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 <greg.land...@gmail.com> Date : mercredi, 4 novembre 2020 à 08:38 À : Lewis Martin <lewis.marti...@gmail.com> Cc : RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Objet : [*External*] Re: [Rdkit-discuss] GPU Implementation of shape-based 3D overlap on rdkit? 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 Lewis Martin <lewis.marti...@gmail.com<mailto:lewis.marti...@gmail.com>> 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? Thanks :) Lewis On Wed, 4 Nov 2020 at 3:52 am, Andy Jennings <andy.j.jenni...@gmail.com<mailto: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<mailto: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<mailto: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 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Sent from Gmail Mobile _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss *********************************************************************************** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ***********************************************************************************
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