FPSim2, a simple Python3 molecular similarity tool

FPSim2 is a new tool for fast similarity search on big compound datasets (>100 million) being developed at ChEMBL. We started developing it as we needed a Python3 library able to run either in memory or out-of-core fast similarity searches on such dataset sizes.

It's written in Python/Cython and features:

A fast population count algorithm (builtin-popcnt-unrolled) from https://github.com/WojciechMula/sse-popcount using SIMD instructions.
Bounds for sub-linear speed-ups from 10.1021/ci600358f
A compressed file format with optimised read speed based in PyTables and BLOSC
Use of multiple cores in a single search
In memory and on disk search modes
Simple and easy to use

Source code is available on github and Conda packages are also available for either mac or linux. To install it type:

conda install rdkit -c rdkit

conda install fpsim2 -c efelix

Try it with docker (much better performance than binder):

docker pull eloyfelix/fpsim2
docker run -p 9999:9999 eloyfelix/fpsim2
open http://localhost:9999/notebooks/demo.ipynb in a browser

Or if you prefer to try it without installing anything (yet)... Click on the binder image!

Data files used in the demos are also available to download.

I would also like to thank Andrew Dalke and Greg Landrum for their blogs, they have been very useful resources!

Comments

Unknown said…

very cool! how does it compare to chemfp?

24 January 2019 at 20:30

Eloy said…

thanks!

I can only compare it to chemfp 1.5 version, which is the opensource one.

FPSim2 is Python3 compatible, can use multiple threads in a single query and has a fast loading compressed file format.
SMILES, InChI and molfiles can be used as an input for a search, but this also comes with a cost.
FPSim2 can also run searches without loading all FPs in memory at once. This enables Raspberry Pi to run Unichem (>150 million) similarity searches :)

chemfp, as a more mature software has many more extra features like calculating full similarity matrices for example.

FPSim2 still needs some optimisations, features and a benchmark after some of this work is done.

25 January 2019 at 15:43

Miquel Duran-Frigola said…

Very nice tool. I am trying to move from chemfp to using FPSim2... Are you planning to include the calculation of similarity matrices? Thanks!

27 August 2019 at 08:31

Eloy said…

Glad you find it useful! This is a feature that we considered to implement but it won't probably happen before next ChEMBL (26) release.

27 August 2019 at 18:39

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