.. template taken from SciPy who took it from Pandas (keep the chain going)

.. module:: openfe

OpenFE Documentation
~~~~~~~~~~~~~~~~~~~~
The **OpenFE** ecosystem is a free and open-source framework for planning, running, and analyzing alchemical free energy calculations.

.. grid:: 1 3 3 3
    :gutter: 3

    .. grid-item-card:: :fas:`rocket` Get Started
        :text-align: center
        :link: tutorials/rbfe_cli_tutorial
        :link-type: doc

        Run a free energy calculation with our CLI tutorial.


    .. grid-item-card:: :fas:`gears` Protocols
        :text-align: center
        :link: guide/protocols/index
        :link-type: doc

        Free Energy Protocols available in **openfe**.

    .. grid-item-card:: :fas:`circle-question` Troubleshooting
        :text-align: center
        :link: guide/troubleshooting
        :link-type: doc

        FAQs and troubleshooting guide.


.. toctree::
   :maxdepth: 2
   :hidden:

   installation
   guide/index
   tutorials/index
   cookbook/index
   reference/index
   CHANGELOG


**Useful Links**:
`OpenFE Website <https://openfree.energy/>`__ |
`Example Notebooks Repo <https://github.com/OpenFreeEnergy/ExampleNotebooks/>`__ |
`Source Repo <https://github.com/OpenFreeEnergy/openfe/>`__ |
`Issue Board <https://github.com/OpenFreeEnergy/openfe/issues/>`__


OpenFE Ecosystem Projects:
^^^^^^^^^^^^^^^^^^^^^^^^^^

**openfe** is Open Free Energy's user-facing software for performing alchemical free energy calculations.
Below are other software projects the Open Free Energy team maintains, many of which are used by **openfe** itself.

* `konnektor <https://github.com/OpenFreeEnergy/konnektor/>`_: free energy network planning, modification, and analysis
* `kartograf <https://github.com/OpenFreeEnergy/kartograf/>`_: atom mappings focusing on 3D geometries
* `Lomap <https://github.com/OpenFreeEnergy/Lomap/>`_: planning perturbation networks for free energy calculations
* `cinnabar <https://github.com/OpenFreeEnergy/cinnabar/>`_ (formerly arsenic): plotting free energy calculation results
* `gufe <https://gufe.openfree.energy/en/latest/>`_ : data structures and models underlying the OpenFE ecosystem

Community-Developed Projects:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

* `alchemiscale <https://docs.alchemiscale.org/en/stable/>`_: high-throughput alchemical free energy execution, developed by `Datryllic <https://datryllic.com/>`_.
* `feflow <https://github.com/OpenFreeEnergy/feflow>`_: Protocols and tooling based on openmmtools/perses and OpenFE, including a nonequilibrium cycling protocol with support for protein mutations.

Ecosystem Rules and Guidelines:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

* `Code of Conduct <https://github.com/OpenFreeEnergy/openfe/?tab=coc-ov-file>`_
* `Contributing Guide <https://github.com/OpenFreeEnergy/openfe/?tab=contributing-ov-file>`_