Mercurial > repos > bgruening > openbabel_obgrep

comparison ob_addh.py @ 11:78640d0127ce 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 08:36:19 -0400
parents b0311f002a5f
children 2912ebf12ef2
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10:f27e2eaffb5f 11:78640d0127ce
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')