jax_dna.energy.dna2.coaxial_stacking
====================================

.. py:module:: jax_dna.energy.dna2.coaxial_stacking

.. autoapi-nested-parse::

   Coaxial stacking energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.dna2.coaxial_stacking.CoaxialStackingConfiguration
   jax_dna.energy.dna2.coaxial_stacking.CoaxialStacking


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

.. py:class:: CoaxialStackingConfiguration

   Bases: :py:obj:`jax_dna.energy.configuration.BaseConfiguration`


   Configuration for the coaxial stacking energy function.


   .. py:attribute:: dr_low_coax
      :type:  float | None
      :value: None



   .. py:attribute:: dr_high_coax
      :type:  float | None
      :value: None



   .. py:attribute:: k_coax
      :type:  float | None
      :value: None



   .. py:attribute:: dr0_coax
      :type:  float | None
      :value: None



   .. py:attribute:: dr_c_coax
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_coax_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_coax_4
      :type:  float | None
      :value: None



   .. py:attribute:: a_coax_4
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_coax_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_coax_1
      :type:  float | None
      :value: None



   .. py:attribute:: a_coax_1
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_coax_5
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_coax_5
      :type:  float | None
      :value: None



   .. py:attribute:: a_coax_5
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_coax_6
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_coax_6
      :type:  float | None
      :value: None



   .. py:attribute:: a_coax_6
      :type:  float | None
      :value: None



   .. py:attribute:: a_coax_1_f6
      :type:  float | None
      :value: None



   .. py:attribute:: b_coax_1_f6
      :type:  float | None
      :value: None



   .. py:attribute:: b_low_coax
      :type:  float | None
      :value: None



   .. py:attribute:: dr_c_low_coax
      :type:  float | None
      :value: None



   .. py:attribute:: b_high_coax
      :type:  float | None
      :value: None



   .. py:attribute:: dr_c_high_coax
      :type:  float | None
      :value: None



   .. py:attribute:: b_coax_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_coax_4_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_coax_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_coax_1_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_coax_5
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_coax_5_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_coax_6
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_coax_6_c
      :type:  float | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('dr_low_coax', 'dr_high_coax', 'k_coax', 'dr0_coax', 'dr_c_coax', 'theta0_coax_4',...



   .. py:method:: init_params() -> CoaxialStackingConfiguration

      Initializes the dependent parameters in configuration.

      Should be implemented in the subclass if dependent parameters are present.



.. py:class:: CoaxialStacking

   Bases: :py:obj:`jax_dna.energy.base.BaseEnergyFunction`


   Coaxial stacking energy function for DNA1 model.


   .. py:attribute:: params
      :type:  CoaxialStackingConfiguration


   .. py:method:: pairwise_energies(body_i: jax_dna.energy.dna2.nucleotide.Nucleotide, body_j: jax_dna.energy.dna2.nucleotide.Nucleotide, unbonded_neighbors: jax_dna.utils.types.Arr_Unbonded_Neighbors_2) -> jax_dna.utils.types.Arr_Unbonded_Neighbors

      Computes the coaxial stacking energy for each unbonded pair.



   .. py:method:: __call__(body: jax_dna.energy.dna2.nucleotide.Nucleotide, seq: jax_dna.utils.types.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.