Mercurial > repos > bgruening > openbabel_remions

comparison remove_protonation_state.py @ 13:3153b6f3087c 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 14:43:01 +0000
parents 354c048550f7
children f70b83b730ac
comparison
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12:354c048550f7 13:3153b6f3087c
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__()