Introduction to RDKit

Your First Steps in Cheminformatics: An RDKit Tutorial on Google Colab

Welcome to the world of cheminformatics! If you've ever wanted to analyze, visualize, or manipulate chemical structures using code, you're in the right place. This guide will introduce you to RDKit, an essential open-source toolkit for cheminformatics, and show you how to get started in minutes using Google Colab.

What is RDKit and Why Use It?

RDKit is a powerful collection of software and libraries specifically designed for working with chemical information. You can use it to:

• Read and write various chemical file formats.

• Generate 2D and 3D structures from chemical identifiers like SMILES.

• Calculate molecular properties and descriptors (e.g., molecular weight, LogP).

• Perform substructure searches to find specific patterns within molecules.

• Compare molecules for similarity.

We'll use Google Colab, a free, cloud-based Python environment that runs in your browser. This means you don't need to install anything on your computer to get started!

Key concepts learners should know before starting:

• Python basics (lists, dicts, functions, imports).

• Jupyter/Colab usage (run cells, upload files).

• Chemical notation: SMILES strings (linear chemical text encoding), InChI optional. If unfamiliar, check our previous Tutorial on SMILES.

You can access the Google Colab here; it contains all the code used in this tutorial: Google Colab

Step 1: Setting Up Your Environment Getting started in Google Colab is incredibly simple. The first step is to install the RDKit library.

Go to colab.research.google.com and create a new notebook.

In the first cell, type the following command and run it by pressing Shift+Enter. 

The ! tells Colab to run this as a command-line command instead of Python code.

Install the RDKit library using pip

!pip install rdkit-pypi

You will have the output below (Figure 1).

Step 2: To confirm the installation, let's import the library and check its version.

import rdkit

print(rdkit.__version__)

If this runs without errors and prints a version number (Figure 2), you're all set!