On 04/11/2020 04:26, Lewis Martin wrote:
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/e
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 Lew
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From: Lewis Martin
Sent: 03 November 2020 19:27
To: RDKit Discuss
Subject: Re: [Rdkit-discuss] GPU Implementation of sh
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 m
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 s
Hi Andy,
At the moment the RDKit doesn't have either high-quality shape-based
alignment code[1] or GPU support.
I think having good shape-based alignment available would be a really
useful complement to the Open3DAlign code that's already there, but it's
certainly not a small project.
-greg
[1]
Hi,
I see that back in 2014 there was some discussion of using CUDA inside of
RDKit and how it may be possible to produce a FastROCS-like open source
alternative. I was curious if anyone had made such a breakthrough. Since
GPU availability is now so common, and datasets are becoming so large, I
fi
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