StereoMolGraph Experiments

The experiments accompany the following paper and preprint:

• Papusha, M. and Leonhard, K. StereoMolGraph: Stereochemistry-Aware Molecular and Reaction Graphs. Journal of Chemical Information and Modeling 2026, 66 (7), 3830-3839. https://doi.org/10.1021/acs.jcim.5c02523
• Papusha, M. and Leonhard, K. StereoMolGraph: Stereochemistry-Aware Molecular and Reaction Graphs. ChemRxiv (preprint). https://chemrxiv.org/doi/full/10.26434/chemrxiv-2025-0g4wn/v2

StereoMolGraph source code: https://github.com/maxim-papusha/StereoMolGraph

Contents

• data/: input structures and reference datasets used in the notebooks.
• notebooks/: exploratory and validation notebooks, including molecule comparison, InChI edge cases, pericyclic examples, visualization, and transition-metal stereochemistry examples.
• pyproject.toml: project metadata and Python dependencies for running the notebooks.

Environment

The project targets Python 3.13+.

Install the environment with:

pip install -e .

Key dependencies include stereomolgraph, rdkit, chython, pubchempy, pandas, ipywidgets, and py3dmol.

Data Sources

• data/compounds_2d.sdf was obtained from the CIPValidationSuite/ValidationSuite repository: https://github.com/CIPValidationSuite/ValidationSuite
• The CIP validation data are associated with: Hanson, R. M.; Musacchio, S.; Mayfield, J. W.; Vainio, M. J.; Yerin, A.; Redkin, D. Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. Journal of Chemical Information and Modeling 2018, 58 (9), 1755-1765. https://doi.org/10.1021/acs.jcim.8b00324
• The InChI known-issues files were obtained from InChI_1_06/INCHI-1-DOC/KNOWNISSUES.pdf in the IUPAC InChI repository: https://github.com/IUPAC-InChI/InChI_1_06/blob/master/INCHI-1-DOC/KNOWNISSUES.pdf
• The InChI known-issues reference is also described in: Goodman, J. M.; Pletnev, I.; Thiessen, P.; et al. InChI version 1.06: now more than 99.99% reliable. Journal of Cheminformatics 2021, 13, 40. https://doi.org/10.1186/s13321-021-00517-z

Notes

The data/ directory includes smiles.txt together with the validation reference files used by the notebooks.