iphasimulator.workflows.md_benchmark
====================================

.. py:module:: iphasimulator.workflows.md_benchmark

.. autoapi-nested-parse::

   Batch MD benchmark workflow for PHA validation systems.



Attributes
----------

.. autoapisummary::

   iphasimulator.workflows.md_benchmark.SYSTEMS
   iphasimulator.workflows.md_benchmark.CHARGE_METHODS
   iphasimulator.workflows.md_benchmark.DEFAULT_REPO_ROOT


Classes
-------

.. autoapisummary::

   iphasimulator.workflows.md_benchmark.BenchmarkTarget


Functions
---------

.. autoapisummary::

   iphasimulator.workflows.md_benchmark.discover_targets
   iphasimulator.workflows.md_benchmark.selected_system_names
   iphasimulator.workflows.md_benchmark.run_benchmark
   iphasimulator.workflows.md_benchmark.parse_args
   iphasimulator.workflows.md_benchmark.main


Module Contents
---------------

.. py:data:: SYSTEMS
   :value: ('P3HB_4', 'P3HB_8', 'P3HO_4', 'P3HO_8', 'P3HDD_4', 'P3HDD_8')


.. py:data:: CHARGE_METHODS
   :value: ('abcg2', 'bcc', 'gas', 'mul')


.. py:data:: DEFAULT_REPO_ROOT

.. py:class:: BenchmarkTarget

   Input and output paths for one benchmark system.


   .. py:attribute:: name
      :type:  str


   .. py:attribute:: sdf_path
      :type:  pathlib.Path


   .. py:attribute:: output_dir
      :type:  pathlib.Path


   .. py:property:: gaff2_dir
      :type: pathlib.Path



   .. py:property:: prmtop_path
      :type: pathlib.Path



   .. py:property:: inpcrd_path
      :type: pathlib.Path



   .. py:property:: openmm_dir
      :type: pathlib.Path



   .. py:property:: gromacs_dir
      :type: pathlib.Path



.. py:function:: discover_targets(system_names: tuple[str, ...], *, repo_root: pathlib.Path = DEFAULT_REPO_ROOT) -> list[BenchmarkTarget]

.. py:function:: selected_system_names(args: argparse.Namespace) -> tuple[str, ...]

.. py:function:: run_benchmark(args: argparse.Namespace) -> int

.. py:function:: parse_args(argv: list[str] | None = None) -> argparse.Namespace

.. py:function:: main(argv: list[str] | None = None) -> None