Greg Landrum
@greglandrum.bsky.social
Cheminformatician, developer, climber, runner, hiker, cook
ORCID: 0000-0001-6279-4481
ORCID: 0000-0001-6279-4481
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set I – RDKit blog
Registering and working with a 3D data set using lwreg
greglandrum.github.io
November 8, 2025 at 4:38 PM
This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I know some people have had problems accessing the discord servers we use for the UGMs, so I'm trying an experiment with setting up a Zulip server for the #RDKit.
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
RDKit
Zulip organization for the RDKit community
rdkit.zulipchat.com
November 6, 2025 at 5:54 AM
I know some people have had problems accessing the discord servers we use for the UGMs, so I'm trying an experiment with setting up a Zulip server for the #RDKit.
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
This week I updated an older #RDKit blog post to show how to use the RDKit in your own C++ projects on Windows. That post now covers Linux, the Mac, and Windows.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
October 23, 2025 at 1:25 PM
This week I updated an older #RDKit blog post to show how to use the RDKit in your own C++ projects on Windows. That post now covers Linux, the Mac, and Windows.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
October 21, 2025 at 3:25 PM
Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany.
Pre-registration will open in early 2026.
Pre-registration will open in early 2026.
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Displaying atom maps and highlighting with reactions – RDKit blog
How to display info about a reaction transformation on a set of specific reactants and products.
greglandrum.github.io
October 17, 2025 at 6:41 PM
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I forgot to post over the weekend...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
Rendering intramolecular H bonds in 2D – RDKit blog
A simple approach to get nonbonded atoms close to each other.
greglandrum.github.io
October 6, 2025 at 3:53 AM
I forgot to post over the weekend...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds.
greglandrum.github.io/rdkit-blog/p...
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...
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
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...
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
It's great to see that the piles of money and enormous amounts of electricity and other resources used to train these models has produced such stunning and useful results. And I'm SUPER glad that google now always shows me this garbage.
September 25, 2025 at 3:40 PM
It's great to see that the piles of money and enormous amounts of electricity and other resources used to train these models has produced such stunning and useful results. And I'm SUPER glad that google now always shows me this garbage.
It's always great to see a new release of ChEMBL appear!
September 24, 2025 at 4:52 AM
It's always great to see a new release of ChEMBL appear!
This week I updated an older #RDKit blog post that demonstrates how to set things up so that you can easily use the RDKit in your own C++ code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
September 20, 2025 at 2:45 AM
This week I updated an older #RDKit blog post that demonstrates how to set things up so that you can easily use the RDKit in your own C++ code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
It's hard to believe that we're living in the future when things like this keep happening:
me: "Hey Siri, put onions on the shopping list"
Siri: "Ok, I put bananas on the shopping list"
me: "Hey Siri, put onions on the shopping list"
Siri: "Ok, I put bananas on the shopping list"
September 18, 2025 at 3:42 PM
It's hard to believe that we're living in the future when things like this keep happening:
me: "Hey Siri, put onions on the shopping list"
Siri: "Ok, I put bananas on the shopping list"
me: "Hey Siri, put onions on the shopping list"
Siri: "Ok, I put bananas on the shopping list"
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...
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
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...
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...
This week's #RDKit blog post is a short one looking at the scaling of conformer generation time with the number of threads used.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Scaling conformer generation – RDKit blog
How many cores should I use for conformer generation?
greglandrum.github.io
August 30, 2025 at 4:09 AM
This week's #RDKit blog post is a short one looking at the scaling of conformer generation time with the number of threads used.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Today's #RDKit blog post gets into the weeds of how inconsistent information in a common file format is handled by the RDKit.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
How the 2D/3D flag in Mol blocks is used – RDKit blog
Specifications meet the real world
greglandrum.github.io
August 22, 2025 at 6:23 AM
Today's #RDKit blog post gets into the weeds of how inconsistent information in a common file format is handled by the RDKit.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I really like this description
The difference between doing a project and presenting it. An observation can lead to many avenues of explorations before focus turns to a specific discovery. Presenting it, in a talk / paper, follows inversely, with broad perspectives coming before & after the specific discovery.
August 18, 2025 at 11:57 AM
I really like this description
well, I hope this little glitch is resolved soon.😕
August 12, 2025 at 2:31 PM
well, I hope this little glitch is resolved soon.😕
What good is all the investment that Microsoft is making in AI if Windows keeps showing me that damn hummingbird image even though I click the "I don't like this" button EVERY SINGLE TIME it shows up?
August 12, 2025 at 11:31 AM
What good is all the investment that Microsoft is making in AI if Windows keeps showing me that damn hummingbird image even though I click the "I don't like this" button EVERY SINGLE TIME it shows up?
I’m on vacation, so I asked an LLM to write this week’s #RDKit blog post.
Here’s how it went
greglandrum.github.io/rdkit-blog/p...
Here’s how it went
greglandrum.github.io/rdkit-blog/p...
An LLM experiment – RDKit blog
What happens if you ask an LLM to generate an RDKit blog post?
greglandrum.github.io
July 31, 2025 at 2:55 PM
I’m on vacation, so I asked an LLM to write this week’s #RDKit blog post.
Here’s how it went
greglandrum.github.io/rdkit-blog/p...
Here’s how it went
greglandrum.github.io/rdkit-blog/p...
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...
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
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...
Thanks to @wpwalters.bsky.social for the inspiration for this one.
greglandrum.github.io/rdkit-blog/p...
Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...
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
Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post looks at two different approaches for picking a small number of diverse compounds from a large set. Sometimes you don't need to use the fancy way.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Picking a small set of diverse molecules from a large set – RDKit blog
There’s more than one way
greglandrum.github.io
July 10, 2025 at 6:38 AM
The new #RDKit blog post looks at two different approaches for picking a small number of diverse compounds from a large set. Sometimes you don't need to use the fancy way.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post is another exploration of the impact of molecule size on similarity; this time looking at single-atom changes.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
The impact of molecular size on similarity between very closely related molecules. – RDKit blog
How molecule size affects the impact of single-atom changes on molecular similarity.
greglandrum.github.io
July 5, 2025 at 5:20 AM
The new #RDKit blog post is another exploration of the impact of molecule size on similarity; this time looking at single-atom changes.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
The new #RDKit blog post, inspired by a question from @valencekjell.com, looks at the impact of molecular size on similarity thresholds.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
The impact of molecular size on similarity. – RDKit blog
An exploration of how molecular size influences fingerprint similarity.
greglandrum.github.io
June 20, 2025 at 4:24 AM
The new #RDKit blog post, inspired by a question from @valencekjell.com, looks at the impact of molecular size on similarity thresholds.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
This week's #RDKit blog post shows how to use some of the information added to molecules that come from the chemical reactions code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Connecting reaction products to the reacting molecules. – RDKit blog
An example of using the extra information that reaction enumeration provides.
greglandrum.github.io
June 15, 2025 at 4:11 AM
This week's #RDKit blog post shows how to use some of the information added to molecules that come from the chemical reactions code.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...