# HG changeset patch # User bgruening # Date 1591203431 14400 # Node ID 4ba7350f00adb56f4f2f13db721c087136bfa86f # Parent 7be0793dd4480cd5fc0a3bcf50c4641372628a6f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" diff -r 7be0793dd448 -r 4ba7350f00ad rbdock.py --- a/rbdock.py Sat Apr 25 08:59:22 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() diff -r 7be0793dd448 -r 4ba7350f00ad rxdock_macros.xml --- a/rxdock_macros.xml Sat Apr 25 08:59:22 2020 -0400 +++ b/rxdock_macros.xml Wed Jun 03 12:57:11 2020 -0400 @@ -6,7 +6,7 @@ - rxdock + rxdock diff -r 7be0793dd448 -r 4ba7350f00ad sort_filter.xml --- a/sort_filter.xml Sat Apr 25 08:59:22 2020 -0400 +++ b/sort_filter.xml Wed Jun 03 12:57:11 2020 -0400 @@ -1,4 +1,4 @@ - + using the sdsort provided with rxDock rxdock_macros.xml