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...
Yep, network effects mean that there are very significant benefits to staying on the dominant platform
More terrible UI, this time from the @github.com app.
I'm in landscape mode, vertical space is the limiter, but look at the incredible amount that is being wasted. Never mind that much of the info doesn't need to be displayed on that screen.
🤷I basically just read and "save for later" (which is HIGHLY aspirational).
You can add articles to separate boards to organize things, but I apparently haven't done that in 8+ years, so I guess it's one of those features I should use, but don't
"You're right, there should be a file called important data.xlsx in this folder. I'm sorry that I deleted it, but I will create a new one for you right now."
I'm completely addicted to RSS, so I use Feedly for this.
Oh, awesome. I can't wait to start finding hallucinated files in my OneDrive folders.
0) Hogwarts
In this week's #RDKit blog post I assemble a new data set of compounds from patents.
greglandrum.github.io/rdkit-blog/p...
If I had any choice in the matter, I would stop using Word, PowerPoint, and Excel just because I am SO F*CKING TIRED of the constant "nudges" to use OneDrive.
Hopefully it's rare enough that you don't end up getting complaints when your new implementation isn't bug-compatible with the old one.
First: "This new position is such a great opportunity, how could I possibly turn it down?"
Not all that much later: "Oh, the meetings... Please just kill me now."
I really enjoy my birthday, but this time I have had a particular Sammy Hagar song popping into my head for the last few days, and I'm very much ready to be done with it
The last #RDKit blog post of the year is a brief look back at 2025.
greglandrum.github.io/rdkit-blog/p...
Damn, forgot the alt text on the image: “view out over the ocean with a table and laptop in the foreground. Maybe that’s the text for a blog post on the screen”
I’m hard at work on this week’s blog post.
I keep taking pictures like this in this gorge. Goodness do I love 🧗here.
Today's #RDKit blog post is a tutorial/explanation about which atoms are considered as candidates for tetrahedral chirality.
greglandrum.github.io/rdkit-blog/p...
Wow, the LinkedIn year in review was even dumber than I thought it was going to be.
Maybe not everyone needs to do this.
So now I have, unfortunately, once again given up on Polaris being a source of useful open data and I will just get the data from the paper's CI and do my own curation.
I'll check back for my next new project and see if the "authenticate to access open data" dark pattern is finally gone.
5/5
I remember you saying that there was going to be a way to access the supposedly open data you are hosting without logging in first, but it certainly doesn't work if I follow the standard instructions on the website.
4/n
Then I find the dataset (easy!) and follow your instructions to load it.
This immediately fails because I'm not logged in.
3/n
So I start by setting up a conda environment and installing the usual packages.
Then I install the polaris code based on the instructions on your website - easy since it's conda... yay!
2/n
@polarishub.io I'm starting a new project and wanted to use the Fang (a.k.a. Biogen) data set. Since I'm starting from scratch, this tim I figured I'd try grabbing it from polaris instead of doing my own curation. 1/n
This week's #RDKit blog post, like last week's, looks at creating your own synthon spaces. Last week was BRICS, this week we use some combichem reactions:
greglandrum.github.io/rdkit-blog/p...
damn you!
Yeah, I like the VMS style ones better, and including them is a BRILLIANT idea
"blah.md" is a nice to have.
Feature request for version 2: please also allow "blah.txt"
I'd love to switch, but I don't want to have to change my entire workflow
I read the first sentence and thought "oh please let that not be the RDKit", then I got to "support guy" and breathed a giant sigh of relief.
At least this time it's not us. :-)
