RDKit Substructure Search with SMARTS

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Molecule Substructure Search with RDKit

∟RDKit Substructure Search with SMARTS

This section provides a tutorial example on how to perform substructure search with a MARTS parttern using RDKit library.

RDKit also supports substructure search with SMARTS (SMiles ARbitrary Target Specification) pattern, which is an extension of SMILES (Simplified Molecular Input Line Entry System).

SMARTS is a language for describing molecular substructure patterns and widely used in cheminformatics.

Here is a nice short example of doing substructure search with SMARTS using RDKit library, revised from "A Brief Introduction to SMARTS" by Daniel Russo at https://russodanielp.github.io/blog/a-brief-introduction-to-smarts/. The image generated by the line will be displayed automatically Jupyter Notebook.

from rdkit import Chem
from rdkit.Chem import Draw
mols = ['CC(=O)Nc1ccc(O)cc1', 'CC(N)Cc1ccccc1', 'CC(CS)C(=O)N1CCCC1C(=O)O']
mols = list(map(Chem.MolFromSmiles, mols))
sub = Chem.MolFromSmarts('[#6]!:[#6]')
highlights = [[a[0] for a in m.GetSubstructMatches(sub)] for m in mols]
Draw.MolsToGridImage(mols, highlightAtomLists=highlights)

Note that 2 Python nice features are used in example:

map(f, list) Method - Returns a set of objects by calling the given function on the given list of input data.
[exp for i in list if condition] - Called "List Comprehension", returns a list of results from a given expression on a given loop filtered by a given condition.