pyFRESEAN

Latest release
Status
Community

A Python package for FRESEAN based analysis

pyFRESEAN is bound by a Code of Conduct.

Quick start

import MDAnalysis as mda
from pyfresean import FRESEAN, Align, Unwrap

u = mda.Universe("topol.tpr", "traj.trr")
sel = u.select_atoms("all")
u_ref = mda.Universe("min.xyz")

# optional preprocessing (standard MDA trajectory transforms)
u.trajectory.add_transformations(
    Unwrap(u.atoms),
    Align(
        sel,
        reference_positions=u_ref.atoms.positions,
        place_com_in_box=False,  # gas phase
    ),
)

analysis = FRESEAN(
    u,
    select="all",
    n_constraints=6,
    n_corr=500,
    dt=0.004,
    sigma=10.0,
)
analysis.run()

print(analysis.results.freqs)
print(analysis.results.eigenvalues)
print(analysis.results.vdos_total)

See also the minimal notebooks in examples/.

Tests

pip install -e ".[test]"
pytest                    # unit tests (default)
pytest -m pytutorial_ref   # vs Python tutorial reference (~90 s; may download trajectory)
pytest -m c_ref           # vs FRESEAN COARSE (C) reference

Reference data:

• pyfresean/tests/data/fresean_pytutorial_ref/ — Python tutorial comparisons
• pyfresean/tests/data/fresean_c_ref/ — FRESEAN COARSE (C) comparisons

On CI, every pull request runs unit tests plus all pytutorial_ref and c_ref regressions. Download the c-ref-plots-* artifact from the workflow run (Actions tab) for eigenvalue and VDoS PNG comparisons.

Installation

To build pyFRESEAN from source, we highly recommend using virtual environments. If possible, we strongly recommend that you use Anaconda as your package manager. Below we provide instructions both for conda and for pip.

With conda

Ensure that you have conda installed.

Create a virtual environment and activate it:

conda create --name pyfresean
conda activate pyfresean

Install the development and documentation dependencies:

conda env update --name pyfresean --file devtools/conda-envs/test_env.yaml
conda env update --name pyfresean --file docs/requirements.yaml

Build this package from source:

pip install -e .

If you want to update your dependencies (which can be risky!), run:

conda update --all

And when you are finished, you can exit the virtual environment with:

conda deactivate

With pip

To build the package from source, run:

pip install .

If you want to create a development environment, install the dependencies required for tests and docs with:

pip install ".[test,doc]"

Copyright

The pyFRESEAN source code is hosted at https://github.com/HeydenLabASU-collab/pyFRESEAN and is available under the MIT License (see the file LICENSE).

Copyright (c) 2026, Amruthesh Thirumalaiswamy

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using pyFRESEAN in published work.