Mercurial > repos > bgruening > openbabel_structure_distance_finder
comparison ob_genProp.py @ 0:c066b5accacf draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
| author | bgruening |
|---|---|
| date | Wed, 25 Mar 2020 16:47:13 -0400 |
| parents | |
| children | 4c9d6b47045c |
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| -1:000000000000 | 0:c066b5accacf |
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| 1 #!/usr/bin/env python | |
| 2 """ | |
| 3 Input: Molecular input file. | |
| 4 Output: Physico-chemical properties are computed and stored as metadata in the sdf output file. | |
| 5 Copyright 2012, Bjoern Gruening and Xavier Lucas | |
| 6 """ | |
| 7 import sys, os | |
| 8 import argparse | |
| 9 import openbabel | |
| 10 openbabel.obErrorLog.StopLogging() | |
| 11 import pybel | |
| 12 import cheminfolib | |
| 13 | |
| 14 | |
| 15 def parse_command_line(argv): | |
| 16 parser = argparse.ArgumentParser() | |
| 17 parser.add_argument('--iformat', default='sdf' , help='input file format') | |
| 18 parser.add_argument('-i', '--input', required=True, help='input file name') | |
| 19 parser.add_argument('--oformat', default='sdf', choices = ['sdf', 'table'] , help='output file format') | |
| 20 parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table') | |
| 21 parser.add_argument('-o', '--output', required=True, help='output file name') | |
| 22 return parser.parse_args() | |
| 23 | |
| 24 def compute_properties(args): | |
| 25 if args.oformat == 'sdf': | |
| 26 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) | |
| 27 else: | |
| 28 outfile = open(args.output, 'w') | |
| 29 if args.header: | |
| 30 mol = next(pybel.readfile(args.iformat, args.input)) | |
| 31 metadata = cheminfolib.get_properties_ext(mol) | |
| 32 outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) ) | |
| 33 | |
| 34 for mol in pybel.readfile(args.iformat, args.input): | |
| 35 if mol.OBMol.NumHvyAtoms() > 5: | |
| 36 metadata = cheminfolib.get_properties_ext(mol) | |
| 37 if args.oformat == 'sdf': | |
| 38 [ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ] | |
| 39 outfile.write(mol) | |
| 40 else: | |
| 41 outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) ) | |
| 42 outfile.close() | |
| 43 | |
| 44 def __main__(): | |
| 45 """ | |
| 46 Physico-chemical properties are computed and stored as metadata in the sdf output file | |
| 47 """ | |
| 48 args = parse_command_line(sys.argv) | |
| 49 compute_properties(args) | |
| 50 | |
| 51 if __name__ == "__main__" : | |
| 52 __main__() |