OpenFreeEnergy · richardjgowers · Aug 30, 2023 · Aug 22, 2023 · Aug 22, 2023 · Aug 22, 2023
diff --git a/docs/conf.py b/docs/conf.py
@@ -45,6 +45,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.autosummary",
     "docs._ext.sass",
+    "sphinx.ext.mathjax",
 ]
 
 intersphinx_mapping = {
@@ -70,7 +71,9 @@
 autodoc_default_options = {
     "members": True,
     "member-order": "bysource",
-    "inherited-members": "GufeTokenizable,BaseModel"
+    "inherited-members": "GufeTokenizable,BaseModel",
+    "undoc-members": True,
+    "special-members": "__call__",
 }
 toc_object_entries_show_parents = "hide"
 

diff --git a/docs/cookbook/index.rst b/docs/cookbook/index.rst
@@ -60,7 +60,7 @@ The typical way to use the Python API is to load a number of molecules you want
                             Atom mappings from another tool.
 
                             .. rst-class:: arrow-down
-                        -
+                        - :any:`Ligand Network Loaders`
 
                     -   -
                             .. rst-class:: flowchart-spacer
@@ -70,7 +70,7 @@ The typical way to use the Python API is to load a number of molecules you want
                             Hand-write an atom mapping.
 
                             .. rst-class:: arrow-down
-                        -
+                        - :any:`Ligand Network Loaders`
 
                 - :class:`LigandNetwork`
                     A network of ligand transformations.

diff --git a/docs/reference/api/alchemical_data_objects.rst b/docs/reference/api/alchemical_data_objects.rst
diff --git a/docs/reference/api/alchemical_network_planning.rst b/docs/reference/api/alchemical_network_planning.rst
@@ -1,35 +1,41 @@
 .. _Alchemical Network Planning:
 
-Alchemical Network Planning
-===========================
+Simulation Campaign Planning
+============================
 
-Alchemical network planners are objects that pull all the ideas in OpenFE
-into a quick setup for simulation. The goal is to create the
-:class:`.AlchemicalNetwork` that represents an entire simulation campaign,
-starting from a bare amount of user input. This also requries several helper
-classes along the way.
+While a :class:`LigandNetwork` describes a network of ligands and their atom
+mappings, a :class:`AlchemicalNetwork` describes a single replicate of a
+simulation campaign. It includes all the information needed to perform the
+simulation, and so implicitly includes the :class:`LigandNetwork`.
 
-Alchemical Network Planners
----------------------------
+Alchemical Simulations
+~~~~~~~~~~~~~~~~~~~~~~
 
-.. module:: openfe.setup
-   :noindex:
+Descriptions of anticipated alchemical simulation campaigns.
+
+.. module:: openfe
+    :noindex:
 
 .. autosummary::
     :nosignatures:
     :toctree: generated/
 
-    RBFEAlchemicalNetworkPlanner
-    RHFEAlchemicalNetworkPlanner
-
+    Transformation
+    AlchemicalNetwork
 
-Chemical System Generators
---------------------------
+Alchemical Network Planners
+---------------------------
+Alchemical network planners are objects that pull all the ideas in OpenFE
+into a quick setup for simulation. The goal is to create the
+:class:`.AlchemicalNetwork` that represents an entire simulation campaign,
+starting from a bare amount of user input.
 
-.. module:: openfe.setup.chemicalsystem_generator
+.. module:: openfe.setup
+    :noindex:
 
 .. autosummary::
     :nosignatures:
     :toctree: generated/
 
-    EasyChemicalSystemGenerator
+    RBFEAlchemicalNetworkPlanner
+    RHFEAlchemicalNetworkPlanner
diff --git a/docs/reference/api/data.rst b/docs/reference/api/data.rst
@@ -0,0 +1,13 @@
+Data Objects and Serialization
+==============================
+
+.. module:: gufe.tokenization
+
+Almost every OpenFE data object inherits from :class:`GufeTokenizable`, which
+enforces immutability and provides functions for data serialization.
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+    GufeTokenizable
diff --git a/docs/reference/api/defining_and_executing_simulations.rst b/docs/reference/api/defining_and_executing_simulations.rst
@@ -7,41 +7,41 @@ Executing Simulations
 ---------------------
 
 .. module:: openfe
-   :noindex:
+    :noindex:
 
 .. autosummary::
-   :nosignatures:
-   :toctree: generated/
+    :nosignatures:
+    :toctree: generated/
 
-   execute_DAG
+    execute_DAG
 
 General classes
 ---------------
 
 .. module:: openfe
-   :noindex:
+    :noindex:
 
 .. autosummary::
-   :nosignatures:
-   :toctree: generated/
+    :nosignatures:
+    :toctree: generated/
 
-   ProtocolDAG
-   ProtocolUnitResult
-   ProtocolUnitFailure
-   ProtocolDAGResult
+    ProtocolDAG
+    ProtocolUnitResult
+    ProtocolUnitFailure
+    ProtocolDAGResult
 
 Specialised classes
 -------------------
 
 These classes are abstract classes that are specialised (subclassed) for an individual Protocol.
 
 .. module:: openfe
-   :noindex:
+    :noindex:
 
 .. autosummary::
-   :nosignatures:
-   :toctree: generated/
+    :nosignatures:
+    :toctree: generated/
 
-   Protocol
-   ProtocolUnit
-   ProtocolResult
+    Protocol
+    ProtocolUnit
+    ProtocolResult
diff --git a/docs/reference/api/index.rst b/docs/reference/api/index.rst
@@ -6,7 +6,8 @@ OpenFE API Reference
 .. toctree::
     :maxdepth: 2
 
-    alchemical_data_objects
+    data
+    systems_and_components
     ligand_network
     alchemical_network_planning
     defining_and_executing_simulations