diff --git a/docs/guide/introduction.rst b/docs/guide/introduction.rst index 5432a1fa..f038ee45 100644 --- a/docs/guide/introduction.rst +++ b/docs/guide/introduction.rst @@ -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 `. + scheme can be configured using the :ref:`YAML settings `. 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 ` + for more details. For example, you can create a relative binding free energy (RBFE) network using diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst index 051e0b27..81037364 100644 --- a/docs/tutorials/index.rst +++ b/docs/tutorials/index.rst @@ -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 ` 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 `_ 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 ` 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 diff --git a/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py index 37354c05..4ff729b8 100644 --- a/openfecli/commands/plan_rbfe_network.py +++ b/openfecli/commands/plan_rbfe_network.py @@ -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 diff --git a/openfecli/commands/plan_rhfe_network.py b/openfecli/commands/plan_rhfe_network.py index 254343ad..41d92756 100644 --- a/openfecli/commands/plan_rhfe_network.py +++ b/openfecli/commands/plan_rhfe_network.py @@ -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: