mythos.simulators.io
====================

.. py:module:: mythos.simulators.io

.. autoapi-nested-parse::

   Common data structures for simulator I/O.



Classes
-------

.. autoapisummary::

   mythos.simulators.io.SimulatorTrajectory


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

.. py:class:: SimulatorTrajectory

   A trajectory of a simulation run.


   .. py:attribute:: rigid_body
      :type:  jax_md.rigid_body.RigidBody


   .. py:attribute:: metadata
      :type:  jax.numpy.ndarray | None
      :value: None



   .. py:method:: __post_init__() -> None


   .. py:method:: with_state_metadata(metadata: Any) -> SimulatorTrajectory

      Set the same metadata for all states in the trajectory.



   .. py:method:: filter(filter_fn: collections.abc.Callable[[Any], bool]) -> SimulatorTrajectory

      Filter the trajectory based on metadata.

      :param filter_fn: A function that takes in metadata and returns a boolean
                        indicating whether to keep the state.

      :returns: A new SimulatorTrajectory with only the states that pass the filter.



   .. py:method:: slice(key: int | slice | jax.numpy.ndarray | list) -> SimulatorTrajectory

      Slice the trajectory.



   .. py:method:: length() -> int

      Return the length of the trajectory.

      Note, that this may have been more natural to implement as the built-in
      __len__ method. However, the chex.dataclass decorator overrides that
      method to be compatabile with the abc.Mapping interface

      See here:
      https://github.com/google-deepmind/chex/blob/8af2c9e8a19f3a57d9bd283c2a34148aef952f60/chex/_src/dataclass.py#L50



   .. py:method:: __add__(other: SimulatorTrajectory) -> SimulatorTrajectory

      Concatenate two trajectories.



   .. py:method:: to_file(filepath: pathlib.Path, box_size: mythos.utils.types.Vector3D = (0, 0, 0)) -> None

      Write the trajectory to an oxDNA file.

      Note that the SimulatorTrajectory does not store several of the fields
      necessary to fully reconstruct an oxDNA trajectory file (e.g. times, box
      size, velocities, angular momenta, and energies). Thus, times are filled
      with a monotonic sequence, while the rest of these fields are filled
      with 0's. The resultant file can be used for inspection and
      visualization of non-time-dependent state-by-state spatial information
      only.

      :param filepath: The path to write the trajectory file to.
      :param box_size: The box size in 3 dimensions to write to the file. defaults to (0,0,0).