Using The RDKit

The RDKit is currently the de facto standard of chemoinformatics in Python.

Though full of useful functionality, The RDKit is less well documented than some of the other packages we recommend. It is also less stable, meaning that there are changes to the code between updates which may affect your scripts. This is getting better over time, but bear this in mind: record which version you are using, and if something breaks, you will have to look up how to fix it. That said, the basics have been stable for a while now, so you may not have much to worry about unless you get deep into it.

There is a huge amount you can do with The RDKit. This page covers the basics (and possibly some advanced things more specific to what we do).

Documentation

The RDKit documentation can be found here. More user-friendly, up-to-date, tutorial-style documentation is also being developed on The RDKit Blog. An older blog is also available here, however, the code examples may be out of date.

Installation

Conda

conda install -c conda-forge rdkit

Pip

pip install rdkit

Importing

You tend to import specific functionality from The RDKit like this:

from rdkit import Chem

Create a Molecule Object from SMILES

TBC

Inter-convert Molecular Representations

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Molecular Properties

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Iterate Over A Molecule's Atoms

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Substructure Searching/Matching

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Drawing Molecules

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Fingerprinting

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Molecular Similarity

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Reactions

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Creating Reactions

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Performing Reactions

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