RDKit blog

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