StereoMolGraph: Stereochemistry-Aware Molecular and Reaction Graphs

Conventional molecular graphs are often unable to reliably
encode
stereochemistry, especially for symmetric molecules, nontetrahedral
centers, and transition states. To overcome this, we present StereoMolGraph,
an open-source Python library implementing a stereochemistry-aware
graph representation for molecules and condensed graphs of reactions.
Our method uses permutation-invariant local stereodescriptors, grounded
in group theory, to provide an extensible representation of chirality.
Based on this we introduce methods allowing for robust comparison
of stereoisomers, including the identification of enantiomerism and
diastereomerism, and support fleeting stereochemistry in transition
states. We demonstrate the library’s utility for complex organic
molecules and metal complexes and analysis of distinct chiral reaction
pathways. With RDKit interoperability and visualization features,
StereoMolGraph offers a practical and transparent tool for advanced
stereochemically aware chemoinformatics workflows.