349 5.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4583 25.1339 6.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0123 26.0899 5.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4676 30.8241 0.4170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8412 32.3751 -0.5420 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2388 32.9722 1.4960 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2847 33.4632 3.4970 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6273 27.9210 4.8320 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8230 23.4168 3.6560 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1441 22.5778 4.6930 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5192 24.2169 5.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0522 28.2910 4.7350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8817 31.5647 4.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4982 30.5088 4.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0329 29.7742 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0645 27.6908 2.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5623 28.1183 3.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5506 28.9693 0.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9492 28.3958 1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0540 29.8010 5.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7656 28.5900 5.4903 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0962 26.0040 3.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.7524 24.4932 2.1715 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6062 23.0393 2.7052 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 24.4781 3.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7376 22.7384 3.1952 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1884 21.0868 3.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3042 22.0856 2.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8011 25.7764 6.8076 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4051 24.5711 6.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1871 25.7386 5.1495 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2964 26.7805 5.6864 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2433 33.2980 -0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0822 31.6679 -1.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8759 34.3850 3.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8862 33.2055 4.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2045 28.9156 3.8635 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6528 27.3942 4.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3454 28.8348 5.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 19 1 0 0 0 0 + 1 20 1 0 0 0 0 + 2 22 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 8 1 0 0 0 0 + 4 3 1 0 0 0 0 + 4 28 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 30 1 6 0 0 0 + 6 7 1 0 0 0 0 + 6 31 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 19 2 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 37 1 0 0 0 0 + 12 11 1 0 0 0 0 + 13 38 1 0 0 0 0 + 13 39 1 0 0 0 0 + 13 40 1 0 0 0 0 + 14 12 2 0 0 0 0 + 15 25 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 26 1 0 0 0 0 + 17 26 1 0 0 0 0 + 17 44 1 0 0 0 0 + 17 45 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 10 1 0 0 0 0 + 18 16 2 0 0 0 0 + 18 47 1 0 0 0 0 + 20 48 1 0 0 0 0 + 20 49 1 0 0 0 0 + 21 1 2 0 0 0 0 + 21 2 1 0 0 0 0 + 22 50 1 0 0 0 0 + 22 51 1 0 0 0 0 + 23 9 1 0 0 0 0 + 23 10 1 0 0 0 0 + 23 27 1 0 0 0 0 + 24 12 1 0 0 0 0 + 24 13 1 0 0 0 0 + 25 14 1 0 0 0 0 + 27 52 1 0 0 0 0 + 27 53 1 0 0 0 0 + 27 54 1 0 0 0 0 +M END +$$$$ |