mythos.observables.rise
=======================

.. py:module:: mythos.observables.rise

.. autoapi-nested-parse::

   Rise observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.rise.TARGETS
   mythos.observables.rise.single_rise_mapped


Classes
-------

.. autoapisummary::

   mythos.observables.rise.Rise


Functions
---------

.. autoapisummary::

   mythos.observables.rise.single_rise


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

.. py:data:: TARGETS

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

   Computes the rise between adjacent base pairs.


.. py:data:: single_rise_mapped

.. py:class:: Rise

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


   Computes the rise for each state.

   The rise between two adjacent base pairs is defined as the distance of the displacement
   vector between their midpoints projected onto the local helical axis. The rise per state
   is the average rise over all (specified) pairs of adjacent base pairs (i.e. quartets)

   :param quartets: a (n_bp, 2, 2) array containing the pairs of adjacent base pairs
                    for which to compute the rise
   :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 rise in Angstroms.

      :param trajectory: the trajectory to calculate the rise for
      :type trajectory: jd_sio.Trajectory

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