polymerist.mdtools.openmmtools.serialization
============================================

.. py:module:: polymerist.mdtools.openmmtools.serialization

.. autoapi-nested-parse::

   For reading OpenMM components from files and writing OpenMM components to files



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/polymerist/mdtools/openmmtools/serialization/paths/index
   /autoapi/polymerist/mdtools/openmmtools/serialization/state/index
   /autoapi/polymerist/mdtools/openmmtools/serialization/system/index
   /autoapi/polymerist/mdtools/openmmtools/serialization/topology/index


Attributes
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.serialization.StateLike
   polymerist.mdtools.openmmtools.serialization.DEFAULT_STATE_PROPS


Classes
-------

.. autoapisummary::

   polymerist.mdtools.openmmtools.serialization.SimulationPaths


Functions
---------

.. autoapisummary::

   polymerist.mdtools.openmmtools.serialization.load_state_flexible
   polymerist.mdtools.openmmtools.serialization.serialize_state_from_context
   polymerist.mdtools.openmmtools.serialization.apply_state_to_context
   polymerist.mdtools.openmmtools.serialization.serialize_system
   polymerist.mdtools.openmmtools.serialization.serialize_openmm_pdb
   polymerist.mdtools.openmmtools.serialization.serialize_topology_from_simulation


Package Contents
----------------

.. py:class:: SimulationPaths

   Encapsulates Paths to various files associated with an OpenMM Simulation


   .. py:attribute:: parameters_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: paths_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: system_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: topology_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: state_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: checkpoint_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: trajectory_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: state_data_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: time_data_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:attribute:: spatial_data_path
      :type:  Optional[pathlib.Path]
      :value: None



   .. py:method:: init_top_and_sys_paths(out_dir: pathlib.Path, prefix: str, record: bool = True) -> tuple[pathlib.Path, pathlib.Path]

      Initialize Topology and System output paths for a given directory



   .. py:method:: from_dir_and_parameters(out_dir: pathlib.Path, prefix: str, sim_params: polymerist.mdtools.openmmtools.parameters.SimulationParameters, touch: bool = True) -> SimulationPaths
      :classmethod:


      Create file directory and initialize simulationPaths object from a set of SimulationParameters



.. py:data:: StateLike

.. py:data:: DEFAULT_STATE_PROPS
   :type:  dict[str, bool]

.. py:function:: load_state_flexible(state: Optional[StateLike] = None) -> Optional[openmm.State]

   Allows one to flexibly load an OpenMM state, either from a State object or file-like object


.. py:function:: serialize_state_from_context(state_path: pathlib.Path, context: openmm.Context, state_params: dict[str, bool] = None) -> None

   For saving State data within an existing OpenMM Context to file


.. py:function:: apply_state_to_context(context: openmm.Context, state: openmm.State) -> None

   For applying saved State data to an existing OpenMM Context


.. py:function:: serialize_system(sys_path: pathlib.Path, system: openmm.System) -> None

   For saving an existing OpenMM System to file


.. py:function:: serialize_openmm_pdb(pdb_path: pathlib.Path, topology: openmm.app.Topology, positions: Union[numpy.typing.NDArray, list[openmm.Vec3]], keep_chain_and_res_ids: bool = True, atom_labeller: Optional[polymerist.molfiles.pdb.SerialAtomLabeller] = None, resname_map: Optional[dict[str, str]] = None) -> None

   Configure and write an Protein DataBank File from an OpenMM Topology and array of positions
   Provides options to configure atom ID numbering, residue numbering, and residue naming


.. py:function:: serialize_topology_from_simulation(pdb_path: pathlib.Path, sim: openmm.app.Simulation, keep_ids: bool = False) -> None

   Saves a PDB of the current state of a simulation's Topology