The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
The RDKit toolkit wrapper does not raise the expected exception when creating a molecule from '[NH+:1]([C@:2]([C:3](=[O:4])[O-:10])([C:5]([C:6]([C:7]([C:8]([NH+:9]([H:22])[H:23])([H:20])[H:21])([H:18])[H:19])([H:16])[H:17])([H:14])[H:15])[H:13])([H:11])[H:12]' when the explicit_hydrogens option is set to true.
This allows some of the Season 1 pharmaceutical benchmarking molecules (of which this is an example) to pass through the checks likely incorrectly. The correct exception is raised by OpenEye.
Describe the bug
The RDKit toolkit wrapper does not raise the expected exception when creating a molecule from
'[NH+:1]([C@:2]([C:3](=[O:4])[O-:10])([C:5]([C:6]([C:7]([C:8]([NH+:9]([H:22])[H:23])([H:20])[H:21])([H:18])[H:19])([H:16])[H:17])([H:14])[H:15])[H:13])([H:11])[H:12]'
when theexplicit_hydrogens
option is set to true.This allows some of the Season 1 pharmaceutical benchmarking molecules (of which this is an example) to pass through the checks likely incorrectly. The correct exception is raised by OpenEye.
(cc @JoshHorton , @dotsdl , @j-wags )
To Reproduce
Output The full error message (may be large, that's fine. Better to paste too much than too little.)
Computing environment (please complete the following information):
conda list
openff-toolkit ==0.9.2
,rdkit ==2021.03.1
Additional context Add any other context about the problem here.