Tonight I'm taking the train to Prague for the European edition of the 2025 #RDKit UGM.
I'm really looking forward to meeting a bunch of the community there!
We don't have space for any last-minute in-person registrations, but info on joining the live streams is here:
https://github.com/rdkit/UGM_2025/

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

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

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.)

Join Franciszek Job at EuroSciPy as he presents a scalable framework to unify chemical datasets from sources like PubChem, UniChem & COCONUT.

Canonicalize with RDKit
Scale via Dask
Deduplicate with InChI keys

Ideal for ML pretraining, benchmarking, and chemical data analysis.

Schedule: https://lnkd.in/eaAxwUN2
Tickets: https://lnkd.in/end9aYzE

Today's #RDKit blog post shows a way to store partial charges in SD files. We really should stop using mol2 files.

https://greglandrum.github.io/rdkit-blog/posts/2025-07-24-writing-partial-charges-to-sd-files.html

Today's #RDKit blog post is a heartfelt plea for clearer communication.

https://greglandrum.github.io/rdkit-blog/posts/2025-07-17-naming-similarity-metrics.html

The new #RDKit blog post, inspired by a question from Kjell Jorner, looks at the impact of molecular size on similarity thresholds.
https://greglandrum.github.io/rdkit-blog/posts/2025-06-20-size-and-similarity-1.html

This week's #RDKit blog post shows how to use some of the information added to molecules that come from the chemical reactions code.

https://greglandrum.github.io/rdkit-blog/posts/2025-06-12-using-reaction-info.html

The new #RDKit blog post is a guest post from @jemonat with a tutorial on using Bemis-Murcko scaffolds.

https://greglandrum.github.io/rdkit-blog/posts/2025-06-06-murcko-scaffolds.html

This week I have updated and revised an old blog post showing how to perform extended Hueckel calculations with the #RDKit. This is a fun one for me because it involves work I did back in grad school. :-)
https://greglandrum.github.io/rdkit-blog/posts/2025-05-30-eHT-in-RDKit.html

This #RDKit blog post builds on the earlier one about chemical words; this time I'm using Morgan fingerprint bits as the "words".

https://greglandrum.github.io/rdkit-blog/posts/2025-05-22-common-chemical-words-2.html

The new #RDKit blog posts demonstrates how to work with your own fingerprints in the PostgreSQL cartridge.

https://greglandrum.github.io/rdkit-blog/posts/2025-05-17-custom-fingerprints-in-postgresql.html

This week's #RDKit blog post revisits and updates a really old post looking at the most common chemical "words".

https://greglandrum.github.io/rdkit-blog/posts/2025-05-09-common-chemical-words-1.html

Hi. I'm a scientist and programmer based in Basel, Switzerland. I'm a long-time advocate of #OpenSource and #OpenScience and am the primary developer of the #RDKit.

The 2025_03_1 release of #RDKit release includes my contribution to speed up part of getting 2D fingerprints for a molecule by ~75x! So if you generate #chemical fingerprints, now is a good time to upgrade.

Reminder that I'm #OpenToWork so if you're hiring for #cheminformatics or #scientificSoftware development, let's talk.

#chemistry #DrugDiscovery #pharma #PythonForChemists

https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_1

I'm excited to present "Finding Tautomers" at the first North American #RDKit User Group Meeting in the #Boston #MA area on Friday April 11!

Reminder that I'm #OpenToWork so if you're in the area and hiring for #cheminformatics or #scientificSoftware development, let me know and we can meet to discuss your needs.

Here's a new post on my first encounter with building a simple deep learning model on manually-compiled adverse drug reactions data (thanks to @baoilleach for feedback) - https://jhylin.github.io/Data_in_life_blog/posts/22_Simple_dnn_adrs/2_ADR_regressor.html

Notes re. data - https://jhylin.github.io/Data_in_life_blog/posts/22_Simple_dnn_adrs/1_ADR_data.html

There's a new #RDKit blog post introducing some new functionality that I'm really excited about: doing efficient substructure and similarity searches in very large chemical libraries:
https://greglandrum.github.io/rdkit-blog/posts/2024-12-03-introducing-synthon-search.html