Mercurial > repos > bgruening > openbabel_obgrep

annotate ob_addh.py @ 1:f7e1b289b811 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 78ac0521d7df684e96c1b9c1ba2a17b02e681608
author bgruening
date Sat, 20 May 2017 20:03:32 -0400
parents b0311f002a5f
children 78640d0127ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
2 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
3 Input: Molecule file
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
4 Output: Molecule file with hydrogen atoms added at the target pH.
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
5 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
6 import sys, os
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
7 import argparse
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
8 import openbabel
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
9 openbabel.obErrorLog.StopLogging()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
10 import pybel
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
11
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
12 def parse_command_line(argv):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
13 parser = argparse.ArgumentParser()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
14 parser.add_argument('--iformat', type=str, default='sdf' , help='input file format')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
15 parser.add_argument('-i', '--input', type=str, required=True, help='input file name')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
16 parser.add_argument('-o', '--output', type=str, required=True, help='output file name')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
17 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
18 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value')
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
19 return parser.parse_args()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
20
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
21 def addh(args):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
23 for mol in pybel.readfile(args.iformat, args.input):
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
24 if mol.OBMol.NumHvyAtoms() > 5:
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
25 mol.removeh()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
26 mol.OBMol.AddHydrogens(args.polar, True, args.pH)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
27 outfile.write(mol)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
28 outfile.close()
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
29
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
30 def __main__():
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
31 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
32 Add hydrogen atoms at a certain pH value
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
33 """
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
34 args = parse_command_line(sys.argv)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
35 addh(args)
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
36
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
37 if __name__ == "__main__" :
b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
bgruening
parents:
diff changeset
38 __main__()