# HG changeset patch # User bgruening # Date 1585935133 14400 # Node ID a428230b38f6bab1e27aa10ee4827bf572349fbf # Parent 1709d2c3dc200938ec865ec17b1af3dc5ec7d4af "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad" diff -r 1709d2c3dc20 -r a428230b38f6 rbdock.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.py Fri Apr 03 13:32:13 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() diff -r 1709d2c3dc20 -r a428230b38f6 rbdock.xml --- a/rbdock.xml Tue Mar 17 09:26:29 2020 -0400 +++ b/rbdock.xml Fri Apr 03 13:32:13 2020 -0400 @@ -1,4 +1,4 @@ - + - perform protein-ligand docking with rDock rdock_macros.xml @@ -13,15 +13,30 @@ #else ln -s '$ligands' ligands.sdf && #end if -rbdock -i ligands.sdf -r receptor.prm -p dock.prm -n $num -o output && -sdsort -n -s -fSCORE output.sd | -#if $score: - sdfilter -f'\$SCORE <= $score' | + +python '$__tool_directory__/rbdock.py' + -n '$num' + #if $seed: + -s '$seed' + #end if + && + +cat rdock_output.sd + +#if $filter.filter_select == "filter": + #if $filter.score: + | sdfilter -f'\$SCORE <= ${filter.score}' + #end if + #if $filter.nscore: + | sdfilter -f'\$SCORE.norm <= ${filter.nscore}' + #end if + #if $filter.top + | sdsort -n -s -fSCORE | sdfilter -f'\$_COUNT <= $filter.top' + #end if #end if -#if $nscore: - sdfilter -f'\$SCORE.norm <= $nscore' | -#end if -sdfilter -f'\$_COUNT <= $top' > '$output' + + > '$output' + ]]> @@ -36,28 +51,57 @@ - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -66,11 +110,34 @@ - + + + + + + + + + + + + + + + + + + + + + + + + @@ -79,12 +146,17 @@ - - - + + + + + + + + diff -r 1709d2c3dc20 -r a428230b38f6 test-data/broken_ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken_ligand.sdf Fri Apr 03 13:32:13 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 + 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