Stereochemistry-Aware Molecular and Reaction Graphs#

StereoMolGraph StereoMolGraph

pypi python license tests github doi

Welcome to the documentation for StereoMolGraph.

This package provides a collection of graph classes for the representation of molecules and chemical reactions in a modular. The core focus is to allow the user to work with chiral molecules in a consistent way with a simple interface. All arising algorithmic difficulties are taken care of by the internal implementations.

Its treatment of stereochemistry is based on rigorously defined local stereodescriptors, which are derived from group-theoretical principles.

Building on this formal foundation, a range of graph algorithms is implemented in a stereochemistry-aware manner, enabling consistent handling of symmetry, equivalence, and stereochemical transformations.

Magic Methods#

StereoMolGraph implements the following magic methods:

  • __eq__: based on graph isomorphism and stereochemical equivalence [1]

  • __hash__: based on Circular Stereo Algorithm [2]

Citations#

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

[1]

Maxim Papusha and Kai Leonhard. StereoMolGraph: stereochemistry-aware molecular and reaction graphs. J. Chem. Inf. Model., 2026. doi:10.1021/acs.jcim.5c02523.

[2]

Maxim Papusha and Kai Leonhard. Circular stereo algorithm and fingerprint for chiral resonance invariant molecular representations. ChemRxiv, 2026. doi:10.26434/chemrxiv.15002723/v1.

[3]

Maxim Papusha, Andreas Victor Copan, Brandon Rotavera, and Kai Leonhard. Symmetry numbers: a flexible approach for molecules and transition states. ChemRxiv, 2026. submitted.