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/else
statements), which as i understand it most point cloud registration
algorithms use, such as iterative closest point or anything available
in open3d.
No guarantee ill make any progress of course, but would someone mind
recommending a paper explaining a nice subshape alignment algorithm?
Grant, J.A.; Gallardo, M.A.; Pickup, B.T. (1996) ‘A fast method of
molecular shape comparison: a simple application of a Gaussian
description of molecular shape’, J. Comp. Chem. 17, 1653-1666
[wiley/19961115]
From the abstract:
"A Gaussian description of molecular shape is used to compare the shapes
of two molecules by analytically optimizing their volume intersection."
The Shape-it open-source program might have some code also.
Regards,
F.
Thanks :)
Lewis
On Wed, 4 Nov 2020 at 3:52 am, Andy Jennings
<andy.j.jenni...@gmail.com> wrote:
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 <greg.land...@gmail.com>
wrote:
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] The python implementation of the subshape alignment algorithm is
essentially just a proof-of-concept and not performant enough for
real usage.
On Mon, Nov 2, 2020 at 7:16 PM Andy Jennings
<andy.j.jenni...@gmail.com> wrote:
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 figured that more and more
people would be thinking RDKit + GPU = :-)
Thanks in advance.
Andy _______________________________________________
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