Mercurial > repos > bgruening > openbabel_remions

comparison remove_protonation_state.py @ 12:354c048550f7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:37:04 -0400
parents c9bee3591df9
children 3153b6f3087c
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11:9249b0e0e6bd 12:354c048550f7
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 7 import sys, os
8 import argparse 8 import argparse
9 import openbabel 9
10 from openbabel import openbabel, pybel
10 openbabel.obErrorLog.StopLogging() 11 openbabel.obErrorLog.StopLogging()
11 import pybel
12 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')