Greg Landrum

@dr_greg_landrum
270 Followers
97 Following
19 Posts
Cheminformatician, developer, climber, runner, hiker, cook
Show threadGreg LandrumFeb 17
@freedosproject @jemonat I mis-spoke here: the getting started doc is one big RST file, not a notebook
Show threadGreg LandrumFeb 17
@freedosproject @jemonat I’m not sure this is feasible. We use Sphinx to produce the docs and there’s a fair amount of infrastructure in place to support that (for example, we run Python doctests across the docs to make sure they are still correct when the code changes)
Show threadGreg LandrumFeb 16
@freedosproject @jemonat unless, of course someone can point to a study that shows that technical/scientific documentation is more effective when split into small pieces
Show threadGreg LandrumFeb 16
@freedosproject @jemonat if there’s a way to do that while still maintaining the full notebook for humans who want a tutorial, I’m all for it
Otherwise, the idea of having that tutorial be 15 separate docs is not especially appealing
Greg LandrumSep 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 LandrumAug 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 LandrumJul 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 LandrumJul 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 LandrumJun 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 LandrumJun 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.