hannahbaumann · Nov 10, 2026 · Nov 10, 2026 · Nov 10, 2026 · Nov 10, 2026 · Nov 10, 2026
diff --git a/docs/conf.py b/docs/conf.py
@@ -195,7 +195,7 @@
     else:
         repo = git.Repo.clone_from(
             "https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
-            branch="main",
+            branch="move_cli_charge_howto",
-            branch="move_cli_charge_howto",
+            branch="main",
-            branch="move_cli_charge_howto",
+            branch="main",
             to_path=example_notebooks_path,
         )
 except Exception as e:

diff --git a/docs/guide/introduction.rst b/docs/guide/introduction.rst
@@ -202,7 +202,7 @@ The commands used to generate an :class:`.AlchemicalNetwork` using the CLI are:
    To ensure a consistent set of partial charges are used for each molecule across different transformations, the CLI
    network planners will now automatically generate charges ahead of planning the network. The partial charge generation
    scheme can be configured using the :ref:`YAML settings <userguide_cli_yaml_interface>`. We also provide tooling to
-   generate the partial charges as a separate CLI step which can be run before network planning, see the :ref:`tutorial <charge_molecules_cli_tutorial>`
+   generate the partial charges as a separate CLI step which can be run before network planning, see the :ref:`how-to guide <charge_molecules_cli>`
    for more details.
 
 

diff --git a/docs/guide/setup/index.rst b/docs/guide/setup/index.rst
@@ -49,6 +49,7 @@ See :ref:`dumping transformations <dumping_transformations>` for more details.
 
    * :doc:`/how_to_guides/loading_molecules`
    * :doc:`/how_to_guides/user_charges`
+   * :doc:`/how_to_guides/charge_molecules_cli`
    * :doc:`/how_to_guides/bespoke_parameters`
 
    **Planning: Ligand networks**

diff --git a/docs/guide/setup/input_preparation.rst b/docs/guide/setup/input_preparation.rst
@@ -180,8 +180,8 @@ results.
 
 Partial charges are assigned during protocol setup but can also
 be assigned in advance for reproducibility and to avoid repeated calculations.
-See :doc:`Assigning partial charges </how_to_guides/user_charges>` (Python API) or
-:doc:`Generating Partial Charges with the OpenFE CLI </tutorials/charge_molecules_cli_tutorial>`.
+See Assigning partial charges :doc:`with the Python API </how_to_guides/user_charges>` or
+:doc:`with the CLI </how_to_guides/charge_molecules_cli>`.
 
 .. rubric:: Binding poses
 

diff --git a/docs/how_to_guides/charge_molecules_cli.rst b/docs/how_to_guides/charge_molecules_cli.rst
@@ -0,0 +1,4 @@
+.. _charge_molecules_cli:
+
+.. include:: /ExampleNotebooks/cookbook/charge_molecules_cli.md
+   :parser: myst_parser.sphinx_
diff --git a/docs/how_to_guides/index.rst b/docs/how_to_guides/index.rst
@@ -15,6 +15,7 @@ For the concepts behind each step, see the :doc:`User Guide </guide/index>`.
 
    loading_molecules
    user_charges
+   charge_molecules_cli
    bespoke_parameters
    packmol_memgen_setup
 

diff --git a/docs/tutorials/charge_molecules_cli_tutorial.rst b/docs/tutorials/charge_molecules_cli_tutorial.rst
diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -43,13 +43,6 @@ Post-Simulation Analysis
 
 - :any:`Cinnabar tutorial <plotting_with_cinnabar>`: A tutorial for using the `cinnabar <https://github.com/OpenFreeEnergy/cinnabar>`_ Python package to analyze (e.g. generating MLE estimates of absolute free energies) and plot networks of relative free energy results.
 
-Generating Partial Charges
---------------------------
-
-.. todo: this should be in how_to_guides
-
--  :ref:`Generating Partial Charges CLI tutorial <charge_molecules_cli_tutorial>`: how to use the CLI to assign and store partial charges for mall molecules which can be used throughout the OpenFE ecosystem.
-
 .. toctree::
     :maxdepth: 1
     :hidden:
@@ -67,4 +60,3 @@ Generating Partial Charges
     plotting_with_cinnabar
     task_based_execution_cli
     task_based_execution_python_api
-    charge_molecules_cli_tutorial