I just submitted a #cheminformatics preprint to ChemRxiv, based on the #RDKit count fingerprints, #chemfp, and some one-off R&D code I wrote over the last few months.

"Superimposed Coding of Count Fingerprints to Binary Fingerprints"

In short, my superimposed coding method gives k-recall@k nearest neighbor scores ~0.9 relative to using full count fingerprints and the multiset Tanimoto (aka MinMax, aka Ruzicka similarity). Recall can be over 0.95 w/ 8192 bits!

https://chemfp.com/SuperimposedCounts.pdf

#OpenBabel is dead, long live #RDKit!

https://github.com/RMeli/spyrmsd/issues/149

On a more serius note, it would be cool to have a cheminformatics library that actually works. Don't get me wrong, RDKit is very cool - but you can feel all the underlying problems it has when using it.

#Cheminformatics

Hey, @egonw - I'm working on a preprint.

How do I cite a source code file in the #rdkit and a commit message? FWIW, I use #Zotero.

"The RDKit implementation [of the multiset Tanimoto] was added in 2009, using fuzzy set operations already available for multiset Dice similarity."

"added in 2009" is commit 104efc5b607baa54ce0804c6a76d484bf9f78b57 at https://github.com/rdkit/rdkit/commit/423433a3e47df64af4a31888e835144e8b3a6c07#diff-d7a0f684fa993bfd84319df4d23b199973d13599b94ad6a4b3a6c79ed7d46719

"fuzzy set operations" is a reference to the two operations starting at https://github.com/rdkit/rdkit/blob/af4e6c05eca09efa8e8f61603937e0d997fc1499/Code/DataStructs/SparseIntVect.h#L132

Or am I overthinking?

#RDKit Atom Pair count fingerprints are wild! If you sum the per-record counts you'll see patterns like:

sum num_records
399 489
400 6
401 0
402 0
403 36
404 0
405 3
406 133423
407 9
408 6
409 42
410 6
411 0
412 36
...
493 83
494 1
495 3
496 116222
497 10
498 3
499 47
500 0

Not easy to plot! No doubt due to rings and chains causing highly repetitive path lengths. (406=2x7x29, 496=8x31)

I used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time

📖 https://cthoyt.com/2025/08/26/chembl-history.html

#chembl #chemistry #chemometrics #chemoinformatics #cheminformatics #rdkit #cdk #proteochemometrics

Today's #RDKit blog post gets into the weeds of how inconsistent information in a common file format is handled by the RDKit.

https://greglandrum.github.io/rdkit-blog/posts/2025-08-22-interpreting-the-2d3d-flag.html

chemfp 5.0b2 is out. Get it while it's hot! For Linux:

python -m pip install chemfp==5.0b2 -i https://chemfp.com/packages/

I'm still updating the documentation. See 'What's new in 5.0' at https://chemfp.com/docs/whats_new_in_50.html

* shardsearch - search many target files

* simhistogram - histogram all the scores

* FPB file now handles 1B+ records

* sparse count fingerprints
- new FPC format
- rdkit2fpc to make them with #RDKit
- fpc2fps to convert to binary fps
- fps2fpc for the other way

#cheminformatics

It's official - the upcoming chemfp 5.0 release will have limited support sparse count #cheminformatics fingerprints, in addition to the normal binary fingerprints.

The new format is "FPC", a variant of the FPS format. Details at https://chemfp.com/fpc_format/.

There will also be "rdkit2fpc" for the four #RDKit count fingerprint generators.

Plus "fpc2fps" with several methods to convert sparse count features -> binary.

And "fps2fpc" for the reverse (it's just a list of on-bit indices.)