Hi James,
This is definitely a bug. The problem seems to be connected to the way what
the RDKit calls "ring stereochemistry" is handled when there are spiro
linkages.
Here's the github issue: https://github.com/rdkit/rdkit/issues/1294
I'll take a look.
Best,
-greg
On Tue, Feb 7, 2017 at 8:32 PM, James Davidson <j.david...@vernalis.com>
wrote:
> Dear All,
>
>
>
> I have hit what I think is a problem with stereochemistry
> perception/handling for certain types of pseudochiral and/or spirocyclic
> systems.
>
> Basically I am observing that some types of input tetrahedral
> stereochemical information gets lost when an RDKit molecule is generated.
>
> But I only realised this because I was wanting to generate conformers and
> was seeing stereochemical scrambling…
>
>
>
> Anyway, an example with pictures will probably explain things better:
>
> https://gist.github.com/jepdavidson/fdfbf6366a17f4829de3d4de22f3b442
>
>
>
> Any help/advice appreciated.
>
>
>
> Kind regards
>
>
>
> James
>
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