Mercurial > repos > bgruening > openbabel_compound_convert
comparison ob_addh.py @ 15:4242b4d68e9c draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2024 11:06:27 +0000 |
| parents | 1400d1977e7b |
| children |
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| 14:e2c36f62e22f | 15:4242b4d68e9c |
|---|---|
| 5 """ | 5 """ |
| 6 import argparse | 6 import argparse |
| 7 import sys | 7 import sys |
| 8 | 8 |
| 9 from openbabel import openbabel, pybel | 9 from openbabel import openbabel, pybel |
| 10 | |
| 10 openbabel.obErrorLog.StopLogging() | 11 openbabel.obErrorLog.StopLogging() |
| 11 | 12 |
| 12 | 13 |
| 13 def parse_command_line(argv): | 14 def parse_command_line(argv): |
| 14 parser = argparse.ArgumentParser() | 15 parser = argparse.ArgumentParser() |
| 15 parser.add_argument('--iformat', type=str, default='sdf', help='input file format') | 16 parser.add_argument("--iformat", type=str, default="sdf", help="input file format") |
| 16 parser.add_argument('-i', '--input', type=str, required=True, help='input file name') | 17 parser.add_argument( |
| 17 parser.add_argument('-o', '--output', type=str, required=True, help='output file name') | 18 "-i", "--input", type=str, required=True, help="input file name" |
| 18 parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms') | 19 ) |
| 19 parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value') | 20 parser.add_argument( |
| 21 "-o", "--output", type=str, required=True, help="output file name" | |
| 22 ) | |
| 23 parser.add_argument( | |
| 24 "--polar", | |
| 25 action="store_true", | |
| 26 default=False, | |
| 27 help="Add hydrogen atoms only to polar atoms", | |
| 28 ) | |
| 29 parser.add_argument( | |
| 30 "--pH", type=float, default="7.4", help="Specify target pH value" | |
| 31 ) | |
| 20 return parser.parse_args() | 32 return parser.parse_args() |
| 21 | 33 |
| 22 | 34 |
| 23 def addh(args): | 35 def addh(args): |
| 24 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) | 36 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) |
| 30 outfile.close() | 42 outfile.close() |
| 31 | 43 |
| 32 | 44 |
| 33 def __main__(): | 45 def __main__(): |
| 34 """ | 46 """ |
| 35 Add hydrogen atoms at a certain pH value | 47 Add hydrogen atoms at a certain pH value |
| 36 """ | 48 """ |
| 37 args = parse_command_line(sys.argv) | 49 args = parse_command_line(sys.argv) |
| 38 addh(args) | 50 addh(args) |
| 39 | 51 |
| 40 | 52 |