A graph library for chiral molecules, reactions and transition states
Project description
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 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 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 are welcome — please open an issue on GitHub. Technical questions and feature requests can be added as discussions.
Issues:
Discussions:
- Q&A: https://github.com/maxim-papusha/StereoMolGraph/discussions/new?category=q-a
- Ideas: https://github.com/maxim-papusha/StereoMolGraph/discussions/new?category=ideas
Citation
If you use StereoMolGraph in your work, please cite the corresponding paper:
License
MIT License — see LICENSE.
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