comparison ob_addh.py @ 12:50ca8845e7f5 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:38:56 -0400
parents 75d6c2b7907a
children 12aca74f07d7
comparison
equal deleted inserted replaced
11:854a7a169623 12:50ca8845e7f5
3 Input: Molecule file 3 Input: Molecule file
4 Output: Molecule file with hydrogen atoms added at the target pH. 4 Output: Molecule file with hydrogen atoms added at the target pH.
5 """ 5 """
6 import sys, os 6 import sys, os
7 import argparse 7 import argparse
8 import openbabel 8
9 from openbabel import openbabel, pybel
9 openbabel.obErrorLog.StopLogging() 10 openbabel.obErrorLog.StopLogging()
10 import pybel
11 11
12 def parse_command_line(argv): 12 def parse_command_line(argv):
13 parser = argparse.ArgumentParser() 13 parser = argparse.ArgumentParser()
14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format') 14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format')
15 parser.add_argument('-i', '--input', type=str, required=True, help='input file name') 15 parser.add_argument('-i', '--input', type=str, required=True, help='input file name')