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* make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language
104 lines
3.5 KiB
ReStructuredText
104 lines
3.5 KiB
ReStructuredText
.. template taken from SciPy who took it from Pandas (keep the chain going)
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.. module:: openfe
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=====================================
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Welcome to OpenFE's documentation!
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=====================================
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The **OpenFE** toolkit provides a free and open-source framework for alchemical free energy calculations.
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Using this toolkit you can plan, execute, and analyze free energy calculations using a variety of methods.
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**Useful Links**:
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`OpenFE Website <https://openfree.energy/>`__ |
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`Example Tutorial notebooks <https://github.com/OpenFreeEnergy/ExampleNotebooks/>`__ |
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`Source Repository <https://github.com/OpenFreeEnergy/openfe/>`__ |
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`Issues & Ideas <https://github.com/OpenFreeEnergy/openfe/issues/>`__
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.. grid:: 1 2 2 4
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:gutter: 3
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.. grid-item-card:: :fas:`download` Install openfe
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:text-align: center
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:link: installation
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:link-type: doc
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Follow our installation guide to get **openfe** running on your machine!
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.. grid-item-card:: :fas:`laptop-code` CLI Quickstart
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:text-align: center
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:link: tutorials/rbfe_cli_tutorial
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:link-type: doc
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Get started with **openfe**\'s command line interface.
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.. grid-item-card:: :fas:`person-chalkboard` Tutorials
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:text-align: center
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:link: tutorials/index
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:link-type: doc
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Step-by-step examples showing how to use the OpenFE toolkit.
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.. grid-item-card:: :fas:`book-open-reader` User Guide
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:text-align: center
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:link: guide/index
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:link-type: doc
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Explanations of key concept underlying the OpenFE toolkit.
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.. grid-item-card:: :fas:`table-list` Cookbooks
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:text-align: center
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:link: cookbook/index
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:link-type: doc
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How-to guides for common tasks.
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.. grid-item-card:: :fas:`code` API Reference
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:text-align: center
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:link: reference/index
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:link-type: doc
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Comprehensive details of the **openfe** Python and CLI APIs.
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.. grid-item-card:: :fas:`gears` Protocols
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:text-align: center
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:link: guide/protocols/index
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:link-type: doc
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Details of the specific Free Energy Protocols included in **openfe**.
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.. grid-item-card:: :fas:`clock-rotate-left` Changelog
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:text-align: center
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:link: CHANGELOG
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:link-type: doc
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A history of **openfe** releases.
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.. toctree::
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:maxdepth: 2
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:hidden:
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installation
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tutorials/index
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guide/index
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cookbook/index
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reference/index
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CHANGELOG
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Other OpenFE Ecosystem Projects:
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--------------------------------
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**openfe** is Open Free Energy's user-facing software for performing alchemical free energy calculations.
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Below are other software projects the Open Free Energy team maintains, many of which are used by **openfe** itself.
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* `konnektor <https://github.com/OpenFreeEnergy/konnektor/>`_: free energy network planning, modification, and analysis
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* `kartograf <https://github.com/OpenFreeEnergy/kartograf/>`_: atom mappings focusing on 3D geometries
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* `Lomap <https://github.com/OpenFreeEnergy/Lomap/>`_: planning perturbation networks for free energy calculations
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* `cinnabar <https://github.com/OpenFreeEnergy/cinnabar/>`_ (formerly arsenic): plotting free energy calculation results
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* `gufe <https://gufe.openfree.energy/en/latest/>`_ : data structures and models underlying the OpenFE ecosystem
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Community-Developed Projects:
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-----------------------------
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* `alchemiscale <https://docs.alchemiscale.org/en/stable/>`_: high-throughput alchemical free energy execution, developed by `Datryllic <https://datryllic.com/>`_.
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