From 13b29672ce351da1fc66650cc1b078d9b94638e9 Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Tue, 10 Nov 2026 12:17:22 +0100 Subject: [PATCH 1/5] Move partial charge CLI to how-to guides --- docs/guide/introduction.rst | 2 +- docs/guide/setup/index.rst | 1 + docs/guide/setup/input_preparation.rst | 4 ++-- .../charge_molecules_cli.rst} | 0 docs/how_to_guides/index.rst | 1 + docs/tutorials/index.rst | 8 -------- 6 files changed, 5 insertions(+), 11 deletions(-) rename docs/{tutorials/charge_molecules_cli_tutorial.rst => how_to_guides/charge_molecules_cli.rst} (100%) diff --git a/docs/guide/introduction.rst b/docs/guide/introduction.rst index 68c45c636..cc7dd4566 100644 --- 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 `. 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 ` + generate the partial charges as a separate CLI step which can be run before network planning, see the :ref:`how-to guide ` for more details. diff --git a/docs/guide/setup/index.rst b/docs/guide/setup/index.rst index 885c6d5f6..b72f4649a 100644 --- a/docs/guide/setup/index.rst +++ b/docs/guide/setup/index.rst @@ -49,6 +49,7 @@ See :ref:`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 index 48ab8dfba..fe68d8ddb 100644 --- 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 ` (Python API) or -:doc:`Generating Partial Charges with the OpenFE CLI `. +See Assigning partial charges :doc:`with the Python API ` or +:doc:`with the CLI `. .. rubric:: Binding poses diff --git a/docs/tutorials/charge_molecules_cli_tutorial.rst b/docs/how_to_guides/charge_molecules_cli.rst similarity index 100% rename from docs/tutorials/charge_molecules_cli_tutorial.rst rename to docs/how_to_guides/charge_molecules_cli.rst diff --git a/docs/how_to_guides/index.rst b/docs/how_to_guides/index.rst index 970218c62..28d6b5650 100644 --- 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 `. loading_molecules user_charges + charge_molecules_cli bespoke_parameters packmol_memgen_setup diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst index 7ff721342..8878f40e0 100644 --- a/docs/tutorials/index.rst +++ b/docs/tutorials/index.rst @@ -43,13 +43,6 @@ Post-Simulation Analysis - :any:`Cinnabar tutorial `: A tutorial for using the `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 `: 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 From 1ca0233ba1ba44006f05176b41439c8563804d3f Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Tue, 10 Nov 2026 12:19:49 +0100 Subject: [PATCH 2/5] temporarily point to notebooks branch --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 9a471e9a2..117a9c2cd 100644 --- 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", to_path=example_notebooks_path, ) except Exception as e: From 2139e2c66cdb844c2c4d8b68af85ba2251bdbf95 Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Tue, 10 Nov 2026 12:20:28 +0100 Subject: [PATCH 3/5] Fix link --- docs/how_to_guides/charge_molecules_cli.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/how_to_guides/charge_molecules_cli.rst b/docs/how_to_guides/charge_molecules_cli.rst index bc16130aa..dfc60d35e 100644 --- a/docs/how_to_guides/charge_molecules_cli.rst +++ b/docs/how_to_guides/charge_molecules_cli.rst @@ -1,4 +1,4 @@ .. _charge_molecules_cli_tutorial: -.. include:: /ExampleNotebooks/cli_tutorials/cli_charge_molecules.md +.. include:: /ExampleNotebooks/cookbooks/charge_molecules_cli.md :parser: myst_parser.sphinx_ From ee21caafe2a1bfb42d16c40c6ed49dd5a7b9cb08 Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Tue, 10 Nov 2026 13:17:07 +0100 Subject: [PATCH 4/5] Small fix --- docs/how_to_guides/charge_molecules_cli.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/how_to_guides/charge_molecules_cli.rst b/docs/how_to_guides/charge_molecules_cli.rst index dfc60d35e..6332648a1 100644 --- a/docs/how_to_guides/charge_molecules_cli.rst +++ b/docs/how_to_guides/charge_molecules_cli.rst @@ -1,4 +1,4 @@ -.. _charge_molecules_cli_tutorial: +.. _charge_molecules_cli: .. include:: /ExampleNotebooks/cookbooks/charge_molecules_cli.md :parser: myst_parser.sphinx_ From 69d3dbac6a2e95bdbb0d01dd17ddb3016708f034 Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Tue, 10 Nov 2026 13:20:06 +0100 Subject: [PATCH 5/5] Small fix2 --- docs/how_to_guides/charge_molecules_cli.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/how_to_guides/charge_molecules_cli.rst b/docs/how_to_guides/charge_molecules_cli.rst index 6332648a1..8a5c42bd1 100644 --- a/docs/how_to_guides/charge_molecules_cli.rst +++ b/docs/how_to_guides/charge_molecules_cli.rst @@ -1,4 +1,4 @@ .. _charge_molecules_cli: -.. include:: /ExampleNotebooks/cookbooks/charge_molecules_cli.md +.. include:: /ExampleNotebooks/cookbook/charge_molecules_cli.md :parser: myst_parser.sphinx_