Re: [Rdkit-discuss] Ligand conversion problem from 2D to 3D

[Greg L. <gre...@gm...>]

Hi Amy,

On Tue, Feb 6, 2024 at 8:20 PM He, Amy <he...@bu...> wrote:

>
>
> Emre, great to hear from you. I also just wanted to say that not all
> entries in ZINC can be transformed into 3D structures. We encountered a
> couple of instances where the annotated stereo is nonphysical, especially
> at closely-spaced stereo centers in small cycles. I had thought to design a
> check to capture these instances, but eventually I just gave up and
> discarded the entries because no other available methods (including ETKDG)
> or software can build 3D structures for 3D calculations. It would still be
> helpful to consider a check even for 2D calculations.
>
>
Yeah, this is a difficult one. It would be nice to have a check to catch at
least the "simple" cases like these cage structures where there's only one
possible relative stereo possible, but I haven't managed to find it yet.

-greg