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reorder tutorials and add links to cli tutorial

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Josh Horton
2025-02-11 13:41:11 +00:00
parent d6e20f216c
commit 0abc72d3ce
4 changed files with 25 additions and 9 deletions
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4
docs/guide/introduction.rst
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@@ -70,7 +70,9 @@ 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>`.
scheme can be configured using the :ref:`YAML settings <userguide_cli_yaml_interface>`. We also provide tooling to
generating the partial charges as a separate CLI step which can be run before network planning, see the :ref:`tutorial <charge_molecules_cli_tutorial>`
for more details.
For example, you can create a relative binding free energy (RBFE) network using

16
docs/tutorials/index.rst
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@@ -9,6 +9,12 @@ OpenFE has several tutorial notebooks which are maintained on our
Here is a list of key tutorials which cover the different aspects of the
OpenFE tooling:
Generating Partial Charges
--------------------------
The :ref:`Generating Partial Charges CLI tutorial <charge_molecules_cli_tutorial>` demonstrates
how the command line interface can be used to assign and store partial charges for small molecules which
can be used throughout the OpenFE eco-system.
Relative Free Energies
----------------------
@@ -61,22 +67,16 @@ 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.
Generating Partial Charges
--------------------------
The :any:`Generating Partial Charges CLI tutorial <charge_molecules_cli_tutorial>` demonstrates
how the command line interface can be used to assign and store partial charges for small molecules which
can be used throughout the OpenFE eco-system.
.. toctree::
:maxdepth: 1
:hidden:
charge_molecules_cli_tutorial
rbfe_cli_tutorial
rbfe_python_tutorial
showcase_notebook
md_tutorial
ahfe_tutorial
plotting_with_cinnabar
charge_molecules_cli_tutorial

7
openfecli/commands/plan_rbfe_network.py
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@@ -158,6 +158,13 @@ def plan_rbfe_network(
The generated Network will be stored in a folder containing for each
transformation a JSON file, that can be run with quickrun.
.. note::
To ensure a consistent set of partial charges are used for each molecule across different transformations, this
tool will automatically generate charges ahead of planning the network. ``am1bcc`` charges will be generated via
``ambertools``, this can also be customized using the settings yaml file.
By default, this tool makes the following choices:
* Atom mappings performed by LOMAP, with settings max3d=1.0 and

7
openfecli/commands/plan_rhfe_network.py
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@@ -122,6 +122,13 @@ def plan_rhfe_network(molecules: List[str], yaml_settings: str, output_dir: str,
to run the planned transformations with the quickrun tool. For more
sophisticated setups, please consider using the python layer of openfe.
.. note::
To ensure a consistent set of partial charges are used for each molecule across different transformations, this
tool will automatically generate charges ahead of planning the network. ``am1bcc`` charges will be generated via
``ambertools``, this can also be customized using the settings yaml file.
The tool will parse the input and run the rbfe network planner, which
executes following steps: