Hi Amy,
On Tue, Feb 6, 2024 at 8:20 PM He, Amy 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
Hi Greg,
Thanks so much for your kind suggestions. That also helped with our projects!
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,
Hi Emre,
Both of those compounds look like they have conflicting stereochemistry
information in the ring systems, i.e. the stereo which is specified cannot
actually exist. There's something else going on as well (that looks like a
bug) but this is already a big enough problem.
The easiest thing
Thank you so much for your help. I managed to convert most of the molecules
from 2D to 3D, but no matter which ETKDG version, which embedding parameter
I try, I cannot convert these two molecules; ZINC000101210593,
ZINC000196058327. Is there an alternative feature or method I can try? I
would be
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