Thanks for the response, Greg!
When I set cleanIt=false, I get the same results as if I didn't call
assignStereoChemistry() at all. In this case, the fused ring example
(cases 1 and 2 in the GitHub thread) look correct, but, as you noted, the
third case looks wrong.
So I guess the question is, why is the stereo cleanup removing the
stereochemistry in my fused ring example? With hydrogens showing, I'd
expect to have case 1 showing up/down wedges on H and case 2 showing
down/down or up/up. It does this when cleanIt=false (or when I don't call
assignStereoChemistry).
Much appreciated,
Tom
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