#rdkit — Public Fediverse posts

While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?

(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)

#chemistry #cheminformatics #python

Interestingly, only a few days after writing this toot, I somehow wound up with an invitation to use the molab online notebooks from #Marimo (https://marimo.io/).

I am happy to announce that molab notebooks are indeed able to load and run #RDKit; this will help immensely for people like me who are stuck on using stuff from the browser due to various constraints.

If y'all would indulge me a late addition: the appropriate lines in the #RDKit code (https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Draw/__init__.py#L190-L224) can of course be modified to use the B&R blob I introduced in the essay.

What's hampering me from actually trying this out for myself is that due to RDKit not yet being supported by #Pyodide, a lot of the webservices that can run #Python from the browser (e.g. the online version of #jupyter) are also not able to load RDKit. (I have seen at least two proposals to use the JS version of RDKit instead, but I have not managed to make that work either.) Because I had written that essay, and am currently writing this toot from a smartphone (for a number of reasons, I don't have access to a computer I can use), indirectly using RDKit through Wolfram Cloud (basically the online version of Mathematica) is pretty much how I attempt to do cheminformatics experiments on a smartphone. :)

#chemistry #cheminformatics #visualization

I posted a short computational essay on Wolfram Community a little while ago (https://community.wolfram.com/groups/-/m/t/3727989) regarding what I call "molecular heatmaps" for visualizing atomic descriptors. This is based on previous work by #RDKit's Landrum and Riniker (cf. https://doi.org/10.1186/1758-2946-5-43).

Something I did not talk about in that essay is the virtue of reading journal articles that are outside of your usual purview (or, you might even say "comfort zone"). If I had completely restricted myself to the cheminformatics literature, I would not have found out about "blob functions" (cf. https://doi.org/10.1080/10867651.2001.10487549), which are often used in computer graphics. This isn't the first time I was able to profitably use knowledge from one subject to use in another one. It takes conscious effort, but I recommend having a wide reading appetite very warmly.

#chemistry #cheminformatics #visualization

#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

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/

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

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.

#introduction

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

Yes! #rdkit