StereoMolGraph 0.0.0b15

A graph library for chiral molecules, reactions and transition states

StereoMolGraph

StereoMolGraph (SMG) is a lightweight Python library for representing molecules and transition states with explicit, local 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 approximate hashing via Weisfeiler–Lehman color refinement
• 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 on the connectivity and stereochemistry.
• Stereochemistry describes relative spatial arrangement. No absolute stereochemistry.
• Transparent: Simple 2D visualization in IPython notebooks

Examples

Explore the working example notebooks in docs/examples/ (executed in CI). For rendered examples and guides, see the documentation: https://stereomolgraph.readthedocs.io

RDKit interoperability notes

• Hydrogens must be explicit for stereo-safe 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 and feature requests are welcome — please open an issue on GitHub:

• Issues: https://github.com/maxim-papusha/StereoMolGraph/issues

If you have questions or ideas that don’t fit a template, you can still open an issue and tag it appropriately.

Citation

If you use StereoMolGraph in your work, please cite the Zenodo record:

License

MIT License — see LICENSE.