Mercurial > repos > bgruening > openbabel_filter

annotate ob_genProp.py @ 14:ad206086576d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:26:54 +0000
parents 1c0e4c2ac9ce
children 191175b260c8
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46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 Input: Molecular input file.
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Output: Physico-chemical properties are computed and stored as metadata in the sdf output file.
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 """
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 import argparse
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8 import sys
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10 import cheminfolib
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11 import openbabel
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12 from openbabel import pybel
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13 openbabel.obErrorLog.StopLogging()
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16 def parse_command_line(argv):
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 parser = argparse.ArgumentParser()
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18 parser.add_argument('--iformat', default='sdf', help='input file format')
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46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 parser.add_argument('-i', '--input', required=True, help='input file name')
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20 parser.add_argument('--oformat', default='sdf', choices=['sdf', 'table'], help='output file format')
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46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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21 parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table')
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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22 parser.add_argument('-o', '--output', required=True, help='output file name')
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 return parser.parse_args()
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26 def compute_properties(args):
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 if args.oformat == 'sdf':
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 else:
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30 outfile = open(args.output, 'w')
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 if args.header:
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 mol = next(pybel.readfile(args.iformat, args.input))
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 metadata = cheminfolib.get_properties_ext(mol)
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34 outfile.write('%s\n' % '\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))
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36 for mol in pybel.readfile(args.iformat, args.input):
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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37 if mol.OBMol.NumHvyAtoms() > 5:
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38 metadata = cheminfolib.get_properties_ext(mol)
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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39 if args.oformat == 'sdf':
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40 [mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]}) for key in metadata]
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46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 outfile.write(mol)
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 else:
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43 outfile.write('%s\n' % ('\t'.join([str(metadata[key]) for key in metadata])))
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44 outfile.close()
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47 def __main__():
46cd31c2a674 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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48 """
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49 Physico-chemical properties are computed and stored as metadata in the sdf output file
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50 """
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51 args = parse_command_line(sys.argv)
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52 compute_properties(args)
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55 if __name__ == "__main__":
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56 __main__()