Protonated carbonyl groups are certainly a corner case we don't see very often, but when looking into issue #62 I suggested this:
Since I'm looking at this section, I think #6X3:1-[#8X2H0:2] should be #6X3:1-[#8X2H0:2] or #6X3:1-[#8X2H0:2] so that it would match the corresponding bond if the carbonyl oxygen was protonated.
This was drawn to my attention as there are cases for the C=O in a protonated carbonyl, but not for the C-O if the carbonyl was protonated in as ester. I don't actually have a molecule in any set that suggests this is something we should be worried about yet.
Protonated carbonyl groups are certainly a corner case we don't see very often, but when looking into issue #62 I suggested this:
This was drawn to my attention as there are cases for the C=O in a protonated carbonyl, but not for the C-O if the carbonyl was protonated in as ester. I don't actually have a molecule in any set that suggests this is something we should be worried about yet.