Mercurial > repos > bgruening > openbabel_structure_distance_finder

annotate ob_addh.py @ 5:8302ab092300 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:01:11 +0000
parents 49242402887b
children
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c066b5accacf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
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1 #!/usr/bin/env python
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2 """
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3 Input: Molecule file
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4 Output: Molecule file with hydrogen atoms added at the target pH.
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5 """
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6 import argparse
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7 import sys
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9 from openbabel import openbabel, pybel
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11 openbabel.obErrorLog.StopLogging()
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14 def parse_command_line(argv):
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15 parser = argparse.ArgumentParser()
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8302ab092300 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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16 parser.add_argument("--iformat", type=str, default="sdf", help="input file format")
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17 parser.add_argument(
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18 "-i", "--input", type=str, required=True, help="input file name"
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19 )
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20 parser.add_argument(
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21 "-o", "--output", type=str, required=True, help="output file name"
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22 )
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23 parser.add_argument(
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24 "--polar",
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25 action="store_true",
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26 default=False,
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27 help="Add hydrogen atoms only to polar atoms",
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28 )
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29 parser.add_argument(
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30 "--pH", type=float, default="7.4", help="Specify target pH value"
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31 )
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32 return parser.parse_args()
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35 def addh(args):
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36 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
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37 for mol in pybel.readfile(args.iformat, args.input):
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38 if mol.OBMol.NumHvyAtoms() > 5:
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39 mol.removeh()
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40 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
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41 outfile.write(mol)
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42 outfile.close()
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45 def __main__():
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46 """
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47 Add hydrogen atoms at a certain pH value
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48 """
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49 args = parse_command_line(sys.argv)
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50 addh(args)
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53 if __name__ == "__main__":
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54 __main__()