I don't really understand the details of what you're trying to do (and don't currently have the time to dig into it anyway), but perhaps I can help with at least part of this:
On Tue, Aug 20, 2019 at 1:08 PM Andrew Dalke <da...@dalkescientific.com> wrote: > > Problem is, I don't know how to figure out if a given aromatic bond must > be a "-" or "=", or can be both. > I think it's relatively easy to figure out if a particular aromatic bond can only be a single bond; at least for most cases: Here are the cases where the aromatic bonds from an atom must be single bonds: 1) has an explicit double bond - overs exocyclic bonds and bonds in non-aromatic rings 2) is O, Se, or Te and charge ==0 - covers c1cocc1, c1c[se]ccc1, c1c[oH+]ccc1 (not sure if that's actually useful) 3) is N or P and charge==0 and numExplicitHs=1. This ignores weird cases like radicals, C-, [oH+] etc. I think other aromatic bonds can be either single or double (unless they're adjacent to one of these, in which case they have to be double, but that's a "higher order effect"). Is that useful at all?
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