Mercurial > repos > bgruening > rdock_rbdock

annotate rbdock.py @ 4:a428230b38f6 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
author bgruening
date Fri, 03 Apr 2020 13:32:13 -0400
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4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents:
diff changeset
1 import subprocess
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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2 import argparse
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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4 def main():
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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5 parser = argparse.ArgumentParser(description='Simple wrapper for rbdock')
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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6 parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate')
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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7 parser.add_argument('-s', '--seed', type=int, help='Random seed')
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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8 args = parser.parse_args()
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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9
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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10 cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output']
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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11 if args.seed != None:
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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12 cmd += ['-s', str(args.seed)]
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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14 ps = subprocess.Popen(cmd, stdout=subprocess.PIPE)
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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16 error_counter = 0
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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17 for stdout_line in iter(ps.stdout.readline, ''):
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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18 if 'RBT_DOCKING_ERROR' in str(stdout_line):
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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19 error_counter += 1
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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20 if error_counter == 10:
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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21 print(ps.stdout)
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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22 exit(23)
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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23 if ps.poll() != None:
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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24 print(ps.stdout)
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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25 exit(int(ps.poll()))
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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26
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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27 if __name__ == "__main__":
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
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28 main()