jax_dna.simulators.oxdna
========================

.. py:module:: jax_dna.simulators.oxdna

.. autoapi-nested-parse::

   oxDNA simulator module.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/jax_dna/simulators/oxdna/oxdna/index
   /autoapi/jax_dna/simulators/oxdna/utils/index


Attributes
----------

.. autoapisummary::

   jax_dna.simulators.oxdna.BIN_PATH_ENV_VAR
   jax_dna.simulators.oxdna.BUILD_PATH_ENV_VAR
   jax_dna.simulators.oxdna.CMAKE_BIN_ENV_VAR
   jax_dna.simulators.oxdna.ERR_BIN_PATH_NOT_SET
   jax_dna.simulators.oxdna.ERR_BUILD_PATH_NOT_SET
   jax_dna.simulators.oxdna.ERR_BUILD_SETUP_FAILED
   jax_dna.simulators.oxdna.ERR_INPUT_FILE_NOT_FOUND
   jax_dna.simulators.oxdna.ERR_MISSING_REQUIRED_KEYS
   jax_dna.simulators.oxdna.MAKE_BIN_ENV_VAR


Classes
-------

.. autoapisummary::

   jax_dna.simulators.oxdna.oxDNABinarySemaphore
   jax_dna.simulators.oxdna.oxDNABinarySemaphoreActor
   jax_dna.simulators.oxdna.oxDNASimulator


Functions
---------

.. autoapisummary::

   jax_dna.simulators.oxdna._guess_binary_location


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

.. py:data:: BIN_PATH_ENV_VAR
   :value: 'OXDNA_BIN_PATH'


.. py:data:: BUILD_PATH_ENV_VAR
   :value: 'OXDNA_BUILD_PATH'


.. py:data:: CMAKE_BIN_ENV_VAR
   :value: 'CMAKE_BIN_PATH'


.. py:data:: ERR_BIN_PATH_NOT_SET
   :value: 'OXDNA_BIN_PATH environment variable not set'


.. py:data:: ERR_BUILD_PATH_NOT_SET
   :value: 'OXDNA_BUILD_PATH environment variable not set'


.. py:data:: ERR_BUILD_SETUP_FAILED
   :value: 'OXDNA build setup failed wiht return code: {}'


.. py:data:: ERR_INPUT_FILE_NOT_FOUND
   :value: 'Input file not found: {}'


.. py:data:: ERR_MISSING_REQUIRED_KEYS
   :value: 'Missing required keys: {}'


.. py:data:: MAKE_BIN_ENV_VAR
   :value: 'MAKE_BIN_PATH'


.. py:function:: _guess_binary_location(bin_name: str, env_var: str) -> pathlib.Path | None

   Guess the location of a binary.


.. py:class:: oxDNABinarySemaphore

   A semaphore for the oxDNA binary.


   .. py:attribute:: _ready
      :value: False



   .. py:method:: check() -> bool

      Check if the semaphore is ready.



   .. py:method:: set(ready: bool) -> None

      Set the value of the semaphore.



.. py:class:: oxDNABinarySemaphoreActor

   Bases: :py:obj:`oxDNABinarySemaphore`


   A ray actor wrapped oxDNA binary semaphore.


.. py:class:: oxDNASimulator

   Bases: :py:obj:`jax_dna.simulators.base.BaseSimulation`


   A sampler base on running an oxDNA simulation.


   .. py:attribute:: input_dir
      :type:  str


   .. py:attribute:: sim_type
      :type:  jax_dna.utils.types.oxDNASimulatorType


   .. py:attribute:: energy_configs
      :type:  list[jax_dna.energy.configuration.BaseConfiguration] | None
      :value: None



   .. py:attribute:: n_build_threads
      :type:  int
      :value: 4



   .. py:attribute:: logger_config
      :type:  dict[str, Any] | None
      :value: None



   .. py:attribute:: disable_build
      :type:  bool
      :value: False



   .. py:attribute:: check_build_ready
      :type:  collections.abc.Callable[[None], bool]


   .. py:attribute:: set_build_ready
      :type:  collections.abc.Callable[[bool], None]


   .. py:attribute:: build_wait_interval
      :type:  int
      :value: 15



   .. py:method:: __post_init__(*args, **kwds) -> None

      Check the validity of the configuration.



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


   .. py:method:: run(opt_params: list[jax_dna.utils.types.Params] | None = None, seed: numpy.ndarray | None = None, **kwargs) -> jax_dna.input.trajectory.Trajectory

      Run an oxDNA simulation.



   .. py:method:: _update_params(*, new_params: list[dict]) -> None

      Update the simulation.

      This function will recompile the oxDNA binary with the new parameters.



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

      Restore the original parameters.