Re: [Rdkit-discuss] validating stereochemistry

[Brian C. <co...@gm...>]

Good Morning Tim, 

The RDKit EnumerateStereoisomers function accomplishes this through the ‘tryEmbedding’ flag: https://github.com/rdkit/rdkit/blob/d20e5cadc81bf6c7b4e590124866f178f2f2fe28/rdkit/Chem/EnumerateStereoisomers.py#L8

It attempts to generate a 3D conformer for the given stereo configuration and fails the configuration if the conformer isn’t reasonable. Not fast, but it is reliable. 

-Brian

> 
> On Sep 27, 2021, at 8:06 AM, Tim Dudgeon <tdu...@gm...> wrote:
> 
> 
> I have Python code to enumerate undefined chiral centres in a molecule.
> Mostly this works fine, but for some constrained structures this can generate stereochemistry that makes no sense. For instance consider NC1CC2CCC1C2:
> <#1 (2).png>
> 
> 
> These two make sense:
> <#2.png>
> 
> <#3.png>
> 
> 
> But these two don't:
> <#5.png>
> 
> <#4.png>
> 
> 
> Is there a way to filter out the invalid ones?
> 
> Thanks
> Tim
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