rdkit.Chem.rdSubstructLibrary - Substructure Library

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Molecule Substructure Search with RDKit

∟rdkit.Chem.rdSubstructLibrary - Substructure Library

This section provides a quick introduction on rdkit.Chem.rdSubstructLibrary module in RDKit library that provides functionalities to do substructure search with a molecule library.

What Is rdkit.Chem.rdSubstructLibrary Module? rdkit.Chem.rdSubstructLibrary module in RDKit library provides functionalities to do substructure search with a molecule library.

rdkit.Chem.rdSubstructLibrary module contains one main class: rdkit.Chem.rdSubstructLibrary.SubstructLibrary, which has the following main methods:

l = rdSubstructLibrary.SubstructLibrary() - Creates a SubstructLibrary object.

i = 1.AddMol(m) - Adds the given molecule to the library and returns the index of the added molecule.

c = 1.CountMatches(s) - Performs substructure match in the library and returns the number of matched molecules.

i = 1.GetMatches(s) - Performs substructure match in the library and returns a list of matched molecule indexes. The default number of maximum matched molecule indexes is 1000.

m = 1.GetMol(i) - Returns the molecule of a given index.

Here is a short Jupyter Notebook example of using rdkit.Chem.rdSubstructLibrary.SubstructLibrary class for substructure search.

from rdkit import Chem
ms = ["O=C(O)c2cc1ccc(Cl)n1cn2", "O=C(O)c2ccn1c(Cl)ccc1n2"]
ms = list(map(Chem.MolFromSmiles, ms))
i = Chem.Draw.MolsToGridImage(ms)
display(i)

s = Chem.MolFromSmiles('c1nccc2n1ccc2')
i = Chem.Draw.MolToImage(s, size=(120,120))
display("Substructure", i)

from rdkit.Chem import rdSubstructLibrary
l = rdSubstructLibrary.SubstructLibrary()
for m in ms:
  l.AddMol(m)

c = l.CountMatches(s)
print("Number of matches", c)

ms = l.GetMatches(s)
ms = [l.GetMol(m) for m in ms]
i = Chem.Draw.MolsToGridImage(ms)
display(i)