Dealing with molecules

Outline

  1. Introduction to RDKit Part 1

  2. Introduction to RDKit Part 2: Fingerprints and Tanimoto Similarity

  3. RDKit and Pandas

Videos

  • RDKit installation on Google Colab

  • SMILES

  • SMARTS

  • Substructure search

  • Drawing molecules

  • Fingerprints

  • Tanimoto similarity

You no longer need to install an older version of Pandas

This option occasionally stops working for new versions of RDKit or Pandas. In that case you can use mols2grid instead.

Ideas for further coding projects

  • Go back to your solubility prediction projects and determine what molecules have large errors

  • How many of the properties in the solubility dataset can you compute using RDKit?