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Get existing tutorials rendering in Sphinx
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docs/tutorials/assets/RBFE_workflow.drawio.pdf
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docs/tutorials/assets/RBFE_workflow.drawio.pdf
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@@ -11,18 +11,24 @@ For new users, we recommend the following two:
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Relative Free Energies CLI tutorial
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-----------------------------------
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The `Relative Free Energies with the OpenFE CLI <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/rbfe_tutorial/cli_tutorial.md>`_
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The :any:`Relative Free Energies with the OpenFE CLI <rbfe_cli_tutorial>`
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tutorial walks users through how to use the OpenFE command line to calculate
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relative hydration free energies from a small set of benzene modifications.
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Associated with it is also a `notebook <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/rbfe_tutorial/python_tutorial.ipynb>`_
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Associated with it is also a :any:`notebook <rbfe_python_tutorial>`
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for how to achieve the same outcomes using the Python API.
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Python API Showcase
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-------------------
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Our `showcase notebook <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb>`_
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Our :any:`showcase notebook <showcase_notebook>`
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walks users through how to use the main components of OpenFE to create a
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relative binding free energy calculation.
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.. toctree::
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:maxdepth: 1
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rbfe_cli_tutorial
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rbfe_python_tutorial
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showcase_notebook
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2
docs/tutorials/rbfe_cli_tutorial.rst
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2
docs/tutorials/rbfe_cli_tutorial.rst
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.. include:: /ExampleNotebooks/rbfe_tutorial/cli_tutorial.md
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:parser: myst_parser.sphinx_
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3
docs/tutorials/rbfe_python_tutorial.nblink
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3
docs/tutorials/rbfe_python_tutorial.nblink
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{
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"path": "../ExampleNotebooks/rbfe_tutorial/python_tutorial.ipynb"
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}
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6
docs/tutorials/showcase_notebook.nblink
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docs/tutorials/showcase_notebook.nblink
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{
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"path": "../ExampleNotebooks/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb",
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"extra-media": [
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"../ExampleNotebooks/openmm_rbfe/assets"
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]
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}
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