Tom,

On Fri, Apr 7, 2017 at 3:28 AM, Shubbey McBean <shubbeymcb...@gmail.com>
wrote:

> 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).
>

If you wanted a 2D representation of the 3D structure that ignores chemical
conventions, then wedging would be appropriate. So this:
[image: Inline image 1]


Would be drawn as something like this:
[image: Inline image 2]

However, from a chemical perspective, this isn't reasonable: those two
bridging carbons are not chiral centers, so stereochemistry is not normally
indicated. This is why the cleanIt argument to assignStereochemistry()
removes the chiral specification and the bond wedging code does not add a
wedge there.
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