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Creating a patent data set

datasets

exploration

patents

Another collection of sets of related compounds

Wrapping up 2025

general

Completing the streak

About tetrahedral chirality in the RDKit

tutorial

documentation

stereochemistry

Answering a frequently asked question

Building synthon spaces with combinatorial reactions

tutorial

documentation

A frequently requested tutorial part 2

Building synthon spaces with BRICS fragments

tutorial

documentation

A frequently requested tutorial

Thresholds for “random” with 3D similarity methods

datasets

3d

reference

What is noise in 3D?

Working with the LOBSTER Data set III

datasets

3d

superposition

Comparing 3D alignment methods.

Working with the LOBSTER Data set II

datasets

3d

similarity

Conformer generation and comparing 3D fingerprints

Working with the LOBSTER Data set I

datasets

3d

lwreg

Registering and working with a 3D data set using lwreg

How long does it take to do common tasks in the RDKit?

optimization

reference

Setting things up to track performance over time.

Displaying atom maps and highlighting with reactions

drawing

tutorial

reactions

How to display info about a reaction transformation on a set of specific reactants and products.

Similarity search time and thresholds

cartridge

questions

How does the similarity threshold affect search times using the cartridge?

Rendering intramolecular H bonds in 2D

drawing

exploration

A simple approach to get nonbonded atoms close to each other.

Drawing simple protein–ligand interaction diagrams with the RDKit

drawing

exploration

Quick, but useful

2025 RDKit UGM Recap

general

My impressions from the UGM

The 2025 RDKit UGM is next week

general

My excuse for why there’s no blog post this week

Scaling conformer generation

conformers

questions

technical

How many cores should I use for conformer generation?

How the 2D/3D flag in Mol blocks is used

documentation

technical

Specifications meet the real world

A BRICS tutorial

documentation

tutorial

How to use the RDKit’s BRICS implementation for molecular fragmentation and enumeration

Controlling the RDKit’s logging behavior

documentation

technical

How to disable or capture the RDKit’s logging messages

An LLM experiment

exploratoration

LLMs

What happens if you ask an LLM to generate an RDKit blog post?

Storing partial charges in SD files

tutorial

3d

No really, we don’t need mol2 files any more.

Please stop saying “The Tanimoto similarity is”

similarity

fingerprints

rants

A simple tip to explain what you actually did

Picking a small set of diverse molecules from a large set

similarity

fingerprints

tutorial

There’s more than one way

The impact of molecular size on similarity between very closely related molecules.

reference

similarity

fingerprints

How molecule size affects the impact of single-atom changes on molecular similarity.

Sanitization options and molecule parsing.

documentation

technical

Documenting what the available options do.

The impact of molecular size on similarity.

reference

similarity

fingerprints

An exploration of how molecular size influences fingerprint similarity.

Connecting reaction products to the reacting molecules.

tutorial

reactions

An example of using the extra information that reaction enumeration provides.

Murcko Scaffolds Tutorial

tutorial

Counting and visualizing a list of molecules by scaffold

Doing extended Hueckel calculations with the RDKit

tutorial

Including an exploration of charge variability across conformers

Common chemical words II

exploration

fingerprints

This time with Morgan fingeprint bits

Using custom fingerprints in PostgreSQL

cartridge

fingerprints

tutorial

Going beyond the cartridge’s built-in fingerprints

Common chemical words

exploration

Borrowing an idea from Randall Munroe

Constructing molecules more quickly

tutorial

optimization

Avoiding unnecessary work

Specifying what changes in a reaction

tutorial

reactions

You have control, but you have to know how to use it.

Explaining enhanced stereochemistry

prototypes

tutorial

stereochemistry

What does that stereo specification actually mean?

Similarity-search hitlist overlap part 2

reference

similarity

fingerprints

Taking the noise level into account

Interrupting calculations

tutorial

technical

Sometimes things just take too long…

Rendering fingerprint bits

tutorial

drawing

fingerprints

Visualizing the meaning of fingerprint bits

Similarity-search hitlist overlap

reference

similarity

fingerprints

Why it’s interesting to use different fingerprints for similarity searching

Building a similarity comparison set

reference

similarity

Creating reference data for other projects

Constructing SAR tables in Jupyter

tutorial

rgd

Building a common dataset visualization

Drawing on drawings

tutorial

drawing

Making more complex figures with the RDKit molecule drawing code.

Tuning substructure queries

tutorial

substructure

Making querying more flexible without using SMARTS

Highlight atoms in drawings

tutorial

drawing

One way to add information to molecular drawings

Storing molecules in images

tutorial

drawing

PNG as a format for storing molecules.

More on generalized substructure search

tutorial

substructure

Advanced substructure search features

ChEMBL Document Similarity

exploration

similarity

Using compound similarity to define document similarity

A tutorial on properties

tutorial

Storing arbitrary data on molecules, atoms, bonds, etc.

Efficient molecule editing

tutorial

For those cases when you need to do a bit of tweaking.

Using custom atom and bond invariants with fingerprint generators

fingerprints

tutorial

More fine-grained control over the details of how a fingerprint is generated.

Introducing Synthon Searching

release

tutorial

Searching unreasonably large chemical spaces in reasonable amounts of time.

Using lwreg with the RDKit cartridge

cartridge

tutorial

lwreg

Includes a tutorial on installing PostgreSQL and the cartridge with conda.

Using the ACS1996 drawing style in PandasTools

documentation

tutorial

Making small structure drawings more legible

What’s new in 2024.09.1, part II

documentation

release

Second of a series of short posts describing new features since the 2024.03.1 release

What’s new in 2024.09.1, part I

documentation

release

First of a series of short posts describing new features since the 2024.03.1 release

Additive fingerprints

exploration

similarity

fingerprints

Generating molecular fingerprints from fragment fingerprints

Conformer generation and intramolecular H-bonds

tutorial

conformers

Steering conformer generation

The problem(s) with scaffold splits, part 1

machine learning

rants

reference

I get a bit ranty… again.

The impact of single-atom changes on similarity

fingerprints

reference

exploration

Mainly I just wanted to write “topologically complex”.

A stub a day keeps the docstrings at bay

documentation

release

Improving python usability

Using custom standardization rules / Using the python logger from the RDKit

tutorial

documentation

Two topics for the price of one!

Some new ways to speed RDKit calls up using multiple threads

tutorial

Let’s take advantage of modern CPUs

Adding molecules to matplotlib plots

tutorial

You got your molecules in my scatter plots!

Using abbreviations in the RDKit

tutorial

documentation

Making more compact structure drawings.

Calculating the SA_Score and NP_Score descriptors

tutorial

documentation

descriptors

How to use Python code from the RDKit Contrib directory.

Intro to Stereo Groups and Enhanced Stereochemistry

tutorial

stereochemistry

documentation

A powerful way to express partial knowledge.

Using the Multithreaded Mol Readers

tutorial

Another way to do more than one thing at a time.

Introducing RascalMCES

release

tutorial

A fast new implementation of pairwise MCES.

New MCS features in 2023.09.1

release

tutorial

A big collection of fixes and features.

Plotting rows and columns of molecules with MolsMatrixToGridImage

release

tutorial

A new way to draw multiple molecules in a grid

Templates for ring systems

release

tutorial

Improving 2D coordinate generation

What’s new in the 2023.09.1 release, part 1

release

documentation

Generalized substructure search

Rethinking the RDKit versioning model

process

questions

Do we need to be so conservative about rolling out new features?

Variability of x-fold cross validation results

machine learning

exploration

Should multiple splits be run?

The comparative safety of combining data from Ki assays

rants

exploration

the saga contines

The hazards of combining data from IC50 assays

rants

exploration

A data-supported rant

Drawing options explained

documentation

drawing

Making sense of all the options

Understanding conformer generation failures

3d

documentation

Getting more information when the conformer generation doesn’t work

Binary molecules and the cartridge

cartridge

tutorial

exploration

With a diversion into using PostgreSQL like a document store

New stuff from the 2023.03 RDKit release

release

A few highlights

What are the VSA Descriptors?

descriptors

Making sense of something “uninterpretable”

Doing similarity searches with highly folded fingerprints

reference

fingerprints

Are very short fingerprints useful for doing similarity searches?

Setting up an RDKit development environment 1

tutorial

technical

It’s surprisingly straightforward

Using intake for chemistry

tutorial

datasets

A tool for organizing datasets and collections of datasets

Clustering conformers

tutorial

3d

conformers

Tutorial on how to cluster molecular conformers.

Using Feature Maps

tutorial

3d

A useful tool for working with collections of chemical features.

More on constrained embedding

tutorial

3d

Generating conformers where some atomic coordinates are constrained.

Working with conformers

tutorial

3d

Tutorial on how atomic coordinates are stored

Colliding bits III, expanded

reference

fingerprints

Looking at numbers of collisions and their impact on similarity

FingerprintGenerator tutorial

tutorial

fingerprints

A better way to generate molecular fingerprints

R-Group Decomposition Tutorial

tutorial

rgd

Getting started with RGD

R-Group Decomposition: Edge Cases

reference

rgd

More complicated than it seems at first glance.

Colliding bits II, revisited

reference

fingerprints

The impact of bit collisions on machine-learning performance

Descriptor calculation tutorial

tutorial

descriptors

This will eventually be in the docs

Introducing rdDetermineBonds

tutorial

3d

Assigning bonds from 3D coordinates

Timing methods for serializing molecules

reference

optimization

Quickly saving/restoring molecules from text formats

Dealing with multiconformer SD files

3d

conformers

tutorial

If only we could reliably use better file formats

Optimizing conformer generation parameters

3d

conformers

optimization

Improving the speed of the RDKit’s conformer generator

3D maximum common substructure

tutorial

3d

mcs

Taking atomic coordinates into account when doing MCS

Variability of PMI descriptors

3d

questions

Which is more important, stereochemistry or conformational variability?

Searching with generic groups

tutorial

substructure

Using generics to get more specific

Some thoughts on refactoring the MolDraw2D code

technical

A bit of rambling and an overview of some new features

R-group decomposition and molzip

tutorial

rgd

Generating molecules from all possible combinations of R groups

The number of unique fingerprint bits

exploratory

reference

How many distinct atom environments are there in organic molecules?

A Ternary GHOST

exploratory

machinelearning

Extending the threshold-shifting algorithm to three-class problems

Some new features in the SubstructLibrary

tutorial

substructure

Changing the search order, refining searches, and assigning keys

Using single-molecule reactions

tutorial

reactions

A fast and easy way to apply simple reactions

Highlighting changing atoms and bonds in reactions

tutorial

reactions

A compact view of what changed in a product molecule

R-Group Decomposition and Highlighting

tutorial

prototypes

drawing

rgd

Making pretty pictures for SAR analysis

Generalized substructure search

tutorial

substructure

Using advanced query features

Using the RDKit in a C++ program

tutorial

technical

It’s actually pretty easy

Looking at the number of bits set by different fingerprints

fingerprints

reference

How many features do we find?

Simulating count fingerprints

fingerprints

technical

reference

An approximation to make working with count vectors more efficient

Some observations about similarity search thresholds

similarity

reference

Fingerprint efficiency

Fingerprint similarity thresholds for database searches

similarity

reference

FOMO and similarity search

Thresholds for “random” in fingerprints the RDKit supports

fingerprints

similarity

reference

When is it just noise?

Intro to the molecule enumerator

tutorial

substructure

Using some advanced query features

A new way to use the RDKit from other languages

technical

Introducing the RDKit CFFI interface

ETKDG and distance constraints

conformers

exploration

Biasing the conformational search

Looking at random-coordinate embedding

conformers

exploration

3d

An alternative starting point for conformer generation

Sphere exclusion clustering with the RDKit

similarity

tutorial

Very fast clustering for larger datasets

Setting up an environment to make Python contributions to the RDKit

contributing

tutorial

A relatively simple way to become a code contributor

Finding regioisomers

substructure

tutorial

Advanced substructure searching technique

Trying out the new tautomer canonicalization code

prototypes

technical

Enumerating tautomers and picking a canonical one

Some thoughts on the performance of the RDKit cartridge

cartridge

Data, hints, and even a bit of ranting

Similarity maps with the new drawing code

tutorial

A new, and nicer, way to generate similarity maps