Installation

Conda environment

Install Rust first — the build is driven by maturin, which compiles the Rust geometry kernel (phenoms.phenoms_hbond_rs) into the same wheel as the Python package.

conda env create -f environment.yml
conda activate phenoms
pip install -e .

The editable install builds the Rust extension and registers the phenoms CLI entry point in one step. Detection uses the Rust geometry kernel when it’s built; Polars speeds occupancy aggregation only (not the Baker–Hubbard kernel itself). Without a Rust toolchain at install time, PHENOMS falls back to MDTraj for detection.

For local iteration on the Rust source, maturin develop --release from the repo root rebuilds just the extension without reinstalling dependencies.

Using uv

uv venv
source .venv/bin/activate
uv pip install -e .

Optional extras

pip install -e ".[gromacs]"     # MDAnalysis to read GROMACS .tpr topologies
pip install -e ".[benchmark]"   # MDAnalysis for kernel benchmarks

BioPython (PDB B-factor writes via phenoms.write_pdb_bfactors()) is a core dependency and needs no extra.

Verify

python -c "import phenoms; print(phenoms.__version__)"
phenoms --help