Installation

MoleculeKit installs cleanly with pip or conda. We recommend creating an isolated environment regardless of the package manager you use.

With pip

pip install moleculekit

For an isolated environment, create one with venv, conda, or another tool first:

python -m venv .venv
source .venv/bin/activate
pip install moleculekit

With conda

Install Miniforge from conda-forge/miniforge, then:

conda create -n moleculekit
conda activate moleculekit
conda install moleculekit -c acellera -c conda-forge

Verify

from moleculekit.molecule import Molecule
mol = Molecule("3PTB")
print(mol.numAtoms)

Expected output: an integer count of atoms in PDB entry 3PTB.

For contributors: uv

If you are developing moleculekit (running the test suite, building docs, working from a checkout), uv is the recommended tool for managing the project environment:

uv sync --group dev      # install dev + test deps
uv sync --group docs     # add the doc-build deps
uv run pytest            # run the test suite

See the pyproject.toml [dependency-groups] table for the full list of optional dependency groups.