Electronic Notebook: From Intermolecular Poses to Thermodynamics using Subdivided Spheres

This notebook contains supplementary data and workflows for the above article published in ACS Journal of Physical Chemistry B, 2026.

Contents

Subdirectory	Notebook	Description
area_fluctuations/	stddev.ipynb	Standard deviation of pose-cluster weights for N = 0..10.
b2_vs_temperature/	plotting.ipynb	Reduced B₂/B₂ʰˢ of patchy particle P¹₈ vs temperature and ionic strength (fixed and T-dep. dielectric).
mc-vs-duello/	plot.ipynb	Faunus Monte Carlo PMF compared with Duello PMF for the CPPM (P18) model.
pca_free_energy/	pca_analysis.ipynb	PCA of Duello trajectories of Cgn under three Calvados3 variants, with experimental PDB refs.
protein_b2/	plot.ipynb	B₂ for lysozyme and Cgn at pH 7 across three Calvados variants vs experimental B₂.

Reproducing the environment

Dependencies are managed with uv. To recreate the exact environment used for the notebooks:

uv sync
uv run jupyter lab

uv sync reads pyproject.toml and uv.lock and installs the pinned versions into a local .venv.

Linting and formatting

Ruff is included as a dev dependency:

uv run ruff check     # lint notebooks and .py scripts
uv run ruff format    # format notebooks and .py scripts