jax_dna.energy.rna2.stacking
============================

.. py:module:: jax_dna.energy.rna2.stacking

.. autoapi-nested-parse::

   Stacking energy function for RNA2 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.rna2.stacking.StackingConfiguration
   jax_dna.energy.rna2.stacking.Stacking


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

.. py:class:: StackingConfiguration

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


   Configuration for the stacking energy function.


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



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



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



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



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



   .. py:attribute:: dr0_stack
      :type:  float | None
      :value: None



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



   .. py:attribute:: theta0_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: neg_cos_phi1_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_1
      :type:  float | None
      :value: None



   .. py:attribute:: neg_cos_phi2_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_2
      :type:  float | None
      :value: None



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



   .. py:attribute:: ss_stack_weights
      :type:  numpy.ndarray | None


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



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



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



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



   .. py:attribute:: b_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_stack_5_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_stack_6_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_stack_9_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_stack_10_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_neg_cos_phi1_stack
      :type:  float | None
      :value: None



   .. py:attribute:: neg_cos_phi1_c_stack
      :type:  float | None
      :value: None



   .. py:attribute:: b_neg_cos_phi2_stack
      :type:  float | None
      :value: None



   .. py:attribute:: neg_cos_phi2_c_stack
      :type:  float | None
      :value: None



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



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: Stacking

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


   Stacking energy function for DNA1 model.


   .. py:attribute:: params
      :type:  StackingConfiguration


   .. py:method:: compute_v_stack(body: jax_dna.energy.rna2.nucleotide.Nucleotide, bonded_neighbors: jax_dna.utils.types.Arr_Bonded_Neighbors_2) -> jax_dna.utils.types.Arr_Bonded_Neighbors

      Computes the sequence-independent energy for each bonded pair.



   .. py:method:: pairwise_energies(body: jax_dna.energy.rna2.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.rna2.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.