StereoMolGraph

StereoMolGraph (SMG) is a library for graph representation of molecules and reactions with a focus on Stereochemistry. It provides:

• Graph types for molecules and reactions (with/without stereo and stereo changes)
• Includes non tetrahedral stereocenters and changing stereochemistry in reactions
• Fast hashing using Circular Stereo Hash
• Robust equality/isomorphism via a VF2++-style algorithm extended for stereochemistry and reactions
• Bidirectional conversion from / to RDKit
• Construction from 3D coordinates with automatic local stereo inference

Design philosophy

• Unopinionated about bond orders, charge and electronic state
• SMG focuses just on the connectivity and stereochemistry.
• Stereochemistry describes relative spatial arrangement. No absolute stereochemistry.
• Transparent: Simple 2D visualization in IPython notebooks

RDKit interoperability notes

• Hydrogens must be explicit for bidirectional conversion.
• Supports tetrahedral and non tetrahedral stereochemistry during conversion.
• Bond orders, charges, unpaired electrons and other properties are not used!

Installation

Install from PyPI:

pip install stereomolgraph

Feedback and support

Bug reports, feature requests, and questions are welcome through GitHub Issues.

Citations

If you use StereoMolGraph, please cite the relevant publication(s):

1. M. Papusha and K. Leonhard, “StereoMolGraph: Stereochemistry-Aware Molecular and Reaction Graphs,” J. Chem. Inf. Model., 2026, 66, 3830–3839.

2. M. Papusha and K. Leonhard, “Circular Stereo Algorithm and Fingerprint for Chiral Resonance Invariant Molecular Representation,” ChemRxiv, 2026, preprint.

3. M. Papusha, A. V. Copan, B. Rotavera, and K. Leonhard, “Symmetry Numbers: A Flexible Approach for Molecules and Transition States,” ChemRxiv, 2026, preprint.

BibTeX entries

@article{Papusha2026StereoMolGraph,
  author  = {Papusha, Maxim and Leonhard, Kai},
  title   = {{StereoMolGraph}: Stereochemistry-Aware Molecular and Reaction Graphs},
  journal = {Journal of Chemical Information and Modeling},
  year    = {2026},
  volume  = {66},
  number  = {7},
  pages   = {3830--3839},
  doi     = {10.1021/acs.jcim.5c02523},
}

@article{Papusha2026CircularStereoAlgorithm,
  author  = {Papusha, Maxim and Leonhard, Kai},
  title   = {Circular Stereo Algorithm and Fingerprint for Chiral Resonance
             Invariant Molecular Representation},
  journal = {ChemRxiv},
  year    = {2026},
  note    = {Preprint},
  doi     = {10.26434/chemrxiv.15002723/v1},
}

@article{Papusha2026SymmetryNumbers,
  author = {Papusha, Maxim and Copan, Andreas V. and
            Rotavera, Brandon and Leonhard, Kai},
  title  = {Symmetry Numbers: A Flexible Approach for Molecules
            and Transition States},
  journal = {ChemRxiv},
  year   = {2026},
  note   = {Preprint},
  doi     = {10.26434/chemrxiv.15002723/v1},
}

License

MIT License — see LICENSE.