Dear all,
There is also a good example of JAX + rdkit interaction in the pull request
https://github.com/rdkit/rdkit/pull/2654
from Proteneer
BR
Guillaume
De : Greg Landrum
Date : mercredi, 4 novembre 2020 à 08:38
À : Lewis Martin
Cc : RDKit Discuss
Objet : [*External*] Re:
Mark gave a nice overview of the literature for alignment based on gaussian
overlap (thanks Mark!).
The algorithm that's currently implemented in the RDKit is from some former
colleagues and is described here:
http://pubs.acs.org/doi/abs/10.1021/ci0256384
-greg
On Tue, Nov 3, 2020 at 8:28 PM
Dear all,
I just realized that I'd announced this on social media but forgot the
mailing list:
I'm trying something new: livestreams to demo some of the new RDKit
features on 10 November. I'm doing this twice in the hope that everyone
who's interested will be able to make one of them.
9am CET:
Hi Lewis,
The standard shape alignment algorithm that everyone uses is from Grant &
Pickup 1996
(https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%2819961115%2917%3A14%3C1653%3A%3AAID-JCC7%3E3.0.CO%3B2-K).
It’s a Taylor-series-like expansion using spherical Gaussians as
Ive had an initial go at something like this using JAX. I chose JAX since
it has a shallow learning curve, essentially being numpy on a GPU. This is
great for vectorized calculations, but less so for applications that
involve a lot of control flow (ie if/else statements), which as i
understand it
Hi Greg,
Thanks for the response and background. Here's hoping someone is smart
enough to code this up and generous enough to donate it back to the
community.
Best,
Andy
On Mon, Nov 2, 2020 at 8:52 PM Greg Landrum wrote:
> Hi Andy,
>
> At the moment the RDKit doesn't have either high-quality
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