jax_dna.energy.dna2.stacking
============================

.. py:module:: jax_dna.energy.dna2.stacking

.. autoapi-nested-parse::

   Stacking energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.dna2.stacking.Stacking


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

.. py:class:: Stacking

   Bases: :py:obj:`jax_dna.energy.dna1.Stacking`


   Stacking energy function for DNA2 model.


   .. py:attribute:: params
      :type:  jax_dna.energy.dna1.StackingConfiguration


   .. py:method:: pairwise_energies(body: jax_dna.energy.dna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2) -> jax_dna.utils.types.Arr_Bonded_Neighbors

      Computes the stacking energy for each bonded pair.



   .. py:method:: __call__(body: jax_dna.energy.dna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.Discrete_Sequence, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) -> jax_dna.utils.types.Scalar

      Calculate the energy of the system.