Chython [ˈkʌɪθ(ə)n]

Library for processing molecules and reactions in python way.


  • Read/write/convert formats: MDL .RDF (.RXN) and .SDF (.MOL), .MRV, SMILES, INCHI (inchi-trust library), .XYZ, .PDB
  • Standardize molecules and reactions and valid structures checker
  • Supported python-magic
  • Tetrahedron, Allene and CIS-TRANS stereo supporting
  • Perform subgraph search
  • Build/edit molecules and reactions
  • Produce template based reactions and molecules
  • Atom-to-atom mapping checker and rule-based fixer
  • Perform MCS search
  • 2d coordinates generation (based on SmilesDrawer)
  • 2d/3d depiction
  • Produce CGRs (Condensed Graph of Reaction)

Full documentation can be found here.

Chython is fork of CGRtools.


Highly recommended to use python 3.8+. Python 3.6 and 3.7 deprecated.

Note: for using clean2d install NodeJS into system.

  • stable version available through PyPI:

    pip install chython
  • Install chython library DEV version for features that are not well tested:

    pip install -U git+[email protected]#egg=chython


Run unit tests:

git clone && cd chython  # skip if already got sources
pip install -e .
pytest --pyargs chython