polymerist.mdtools.openmmtools.reporters
========================================

.. py:module:: polymerist.mdtools.openmmtools.reporters

.. autoapi-nested-parse::

   Utilities for handlling setup of Simulation Reporters



Attributes
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.reporters.LOGGER
   polymerist.mdtools.openmmtools.reporters.TrajectoryReporter
   polymerist.mdtools.openmmtools.reporters.Reporter
   polymerist.mdtools.openmmtools.reporters.ReporterInitializer
   polymerist.mdtools.openmmtools.reporters.TRAJ_REPORTERS
   polymerist.mdtools.openmmtools.reporters.CHK_REPORTERS
   polymerist.mdtools.openmmtools.reporters.STATE_DAT_REPORTERS
   polymerist.mdtools.openmmtools.reporters.DEFAULT_STATE_DATA_PROPS


Classes
-------

.. autoapisummary::

   polymerist.mdtools.openmmtools.reporters.StateReporter
   polymerist.mdtools.openmmtools.reporters.ReporterConfig
   polymerist.mdtools.openmmtools.reporters.ReporterParameters


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

.. py:data:: LOGGER

.. py:class:: StateReporter(file, reportInterval)

   Bases: :py:obj:`openmm.app.CheckpointReporter`


   CheckpointReporter which is forced to report States; greatly simplifies interface, documentation, and logging


.. py:type:: TrajectoryReporter
   :canonical: Union[PDBReporter, PDBxReporter, DCDReporter]


.. py:type:: Reporter
   :canonical: Union[CheckpointReporter, StateReporter, StateDataReporter, TrajectoryReporter]


.. py:type:: ReporterInitializer
   :canonical: Callable[..., Reporter]


.. py:class:: ReporterConfig

   Interface for generating a Reporter and associated Path in a uniform and standardized way


   .. py:attribute:: label
      :type:  str


   .. py:attribute:: extension
      :type:  str


   .. py:attribute:: reporter_dict
      :type:  dict[str, ReporterInitializer]


   .. py:attribute:: extra_kwargs
      :type:  dict[str, Any]


   .. py:property:: initializer
      :type: ReporterInitializer


      Returns the particular class or initializer


.. py:data:: TRAJ_REPORTERS

.. py:data:: CHK_REPORTERS

.. py:data:: STATE_DAT_REPORTERS

.. py:data:: DEFAULT_STATE_DATA_PROPS

.. py:class:: ReporterParameters

   Parameters for specifying Simulation reporters


   .. py:attribute:: report_checkpoint
      :type:  bool
      :value: True



   .. py:attribute:: report_state
      :type:  bool
      :value: True



   .. py:attribute:: report_trajectory
      :type:  bool
      :value: True



   .. py:attribute:: report_state_data
      :type:  bool
      :value: True



   .. py:attribute:: traj_ext
      :type:  Optional[str]
      :value: 'dcd'



   .. py:attribute:: num_steps
      :type:  Optional[int]
      :value: None



   .. py:attribute:: state_data
      :type:  Optional[dict[str, bool]]


   .. py:attribute:: reporter_paths
      :type:  Optional[dict[str, pathlib.Path]]
      :value: None



   .. py:property:: rep_configs
      :type: list[ReporterConfig]


      Generate Reporter configurations for currently specified reporters


   .. py:method:: init_reporter_paths(out_dir: pathlib.Path, prefix: str) -> None

      Generate paths for all configured and enabled reporters



   .. py:method:: prepare_reporters(report_interval: int) -> list[Reporter]

      Prepare all reporters specified by internal parameters and return Paths linked to said reporters