Re: [Rdkit-discuss] validating stereochemistry

[Tim D. <tdu...@gm...>]

Thanks Brian. Didn't know that existed! Very useful.
As you mention, it is a lot slower to do the check.
Tim

On Mon, Sep 27, 2021 at 1:30 PM Brian Cole <co...@gm...> wrote:

> 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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