mythos.observables.base
=======================

.. py:module:: mythos.observables.base

.. autoapi-nested-parse::

   Base class for observables.



Attributes
----------

.. autoapisummary::

   mythos.observables.base.ERR_RIGID_BODY_TRANSFORM_FN_REQUIRED


Classes
-------

.. autoapisummary::

   mythos.observables.base.BaseObservable


Functions
---------

.. autoapisummary::

   mythos.observables.base.local_helical_axis_with_norm
   mythos.observables.base.local_helical_axis
   mythos.observables.base.get_duplex_quartets


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

.. py:data:: ERR_RIGID_BODY_TRANSFORM_FN_REQUIRED
   :value: 'rigid_body_transform_fn must be provided'


.. py:class:: BaseObservable

   Base class for observables.


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


   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory) -> jax.numpy.ndarray

      Calculate the observable.



.. py:function:: local_helical_axis_with_norm(quartet: jax.numpy.ndarray, base_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) -> jax.numpy.ndarray

   Computes the norm and normalized local helical axis defined by two base pairs.


.. py:function:: local_helical_axis(quartet: jax.numpy.ndarray, base_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) -> jax.numpy.ndarray

   Computes the normalized local helical axis defined by two base pairs.


.. py:function:: get_duplex_quartets(n_nucs_per_strand: int) -> jax.numpy.ndarray

   Computes all quartets (i.e. pairs of adjacent base pairs) for a duplex of a given size.

   :param n_nucs_per_strand: number of nucleotides on each strand
   :type n_nucs_per_strand: int

   :returns: array of all quartets
   :rtype: jnp.ndarray