gufe
====

**gufe** is the Open Free Energy (OpenFE) framework for defining object models used in alchemical free energy calculations.
It is intended for use by free energy method developers, and direct access by end-users should be avoided.

If you are looking to perform free energy calculations, see `openfe <https://docs.openfree.energy/>`_.

Resources
---------

* github repository: https://github.com/OpenFreeEnergy/gufe
* issue tracker: https://github.com/OpenFreeEnergy/gufe/issues
* OpenFE discussions board: https://github.com/OpenFreeEnergy/openfe/discussions

Related Projects
----------------

.. add links

Open Free Energy ecosystem tools that use **gufe**:

* `openfe <https://docs.openfree.energy/>`_: The OpenFE ecosystem's central toolkit for performing free energy calculations.
* `alchemiscale <https://alchemiscale.org/>`_: A distributed execution system for alchemical` networks.
* `lomap <https://lomap.openfree.energy/>`_: Atom mapping tools from the `Mobley Lab <https://mobleylab.org/>`_.
* `kartograf <https://kartograf.openfree.energy/>`_: Atom mapping tools focusing on 3D geometries.
* `konnektor <https://konnektor.openfree.energy/>`_: Network generation tools designed with alchemical networks in mind.
* `cinnabar <https://cinnabar.openfree.energy/>`_: Tools for the analysis of free energy network results.

.. do we want to add packages we depend on, like openff-units, rdkit, openmm?

Contents
--------

.. toctree::
   :maxdepth: 1

   installation
   concepts/index
   how-tos/index

Reference
---------
.. toctree::
   :maxdepth: 1

   api
   CHANGELOG

:ref:`genindex`