Chython

Library for processing molecules and reactions in Python.

pip install chython

Key capabilities:

  • Parse and write SMILES, InChI, IUPAC, MDL (SDF/RDF/MOL), MRV, XYZ, PDB

  • Substructure and MCS search with SMARTS support

  • Standardize, canonicalize, and enumerate tautomers

  • Morgan and linear fingerprints with Tanimoto similarity

  • Atom-to-atom mapping (neural + rule-based)

  • Template-based reaction application

  • Functional and protective group detection and deprotection

  • Stereo handling (tetrahedral, allene, cis-trans)

  • 2D/3D depiction with Jupyter support

  • RDKit interoperability

Cookbook