mythos.observables.pitch
========================

.. py:module:: mythos.observables.pitch

.. autoapi-nested-parse::

   Pitch observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.pitch.TARGETS
   mythos.observables.pitch.single_pitch_angle_mapped


Classes
-------

.. autoapisummary::

   mythos.observables.pitch.PitchAngle


Functions
---------

.. autoapisummary::

   mythos.observables.pitch.compute_pitch
   mythos.observables.pitch.single_pitch_angle


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

.. py:data:: TARGETS

.. py:function:: compute_pitch(avg_pitch_angle: float) -> float

   Computes the pitch given an average pitch angle in radians.

   :param avg_pitch_angle: a value in radians specifying the pitch value
                           averaged over a trajectory
   :type avg_pitch_angle: float

   :returns: the pitch value in base pairs per turn
   :rtype: float


.. py:function:: single_pitch_angle(quartet: jax.numpy.ndarray, base_sites: jax.numpy.ndarray, back_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) -> mythos.utils.types.ARR_OR_SCALAR

   Computes the pitch angle between adjacent base pairs.


.. py:data:: single_pitch_angle_mapped

.. py:class:: PitchAngle

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


   Computes the average pitch angle in radians for each state.

   The pitch is defined by (2*pi) / <angle> where <angle> is the average angle
   between adjacent base pairs across states

   :param quartets: a (n_quartets, 2, 2) array containing the pairs of adjacent base pairs
                    for which to compute pitch angles
   :param displacement_fn: a function for computing displacements between two positions


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


   .. py:attribute:: displacement_fn
      :type:  collections.abc.Callable


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

      Validate the input.



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

      Calculate the average pitch angle in radians.

      :param trajectory: the trajectory to calculate the pitch for
      :type trajectory: jd_traj.Trajectory

      :returns: the average pitch angle in radians for each state,
                so expect a size of (n_states,)
      :rtype: jd_types.ARR_OR_SCALAR