Mercurial > repos > bgruening > openbabel_structure_distance_finder
comparison ob_remIons.py @ 3:49242402887b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author | bgruening |
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date | Mon, 19 Oct 2020 14:40:22 +0000 |
parents | 4c9d6b47045c |
children | 2c5c7da26e08 |
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2:4c9d6b47045c | 3:49242402887b |
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2 """ | 2 """ |
3 Input: molecular input file. | 3 Input: molecular input file. |
4 Output: Molecule file with removed ions and fragments. | 4 Output: Molecule file with removed ions and fragments. |
5 Copyright 2012, Bjoern Gruening and Xavier Lucas | 5 Copyright 2012, Bjoern Gruening and Xavier Lucas |
6 """ | 6 """ |
7 import sys, os | |
8 import argparse | 7 import argparse |
9 | 8 |
10 from openbabel import openbabel, pybel | 9 from openbabel import openbabel, pybel |
11 openbabel.obErrorLog.StopLogging() | 10 openbabel.obErrorLog.StopLogging() |
12 | 11 |
12 | |
13 def parse_command_line(): | 13 def parse_command_line(): |
14 parser = argparse.ArgumentParser() | 14 parser = argparse.ArgumentParser() |
15 parser.add_argument('-iformat', default='sdf' , help='input file format') | 15 parser.add_argument('-iformat', default='sdf', help='input file format') |
16 parser.add_argument('-i', '--input', required=True, help='input file name') | 16 parser.add_argument('-i', '--input', required=True, help='input file name') |
17 parser.add_argument('-o', '--output', required=True, help='output file name') | 17 parser.add_argument('-o', '--output', required=True, help='output file name') |
18 return parser.parse_args() | 18 return parser.parse_args() |
19 | |
19 | 20 |
20 def remove_ions(args): | 21 def remove_ions(args): |
21 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) | 22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) |
22 for mol in pybel.readfile(args.iformat, args.input): | 23 for mol in pybel.readfile(args.iformat, args.input): |
23 if mol.OBMol.NumHvyAtoms() > 5: | 24 if mol.OBMol.NumHvyAtoms() > 5: |
24 mol.OBMol.StripSalts(0) | 25 mol.OBMol.StripSalts(0) |
26 if 'inchi' in mol.data: | |
27 del mol.data['inchi'] # remove inchi cache so modified mol is saved | |
25 # Check if new small fragments have been created and remove them | 28 # Check if new small fragments have been created and remove them |
26 if mol.OBMol.NumHvyAtoms() > 5: | 29 if mol.OBMol.NumHvyAtoms() > 5: |
27 outfile.write(mol) | 30 outfile.write(mol) |
28 outfile.close() | 31 outfile.close() |
32 | |
29 | 33 |
30 def __main__(): | 34 def __main__(): |
31 """ | 35 """ |
32 Remove any counterion and delete any fragment but the largest one for each molecule. | 36 Remove any counterion and delete any fragment but the largest one for each molecule. |
33 """ | 37 """ |
34 args = parse_command_line() | 38 args = parse_command_line() |
35 remove_ions(args) | 39 remove_ions(args) |
36 | 40 |
37 if __name__ == "__main__" : | 41 |
42 if __name__ == "__main__": | |
38 __main__() | 43 __main__() |