Mastodawn

Greg Landrum Sep 8, 2025

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/

GitHub - rdkit/UGM_2025: 2025 RDKit UGM

2025 RDKit UGM. Contribute to rdkit/UGM_2025 development by creating an account on GitHub.

GitHub

Greg Landrum Aug 22, 2025

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

How the 2D/3D flag in Mol blocks is used – RDKit blog

Specifications meet the real world

Greg Landrum Jul 24, 2025

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

Storing partial charges in SD files – RDKit blog

No really, we don’t need mol2 files any more.

Greg Landrum Jul 17, 2025

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

Please stop saying “The Tanimoto similarity is” – RDKit blog

A simple tip to explain what you actually did

Greg Landrum Jun 20, 2025

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

The impact of molecular size on similarity. – RDKit blog

An exploration of how molecular size influences fingerprint similarity.

Greg Landrum Jun 15, 2025

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

Connecting reaction products to the reacting molecules. – RDKit blog

An example of using the extra information that reaction enumeration provides.

Greg Landrum Jun 6, 2025

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

Murcko Scaffolds Tutorial – RDKit blog

Counting and visualizing a list of molecules by scaffold

Greg Landrum Jun 1, 2025

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

Doing extended Hueckel calculations with the RDKit – RDKit blog

Including an exploration of charge variability across conformers

Greg Landrum May 25, 2025

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

Common chemical words II – RDKit blog

This time with Morgan fingeprint bits

Greg Landrum May 17, 2025

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

Using custom fingerprints in PostgreSQL – RDKit blog

Going beyond the cartridge’s built-in fingerprints