#rdkit
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greglandrum.bsky.social
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:
greglandrum.github.io/rdkit-blog/p...
#ChemSky
Introducing Synthon Searching – RDKit blog
Searching unreasonably large chemical spaces in reasonable amounts of time.
greglandrum.github.io
December 3, 2024 at 7:21 AM
greglandrum.bsky.social
Today's #RDKit blog post is a tutorial on editing molecules.
greglandrum.github.io/rdkit-blog/p...
Efficient molecule editing – RDKit blog
For those cases when you need to do a bit of tweaking.
greglandrum.github.io
January 18, 2025 at 4:49 AM
greglandrum.bsky.social
The new #RDKit blog post is another tutorial. This time it's about some advanced substructure search functionality.
greglandrum.github.io/rdkit-blog/p...
More on generalized substructure search – RDKit blog
Advanced substructure search features
greglandrum.github.io
February 8, 2025 at 7:45 AM
greglandrum.bsky.social
Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...
Please stop saying “The Tanimoto similarity is” – RDKit blog
A simple tip to explain what you actually did
greglandrum.github.io
July 17, 2025 at 11:22 AM
greglandrum.bsky.social
We did a new major #RDKit release yesterday. v2026.03.1 is out and the conda-forge builds are available.

As always, especially with major releases, be sure to read the "Backwards incompatible changes" section of the release notes!

github.com/rdkit/rdkit/...
Release 2026_03_1 (Q1 2026) Release · rdkit/rdkit
Release_2026.03.1 (Changes relative to Release_2025.09.1) Acknowledgements (Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with you...
github.com
March 28, 2026 at 4:43 AM
greglandrum.bsky.social
The new #RDKit blog post is another tutorial. This time it's demonstrating the property interface that allows you to associate arbitrary properties to molecules, atoms, bonds, etc.
greglandrum.github.io/rdkit-blog/p...
A tutorial on properties – RDKit blog
Storing arbitrary data on molecules, atoms, bonds, etc.
greglandrum.github.io
January 24, 2025 at 8:23 AM
greglandrum.bsky.social
The new #RDKit blog post is a tutorial on highlighting atoms in molecular drawings.
greglandrum.github.io/rdkit-blog/p...
Highlight atoms in drawings – RDKit blog
One way to add information to molecular drawings
greglandrum.github.io
February 21, 2025 at 5:51 AM
greglandrum.bsky.social
yes! #RDKit
screenshot showing that the 2024.09.3 version of the rdkit is installed
November 30, 2024 at 7:55 AM
greglandrum.bsky.social
The first #RDKit blog post of the year is a short one showing how to change the ways atoms and bonds are represented in fingerprints.
greglandrum.github.io/rdkit-blog/p...
Using custom atom and bond invariants with fingerprint generators – RDKit blog
More fine-grained control over the details of how a fingerprint is generated.
greglandrum.github.io
January 10, 2025 at 7:27 AM
greglandrum.bsky.social
The new #RDKit blog post is an update of an older tutorial on displaying fingerprint bits.
greglandrum.github.io/rdkit-blog/p...
RDKit blog - Rendering fingerprint bits
Visualizing the meaning of fingerprint bits
greglandrum.github.io
March 29, 2025 at 7:49 AM
greglandrum.bsky.social
The new #RDKit blog post builds on the recent one about similarity hit set overlaps by taking similarity noise levels into account.
greglandrum.github.io/rdkit-blog/p...
Similarity-search hitlist overlap part 2 – RDKit blog
Taking the noise level into account
greglandrum.github.io
April 13, 2025 at 4:34 AM
greglandrum.bsky.social
The new #RDKit blog post demonstrates how to easily save molecular structures to PNG and SVG files and retrieve them later.

greglandrum.github.io/rdkit-blog/p...
Storing molecules in images – RDKit blog
PNG as a format for storing molecules.
greglandrum.github.io
February 15, 2025 at 4:34 AM
greglandrum.bsky.social
This week's short #RDKit blog post introduces some new functionality for interrupting long-running calculations.

greglandrum.github.io/rdkit-blog/p...
Interrupting calculations – RDKit blog
Sometimes things just take too long…
greglandrum.github.io
April 6, 2025 at 2:49 PM
greglandrum.bsky.social
This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams.
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
Drawing simple protein–ligand interaction diagrams with the RDKit – RDKit blog
Quick, but useful
greglandrum.github.io
September 26, 2025 at 3:58 PM
greglandrum.bsky.social
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. :-)
greglandrum.github.io/rdkit-blog/p...
Doing extended Hueckel calculations with the RDKit – RDKit blog
Including an exploration of charge variability across conformers
greglandrum.github.io
June 1, 2025 at 6:22 AM
greglandrum.bsky.social
The new #RDKit blog post is an updated tutorial on constructing simple SAR tables in Jupyter notebooks:
greglandrum.github.io/rdkit-blog/p...
Constructing SAR tables in Jupyter – RDKit blog
Building a common dataset visualization
greglandrum.github.io
March 15, 2025 at 5:18 AM
greglandrum.bsky.social
The new #RDKit blog post is a guest post looking at doing Butina clustering on the GPU using nvMolKit.

greglandrum.github.io/rdkit-blog/p...
GPU-Accelerated Clustering with nvMolKit – RDKit blog
A guest post from NVIDIA
greglandrum.github.io
March 2, 2026 at 5:13 AM
greglandrum.bsky.social
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:
github.com/rdkit/UGM_20...
GitHub - rdkit/UGM_2025: 2025 RDKit UGM
2025 RDKit UGM. Contribute to rdkit/UGM_2025 development by creating an account on GitHub.
github.com
September 8, 2025 at 2:23 PM
greglandrum.bsky.social
The last #RDKit blog post of the year is a brief look back at 2025.
greglandrum.github.io/rdkit-blog/p...
Wrapping up 2025 – RDKit blog
Completing the streak
greglandrum.github.io
December 28, 2025 at 6:28 AM
greglandrum.bsky.social
This week's #RDKit blog post shows how to use the built-in drawing code to create a more complex figure.

greglandrum.github.io/rdkit-blog/p...
Drawing on drawings – RDKit blog
Making more complex figures with the RDKit molecule drawing code.
greglandrum.github.io
March 7, 2025 at 10:02 AM
greglandrum.bsky.social
This week's #RDKit blog post revisits and updates a really old post looking at the most common chemical "words".

greglandrum.github.io/rdkit-blog/p...
Common chemical words – RDKit blog
Borrowing an idea from Randall Munroe
greglandrum.github.io
May 10, 2025 at 5:43 AM
greglandrum.bsky.social
Yay! #RDKit
A screenshot showing that my "rdkit_new" conda environment is running the 2025.09.1 RDKit release
September 30, 2025 at 5:20 PM
greglandrum.bsky.social
Confused about enhanced enhanced stereochemistry in cheminformatics? The new #RDKit blog post shows a prototype of a tool to help visualize/explain what an enhanced stereo specification actually means.
greglandrum.github.io/rdkit-blog/p...
Explaining enhanced stereochemistry – RDKit blog
What does that stereo specification actually mean?
greglandrum.github.io
April 18, 2025 at 5:55 AM
greglandrum.bsky.social
Today's #RDKit blog post shows a way to store partial charges in SD files. We really should stop using mol2 files.

Thanks to @wpwalters.bsky.social for the inspiration for this one.

greglandrum.github.io/rdkit-blog/p...
Storing partial charges in SD files – RDKit blog
No really, we don’t need mol2 files any more.
greglandrum.github.io
July 24, 2025 at 12:21 PM
janhjensen.bsky.social
My talk at the #RDKit UGM in Prague youtu.be/TduH7v-biyY?... #compchem
Jan Jensen: Can you find hits by screening only 100 molecules?
YouTube video by RDKit
youtu.be
October 5, 2025 at 9:09 AM