Merge pull request #782 from OpenFreeEnergy/add-tutorials

Clean up tutorials
OpenFreeEnergy · Mar 28, 2024 · a9f05df · a9f05df
2 parents 0ca84d3 + 936f464
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diff --git a/docs/tutorials/ahfe_tutorial.nblink b/docs/tutorials/ahfe_tutorial.nblink
@@ -0,0 +1,6 @@
+{
+   "path": "../ExampleNotebooks/ahfe_tutorial/python_tutorial.ipynb",
+   "extra-media": [
+      "../ExampleNotebooks/ahfe_tutorial/ahfe_cycle.png"
+   ]
+}
diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -5,11 +5,23 @@ Tutorials
 
 OpenFE has several tutorial notebooks which are maintained on our
 `Example Notebooks repository <https://github.com/OpenFreeEnergy/ExampleNotebooks>`_.
-For new users, we recommend the following two:
 
+Here is a list of key tutorials which cover the different aspects of the
+OpenFE tooling:
+
+
+Relative Free Energies
+----------------------
+
+Python API Showcase
+~~~~~~~~~~~~~~~~~~~
+
+Our :any:`shocase notebook <showcase_notebook>` walks users through
+how to use the main Python API components of OpenFE to create a
+relative binding free energy calculation.
 
 Relative Free Energies CLI tutorial
------------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The :any:`Relative Free Energies with the OpenFE CLI <rbfe_cli_tutorial>`
 tutorial walks users through how to use the OpenFE command line to calculate
@@ -18,19 +30,37 @@ relative binding free energies of various ligands against the TYK2 target.
 Associated with it is also a :any:`notebook <rbfe_python_tutorial>`
 for how to achieve the same outcomes using the Python API.
 
-Python API Showcase
--------------------
 
-Our :any:`showcase notebook <showcase_notebook>`
-walks users through how to use the main components of OpenFE to create a
-relative binding free energy calculation.
+Absolute Free Energies
+----------------------
 
-Molecular Dynamics (MD) protocol tutorial
------------------------------------------
+Absolute Solvation Free Energies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The :any:`Absolute Solvation Free Energy Protocol <ahfe_tutorial>` tutorial
+walks users through how to calculate the hydration free energy of a benzene
+ligand.
+
+
+Molecular Dynamics (MD)
+-----------------------
 
 The :any:`MD protocol <md_tutorial>`
-tutorial walks users through how to run an MD simulation of benzene bound to 
-T4-lysozyme L99A in OpenFE.
+tutorial walks users through how to run a conventional (non-alchemical) MD
+simulation of benzene bound to T4-lysozyme L99A in OpenFE.
+
+
+Post Simulation Analysis
+------------------------
+
+Analyzing and Plotting RFE Networks with Cinnabar
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The :any:`Cinnabar tutorial <plotting_with_cinnabar>` demonstrates how to
+use the `Cinnabar Python package <https://github.com/OpenFreeEnergy/cinnabar>`_
+to analyze (e.g. generating MLE estimates of absolute free energies)
+and plot networks of relative free energy results.
+
 
 .. toctree::
     :maxdepth: 1
@@ -40,3 +70,5 @@ T4-lysozyme L99A in OpenFE.
     rbfe_python_tutorial
     showcase_notebook
     md_tutorial
+    ahfe_tutorial
+    plotting_with_cinnabar
diff --git a/docs/tutorials/plotting_with_cinnabar.nblink b/docs/tutorials/plotting_with_cinnabar.nblink
@@ -0,0 +1,3 @@
+{
+   "path": "../ExampleNotebooks/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb"
+}