Molecule Substructure Search with RDKit

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Molecule Substructure Search with RDKit

This chapter provides introductions and tutorial examples on substructure search with RDKit library. Topics include substructure match with HasSubstructMatch() and GetSubstructMatch() methods; using SMARTS patterms as substructures; aligning molecule orientation with substructure; finding MCS (Maximum Common Substructure); building molecule libraries in SMILES format for substructure search.

RDKit m.HasSubstructMatch(s) - Substructure Match

RDKit GenerateDepictionMatching2DStructure(m, s) - Substructure Orientation

RDKit rdMolDraw2D.PrepareAndDrawMolecule - Substructure Highlight

RDKit Substructure Search with SMARTS

rdkit.Chem.rdFMCS - Maximum Common Substructure

rdkit.Chem.rdSubstructLibrary - Substructure Library

Substructure Library in Binary and SMILES Formats

Takeaways:

m.HasSubstructMatch(s) can be used to perform substructure match in a given molecule.
AllChem.GenerateDepictionMatching2DStructure() can be used to align molecule orientation with a given substructure.
rdMolDraw2D.PrepareAndDrawMolecule(...) can be used to prepare molecules to be displayed with highlighted atoms and bonds.
Chem.MolFromSmarts(s) can be used to create substructure pattern from SMARTS in the same way as molecules from SMILES.
rdkit.Chem.rdFMCS.FindMCS(ms) can be used to find the MCS (Maximum Common substructure) for a set of molecules.
rdkit.Chem.rdSubstructLibrary module can used to build a molecule library to reduce substructure search time.
rdkit.Chem.rdSubstructLibrary.CachedTrustedSmilesMolHolder class can be used to build a molecule library in trusted SMILES format to reduce memory usage.