mythos.observables.propeller
============================

.. py:module:: mythos.observables.propeller

.. autoapi-nested-parse::

   Propeller twist observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.propeller.TARGETS
   mythos.observables.propeller.propeller_twist_rad


Classes
-------

.. autoapisummary::

   mythos.observables.propeller.PropellerTwist


Functions
---------

.. autoapisummary::

   mythos.observables.propeller.single_propeller_twist_rad


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

.. py:data:: TARGETS

.. py:function:: single_propeller_twist_rad(bp: jax.numpy.ndarray, base_normals: jax.numpy.ndarray) -> jax.numpy.ndarray

   Computes the propeller twist of a base pair.


.. py:data:: propeller_twist_rad

.. py:class:: PropellerTwist

   Bases: :py:obj:`mythos.observables.base.BaseObservable`


   Computes the propeller twist of a base pair.

   The propeller twist is defined as the angle between the normal vectors
   of h-bonded bases

   Args:
   - bp: a 2-dimensional array containing the indices of the h-bonded nucleotides
   - base_normals: the base normal vectors of the entire body


   .. py:attribute:: h_bonded_base_pairs
      :type:  jax.numpy.ndarray


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

      Validate the input.



   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory) -> mythos.utils.types.ARR_OR_SCALAR

      Calculate the twist of the propeller in degrees.

      :param trajectory: the trajectory to calculate the propeller twist for
      :type trajectory: jd_traj.Trajectory

      :returns: the propeller twist in degrees for each state , so expect a size
                of (n_states,)
      :rtype: jd_types.ARR_OR_SCALAR