Mercurial > repos > bgruening > openbabel_addh
comparison ob_addh.py @ 0:ada6daa717d2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:37:26 -0400 |
| parents | |
| children | 43167f164076 |
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| -1:000000000000 | 0:ada6daa717d2 |
|---|---|
| 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__() |