Mercurial > repos > bgruening > rxdock_rbcavity
changeset 2:7fac8e7a12d5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"
| author | bgruening |
|---|---|
| date | Wed, 03 Jun 2020 12:56:49 -0400 |
| parents | 583dcdbdbf42 |
| children | 0848d3b1a46f |
| files | rbcavity.xml rbdock.py rxdock_macros.xml |
| diffstat | 3 files changed, 2 insertions(+), 30 deletions(-) [+] |
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--- a/rbcavity.xml Sat Apr 25 08:58:47 2020 -0400 +++ b/rbcavity.xml Wed Jun 03 12:56:49 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1"> +<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1.5"> <description>- generate the active site definition needed for rxDock docking</description> <macros> <import>rxdock_macros.xml</import>
--- a/rbdock.py Sat Apr 25 08:58:47 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -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()
--- a/rxdock_macros.xml Sat Apr 25 08:58:47 2020 -0400 +++ b/rxdock_macros.xml Wed Jun 03 12:56:49 2020 -0400 @@ -6,7 +6,7 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="2013.1.0_b93747f3">rxdock</requirement> + <requirement type="package" version="2013.1.1_148c5bd1">rxdock</requirement> </requirements> </xml> </macros>