Hi Tim,
First the best answer: The best solution to this is to use chemfp. It's a
remarkable piece of software.
If you aren't willing to license that, the RDKit's search brute-force
fingerprint search capabilities aren't too bad for in-memory fingerprints.
There's some information in this slide deck, from a presentation I did here
in Basel last year:
https://www.slideshare.net/GregLandrum1/big-chemical-data-no-problem
The parts about similarity search start at slide 44. The "FPB"-based search
on slide 46 uses a chemfp file format, but it provides an upper bound on
what you could expect for an in-memory search.
Nils mentioned the postgresql cartridge too: That's not a terrible way to
do searches, and the individual similarity calculations are pretty quick,
but it's not as fast as using a built-for-purpose similarity search tool.
I still need to writeup some experiments I did at the end of last year on
ways to make things faster... time flies.
-greg
On Thu, May 18, 2017 at 11:15 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> I think I recall Greg mentioning that RDKit can be used for very fast
> similarity search (e.g. all vs. all comparisons or searches against
> multi-million sized datasets).
> If so, is this part the of the standard distro, or something extra
> (chemfp?).
> And can it run inside the cartridge?
> And any benchmarks?
>
> Thanks
> Tim
>
>
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