mirror of
https://github.com/OpenFreeEnergy/openfe.git
synced 2026-06-05 23:04:24 +08:00
66ac2bdc64
* updates to cli from_json * replacing dump instances with to_json * Remove unnecessary imports of JSON_HANDLER * addressing review --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: David L. Dotson <dotsdl@gmail.com>
73 lines
2.8 KiB
ReStructuredText
73 lines
2.8 KiB
ReStructuredText
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``):
|
|
|
|
.. TODO autogenerate using sphinxcontrib-programoutput
|
|
|
|
.. code:: none
|
|
|
|
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
|
|
|
|
.. code:: none
|
|
|
|
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 :ref:`cli-reference`.
|