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> 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> > 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 >>>> _______________________________________________ >>>> Rdkit-discuss mailing list >>>> Rdkit-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> 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 > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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