To close the loop on this: the bug fix is now merged onto master. The ring
stereochemistry code now handles spiro centers.
Here's the little demo of that:
In [2]: print(Chem.CanonSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1'))
O[C@H]1CC[C@]12CC[C@@](Cl)(Br)CC2
Unlike previously (see the bug report) the stereochemistry info is no
longer being lost.
Since the stereochem info is still there it will be used in the conformer
generation/filtering.
-greg
On Wed, Feb 8, 2017 at 4:45 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 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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