Mercurial > repos > bgruening > openbabel_filter

comparison ob_remIons.py @ 13:1c0e4c2ac9ce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 12:02:19 +0000
parents 46cd31c2a674
children ad206086576d
comparison
equal deleted inserted replaced
12:2213bfc4567a 13:1c0e4c2ac9ce
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 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')