Indeed, the only two chemically valid configurations for this molecule seem to
be:
[cid:image001.png@01D92C36.B02214E0]
Impressive that rdkit can detect this kind of contradictions.
G
From: Kangway Chuang (CHUANGK4) via Rdkit-discuss
Sent: 19 January 2023 17:54
To: Ling Chan ; Gianmarco
Agree with Hao above. For the molecules provided, the second example is
geometrically inaccessible given the stereochemical constraints. In this
case, the expected behavior should be an unsuccessful embedding.
Kangway
On Thu, Jan 19, 2023 at 8:49 AM Ling Chan wrote:
> Keep trying with more
Keep trying with more random seeds?
On Thu., Jan. 19, 2023, 07:38 Hao, wrote:
> Hi Gianmarco,
>
> In my experience, this just means that you have an impossible molecule. I
> haven't found any ways around it besides trying to embed. If it fails, try
> to swap the other stereoisomer. I find this
Hi Gianmarco,
In my experience, this just means that you have an impossible molecule. I
haven't found any ways around it besides trying to embed. If it fails, try
to swap the other stereoisomer. I find this particularly prevalent in large
scale datasets where data quality is not very good.
Best,
Hi all,
Anyone can help with this matter?
Thanks,
On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni
wrote:
> Hi all,
>
> I have come across an issue while embedding structures with
> stereochemistry configurations that presumably lead to clashes between
> atoms:
>
> from rdkit import Chem
>
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