handle stereochemistry in reaction rules

[bdelepine]

Stereochemistry is not handled and raises a rpreactor.Utils.ChemConversionError and a traceback.

TODO:

• nicer "warning" message
• add a test with stereo
• implement the stereochemistry

Example:

python -m rpreactor.cli --with_hs true --match_timeout 1 --fire_timeout 1 --with_stereo true  inline --inchi "InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1" --rsmarts "([#6@&v4:1](-[#8&v2:2])(-[#1&v1:3])(-[#6&v4:4])-[#6@@&v4:5](-[#8&v2:6]-[#6@@&v4:7]1(-[#1&v1:8])-[#6@@&v4:9](-[#8&v2:10]-[#1&v1:11])(-[#1&v1:12])-[#6@&v4:13](-[#8&v2:14])(-[#1&v1:15])-[#6&v4:16]-[#8&v2:17]-[#6@@&v4:18]-1(-[#6&v4:19](-[#8&v2:20])(-[#1&v1:21])-[#1&v1:22])-[#1&v1:23])(-[#1&v1:24])-[#8&v2:25]-[#6&v4:26])>>([#6@&v4:1](-[#8&v2:2])(-[#1&v1:3])(-[#6&v4:4])-[#6@@&v4:5](-[#8&v2:6]-[#1&v1])(-[#1&v1:24])-[#8&v2:25]-[#6&v4:26].[#6@@&v4:13]1(-[#8&v2:14])(-[#1&v1:15])-[#6@&v4:9](-[#8&v2:10]-[#1&v1:11])(-[#1&v1:12])-[#6@@&v4:7](-[#8&v2]-[#1&v1])(-[#1&v1:8])-[#6@&v4:18](-[#6&v4:19](-[#8&v2:20])(-[#1&v1:21])-[#1&v1:22])(-[#1&v1:23])-[#8&v2:17]-[#6&v4:16]-1)" 
09/09/2020 15:28:33 -- CRITICAL -- Stereo is not handled at the time being.
Traceback (most recent call last):
  File "/workdir/rpreactor/cli.py", line 251, in compute
    rd_mol = standardize_chemical(rd_mol, with_hs=self._with_hs, with_stereo=self._with_stereo, heavy=True)
  File "/workdir/rpreactor/Utils.py", line 77, in standardize_chemical
    raise ChemConversionError("Stereo is not handled at the time being.")
rpreactor.Utils.ChemConversionError: CHEM-CONVERSION-ERROR: Stereo is not handled at the time being.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/dev_rpreactor/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/opt/conda/envs/dev_rpreactor/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/workdir/rpreactor/cli.py", line 448, in <module>
    __cli()
  File "/workdir/rpreactor/cli.py", line 444, in __cli
    args.func(args)
  File "/workdir/rpreactor/cli.py", line 352, in inline_mode
    r.compute()
  File "/workdir/rpreactor/cli.py", line 253, in compute
    raise ChemConversionError(e) from e
rpreactor.Utils.ChemConversionError: CHEM-CONVERSION-ERROR: CHEM-CONVERSION-ERROR: Stereo is not handled at the time being.