Torsional Fingerprint Support

[SabariKumar]

Hello,
Would it be possible to add functionality to calculate torsional fingerprints on the GPU? I'm particularly interested in GPU accelerated version of rdkit.Chem.TorsionFingerprints.GetTFDMatrix

This would significantly accelerate some of our workflows.

Thanks!

[scal444]

Hey, I'll take a look at the RDKit source to see what goes into that, will get back to you on feasibility!

[scal444]

So, this looks reasonable for us to tackle. Could you let us know what kind of problem sizes you typically work on so we can get an accurate benchmark? In terms of molecule sizes and number of conformers.

[SabariKumar]

Awesome, thanks for the help!
We're typically interested in determining whether several given geometries of a single molecule are actually conformers, and using conformer ensembles as input features.
We're probably interested in doing this on up to hundreds of thousands of molecules, around 25 or so heavy atoms - geom-drugs is probably a good representative dataset for this. We'd probably winnow down from 100 or so conformers on average, and use maybe 15 or so for featurization?

Please let me know if that's enough info, happy to elaborate further if needed.

[scal444]

Thanks, that's good info for benchmarking @evasnow1992 . This may or may not get into our v0.4 release, will definitely be in for v0.5