Mercurial > repos > bgruening > openbabel_remduplicates
comparison remove_protonation_state.py @ 13:12aca74f07d7 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 14:47:33 +0000 |
parents | 50ca8845e7f5 |
children | c5de6c19eb06 |
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12:50ca8845e7f5 | 13:12aca74f07d7 |
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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 2013, Bjoern Gruening and Xavier Lucas | 5 Copyright 2013, 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 def remove_protonation( args ): | 20 |
21 def remove_protonation(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 [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms] | 24 [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms] |
24 outfile.write( mol ) | 25 if 'inchi' in mol.data: |
26 del mol.data['inchi'] # remove inchi cache so modified mol is saved | |
27 outfile.write(mol) | |
25 outfile.close() | 28 outfile.close() |
29 | |
26 | 30 |
27 def __main__(): | 31 def __main__(): |
28 """ | 32 """ |
29 Remove any protonation state from each atom in each molecule. | 33 Remove any protonation state from each atom in each molecule. |
30 """ | 34 """ |
31 args = parse_command_line() | 35 args = parse_command_line() |
32 remove_protonation( args ) | 36 remove_protonation(args) |
33 | 37 |
34 if __name__ == "__main__" : | 38 |
39 if __name__ == "__main__": | |
35 __main__() | 40 __main__() |