CLI basics

The openfe command consists of several subcommands. This is similar to tools like gmx, which has subcommands like gmx mdrun, or conda, which has subcommands like conda install.

To get a list of the subcommands and their descriptions, call openfe (or openfe -h):

Usage: openfe [OPTIONS] COMMAND [ARGS]...

  This is the command line tool to provide easy access to functionality from
  the OpenFE Python library.

Options:
  --version   Show the version and exit.
  --log PATH  logging configuration file
  -h, --help  Show this message and exit.

Network Planning Commands:
  view-ligand-network  Visualize a ligand network
  plan-rbfe-network    Plan a relative binding free energy network, saved as
                       JSON files for the quickrun command.
  plan-rhfe-network    Plan a relative hydration free energy network, saved as
                       JSON files for the quickrun command.

Quickrun Executor Commands:
  gather    Gather result jsons for network of RFE results into a TSV file
  quickrun  Run a given transformation, saved as a JSON file

Miscellaneous Commands:
  fetch  Fetch tutorial or other resource.
  charge-molecules  Generate partial charges for a set of molecules.
  test   Run the OpenFE test suite

The --log option takes a logging configuration file and sets that logging behavior. If you use it, it must come before the subcommand name.

You can find out more about each subcommand by putting --help after the subcommand name, e.g., openfe quickrun --help, which returns

Usage: openfe quickrun [OPTIONS] TRANSFORMATION

  Run the transformation (edge) in the given JSON file.

  Simulation JSON files can be created with the :ref:`cli_plan-rbfe-network`
  or from Python a :class:`.Transformation` can be saved using its ``to_json``
  method::

      transformation.to_json("filename.json")

  That will save a JSON file suitable to be input for this command.

  Running this command will execute the simulation defined in the JSON file,
  creating a directory for each individual task (``Unit``) in the workflow.
  For example, when running the OpenMM HREX Protocol a directory will be
  created for each repeat of the sampling process (by default 3).

Options:
  -d, --work-dir DIRECTORY  directory to store files in (defaults to current
                            directory)
  -o FILE                   output file (JSON format) for the final results
  -h, --help                Show this message and exit.

For more details on various commands, see the CLI Reference.