mythos.energy.dna1.cross_stacking
=================================

.. py:module:: mythos.energy.dna1.cross_stacking

.. autoapi-nested-parse::

   Cross-stacking energy term for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.dna1.cross_stacking.CrossStackingConfiguration
   mythos.energy.dna1.cross_stacking.CrossStacking


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

.. py:class:: CrossStackingConfiguration

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


   Configuration for the cross-stacking energy function.


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



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



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



   .. py:attribute:: r0_cross
      :type:  float | None
      :value: None



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



   .. py:attribute:: theta0_cross_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_1
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_1
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_cross_2
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_2
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_2
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_cross_3
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_3
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_3
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_cross_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_4
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_4
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_cross_7
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_7
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_7
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_cross_8
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_cross_8
      :type:  float | None
      :value: None



   .. py:attribute:: a_cross_8
      :type:  float | None
      :value: None



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



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



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



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



   .. py:attribute:: b_cross_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_1_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_cross_2
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_2_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_cross_3
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_3_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_cross_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_4_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_cross_7
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_7_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_cross_8
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_cross_8_c
      :type:  float | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('dr_low_cross', 'dr_high_cross', 'k_cross', 'r0_cross', 'dr_c_cross', 'theta0_cross_1',...



   .. py:attribute:: dependent_params
      :type:  tuple[str]
      :value: ('b_low_cross', 'dr_c_low_cross', 'b_high_cross', 'dr_c_high_cross', 'b_cross_1',...



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: CrossStacking

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


   Cross-stacking energy function for DNA1 model.


   .. py:attribute:: params
      :type:  CrossStackingConfiguration


   .. py:method:: pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) -> mythos.utils.types.Arr_Unbonded_Neighbors

      Computes the cross stacking energy for each unbonded pair.



   .. py:method:: compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) -> mythos.utils.types.Scalar

      Compute the energy of the system given the nucleotide.