Mercurial > repos > bgruening > openbabel_compound_convert

comparison ob_addh.py @ 13:1400d1977e7b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:48:13 +0000
parents 1c66bf08f687
children 4242b4d68e9c
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12:1c66bf08f687 13:1400d1977e7b
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 """ 2 """
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
7 import argparse 6 import argparse
7 import sys
8 8
9 from openbabel import openbabel, pybel 9 from openbabel import openbabel, pybel
10 openbabel.obErrorLog.StopLogging() 10 openbabel.obErrorLog.StopLogging()
11 11
12
12 def parse_command_line(argv): 13 def parse_command_line(argv):
13 parser = argparse.ArgumentParser() 14 parser = argparse.ArgumentParser()
14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format') 15 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('-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('-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('--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 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
19 return parser.parse_args() 20 return parser.parse_args()
21
20 22
21 def addh(args): 23 def addh(args):
22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) 24 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
23 for mol in pybel.readfile(args.iformat, args.input): 25 for mol in pybel.readfile(args.iformat, args.input):
24 if mol.OBMol.NumHvyAtoms() > 5: 26 if mol.OBMol.NumHvyAtoms() > 5:
25 mol.removeh() 27 mol.removeh()
26 mol.OBMol.AddHydrogens(args.polar, True, args.pH) 28 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
27 outfile.write(mol) 29 outfile.write(mol)
28 outfile.close() 30 outfile.close()
29 31
32
30 def __main__(): 33 def __main__():
31 """ 34 """
32 Add hydrogen atoms at a certain pH value 35 Add hydrogen atoms at a certain pH value
33 """ 36 """
34 args = parse_command_line(sys.argv) 37 args = parse_command_line(sys.argv)
35 addh(args) 38 addh(args)
36 39
37 if __name__ == "__main__" : 40
41 if __name__ == "__main__":
38 __main__() 42 __main__()