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: 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/how_to_guides/charge_molecules_cli.rst b/docs/how_to_guides/charge_molecules_cli.rst new file mode 100644 index 000000000..8a5c42bd1 --- /dev/null +++ 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 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/charge_molecules_cli_tutorial.rst b/docs/tutorials/charge_molecules_cli_tutorial.rst deleted file mode 100644 index bc16130aa..000000000 --- a/docs/tutorials/charge_molecules_cli_tutorial.rst +++ /dev/null @@ -1,4 +0,0 @@ -.. _charge_molecules_cli_tutorial: - -.. include:: /ExampleNotebooks/cli_tutorials/cli_charge_molecules.md - :parser: myst_parser.sphinx_ 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