Mercurial > repos > bgruening > prepare_ligands_for_docking

comparison ob_addh.py @ 0:06340f46ecb8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
author bgruening
date Fri, 10 May 2019 08:55:09 -0400
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children de4c80d17527
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-1:000000000000 0:06340f46ecb8
1 #!/usr/bin/env python
2 """
3 Input: Molecule file
4 Output: Molecule file with hydrogen atoms added at the target pH.
5 """
6 import sys, os
7 import argparse
8 import openbabel
9 openbabel.obErrorLog.StopLogging()
10 import pybel
11
12 def parse_command_line(argv):
13 parser = argparse.ArgumentParser()
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')
16 parser.add_argument('-o', '--output', type=str, required=True, help='output file name')
17 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms')
18 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
19 return parser.parse_args()
20
21 def addh(args):
22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
23 for mol in pybel.readfile(args.iformat, args.input):
24 if mol.OBMol.NumHvyAtoms() > 5:
25 mol.removeh()
26 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
27 outfile.write(mol)
28 outfile.close()
29
30 def __main__():
31 """
32 Add hydrogen atoms at a certain pH value
33 """
34 args = parse_command_line(sys.argv)
35 addh(args)
36
37 if __name__ == "__main__" :
38 __main__()