cosmolkit 0.0.5

Python bindings for COSMolKit

Python Bindings

This directory hosts PyO3-based Python bindings for COSMolKit.

Use the repository-level Python environment:

• uv sync --group dev
• .venv/bin/python -m pip install -e python

Current layout:

• pyproject.toml package metadata for the published Python distribution
• Cargo.toml and src/lib.rs for the Rust extension module crate built with PyO3 + maturin
• no Python shim package; cosmolkit is provided directly by the compiled extension module

Current status:

• the package is still partial and not yet a full public API surface
• low-level bindings now expose:
  • placeholder(), rust_version(), and core_version()
  • Molecule.from_smiles(), Molecule.read_sdf(), atoms(), bonds(), and find_chiral_centers()
  • Molecule.tetrahedral_stereo() for the ordered-ligand tetrahedral stereo representation (spec: tetrahedral_stereo_representation.md)
• Molecule.ensure_conformer() and the higher-level 3D pipeline remain intentionally unimplemented on the COSMolKit side

Examples:

• python/examples/tetrahedral_stereo.py shows the internal tetrahedral stereo representation exposed to Python
• python/examples/io_and_properties.py and the other example files still describe the intended longer-term API shape

Local development:

• uv sync --group dev
• .venv/bin/python -m pip install -e python
• .venv/bin/python -c "import cosmolkit; print(cosmolkit.placeholder())"

Publishing:

• GitHub Actions workflow: .github/workflows/python-publish.yml
• expected PyPI secret: PYPI_API_TOKEN
• trigger: see the workflow file for the current tag/release policy