Mercurial > repos > bgruening > openbabel_remove_protonation_state

annotate ob_remIons.py @ 15:2956017a9244 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 10:53:50 +0000
parents e25b5597cb35
children
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6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
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e25b5597cb35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
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6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 """
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4 Input: molecular input file.
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 Output: Molecule file with removed ions and fragments.
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 Copyright 2012, Bjoern Gruening and Xavier Lucas
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 """
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8 import argparse
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10 from openbabel import openbabel, pybel
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12 openbabel.obErrorLog.StopLogging()
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 def parse_command_line():
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 parser = argparse.ArgumentParser()
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17 parser.add_argument("-iformat", default="sdf", help="input file format")
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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18 parser.add_argument("-i", "--input", required=True, help="input file name")
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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19 parser.add_argument("-o", "--output", required=True, help="output file name")
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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20 parser.add_argument(
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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21 "-idx",
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22 default=False,
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23 action="store_true",
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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24 help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored",
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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25 )
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26 return parser.parse_args()
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 def remove_ions(args):
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30 with open(args.output, "w") as outfile:
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31 for index, mol in enumerate(pybel.readfile(args.iformat, args.input)):
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6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 if mol.OBMol.NumHvyAtoms() > 5:
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33 mol.OBMol.StripSalts(0)
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34 if "inchi" in mol.data:
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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35 del mol.data["inchi"] # remove inchi cache so modified mol is saved
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37 mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n"
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39 if args.idx and args.iformat in ["inchi", "smi"]:
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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40 outfile.write(f"{index}\t{mol}")
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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41 elif mol != "\n":
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42 outfile.write(f"{mol}")
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45 def __main__():
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 """
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47 Remove any counterion and delete any fragment but the largest one for each molecule.
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48 """
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49 args = parse_command_line()
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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50 remove_ions(args)
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53 if __name__ == "__main__":
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54 __main__()