Physics-Constrained Cryo-Electron Microscopy Ensemble Optimizaiton

Description

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Installation

Before installing, use your prefered virtual environment manager to initialize a virtual env. We recommend uv, although any manager should work.

uv venv my-venv-name --python 3.11

Don't forget to activate your environment!

Most dependencies are installed automatically when you install the package. However, although OpenMM is a required dependency, it is not installed automatically as its installation might require specific steps. If you are not worried about the OpenMM installation, you can install it directly from PyPI using pip:

pip install openmm

OpenMM can also be installed using conda, or from source. For more information, see the OpenMM installation instructions.

Lastly, install cryoJAX Ensemble Optimization package by cloning this repo:

git clone [email protected]:DSilva27/cryojax-ensemble-optimization.git
cd cryojax_ensemble_optimization
pip install .

If you intent to use a GPU for JAX operations you might need to install a cuda supported version of JAX manually. We recommend following the official install JAX instructions.

Contributing

If you are contributing to this project please install the package with the following command

pip install -e ".[dev]"

This will install the required dependencies for development, the most important being Ruff and pre-commit. After installation activate your environment and install the pre-commit hooks by running

pre-commit install

Make sure that your code is formatted according to our guidelines by running:

pre-commit run --all-files

This will make sure the code is formatted correcly, fix whatever can be automatically fixed, and tell you if something else needs to be fixed.

Acknowledgements

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