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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file stereomolgraph-0.0.19b0.tar.gz.
File metadata
- Download URL: stereomolgraph-0.0.19b0.tar.gz
- Upload date:
- Size: 55.5 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
69c1397724c806b28f8cb28707b668b097ff3e7b38b76a11db8a7f11b104860e
|
|
| MD5 |
f75e30514be13e6d1514643a029fd0f9
|
|
| BLAKE2b-256 |
b5a38d5aa8cbf05c8ed46a814e9f8db27f07c908b4d76a59d92f2d7b24f7dc78
|
File details
Details for the file stereomolgraph-0.0.19b0-py3-none-any.whl.
File metadata
- Download URL: stereomolgraph-0.0.19b0-py3-none-any.whl
- Upload date:
- Size: 66.1 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: uv/0.11.2 {"installer":{"name":"uv","version":"0.11.2","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
825f000df1d247461c0ad0ccac5dcbc8e5d56aabb06bc5e9c80ac4a4aa926c90
|
|
| MD5 |
2a8bd520ecfb1a27e8564417a2dc217a
|
|
| BLAKE2b-256 |
e38a13f1913bf4de58b50e251d3bfc17af50e55fc1e9e8ff025522b0256e5786
|
