mythos.observables.diameter
===========================

.. py:module:: mythos.observables.diameter

.. autoapi-nested-parse::

   Diameter observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.diameter.TARGETS
   mythos.observables.diameter.ERR_DISPLACEMENT_FN_REQUIRED
   mythos.observables.diameter.single_diameter_mapped


Classes
-------

.. autoapisummary::

   mythos.observables.diameter.Diameter


Functions
---------

.. autoapisummary::

   mythos.observables.diameter.single_diameter


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

.. py:data:: TARGETS

.. py:data:: ERR_DISPLACEMENT_FN_REQUIRED
   :value: 'A displacement function is required for computing the helical diameter.'


.. py:function:: single_diameter(bp: jax.numpy.ndarray, back_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable, sigma_backbone: float) -> mythos.utils.types.ARR_OR_SCALAR

   Computes the helical diameter of a base pair.

   :param bp: a 2-dimensional array containing the indices of the h-bonded nucleotides
   :type bp: jnp.ndarray
   :param back_sites: a 2-dimensional array containing the positions of the backbone sites
   :type back_sites: jnp.ndarray
   :param displacement_fn: a function for computing displacements between two positions
   :type displacement_fn: Callable
   :param sigma_backbone: the excluded volume distance between backbone sites
   :type sigma_backbone: float

   :returns: the helical diameter in Angstroms for each base pair
   :rtype: jd_types.ARR_OR_SCALAR


.. py:data:: single_diameter_mapped

.. py:class:: Diameter

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


   Computes the helical diameter for each state.

   The helical diameter for a given base pair is defined as the furthest extent of the
   excluded volume. The diameter per state is the average over all (specified) base pairs.

   Args:
   - bp: a 2-dimensional array containing the indices of the h-bonded nucleotides
   - displacement_fn: a function for computing displacements between two positions


   .. py:attribute:: h_bonded_base_pairs
      :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, sigma_backbone: float) -> mythos.utils.types.ARR_OR_SCALAR

      Calculate the average helical diameter in Angstroms.

      :param trajectory: the trajectory to calculate the helical diameter for
      :type trajectory: jd_traj.Trajectory
      :param sigma_backbone: the excluded volume distance between backbone sites
      :type sigma_backbone: float

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