mythos.energy.na1.stacking
==========================

.. py:module:: mythos.energy.na1.stacking

.. autoapi-nested-parse::

   Stacking energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.na1.stacking.StackingConfiguration
   mythos.energy.na1.stacking.Stacking


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

.. py:class:: StackingConfiguration

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


   Configuration for the stacking energy function.


   .. py:attribute:: nt_type
      :type:  mythos.utils.types.Arr_Nucleotide | None
      :value: None



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



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



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



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



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



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



   .. py:attribute:: dna_dr0_stack
      :type:  float | None
      :value: None



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



   .. py:attribute:: dna_theta0_stack_4
      :type:  float | None
      :value: None



   .. py:attribute:: dna_delta_theta_star_stack_4
      :type:  float | None
      :value: None



   .. py:attribute:: dna_a_stack_4
      :type:  float | None
      :value: None



   .. py:attribute:: dna_theta0_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: dna_delta_theta_star_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: dna_a_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: dna_theta0_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: dna_delta_theta_star_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: dna_a_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: dna_neg_cos_phi1_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: dna_a_stack_1
      :type:  float | None
      :value: None



   .. py:attribute:: dna_neg_cos_phi2_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: dna_a_stack_2
      :type:  float | None
      :value: None



   .. py:attribute:: dna_ss_stack_weights
      :type:  numpy.ndarray | None
      :value: None



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



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



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



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



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



   .. py:attribute:: rna_dr0_stack
      :type:  float | None
      :value: None



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



   .. py:attribute:: rna_theta0_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: rna_delta_theta_star_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_5
      :type:  float | None
      :value: None



   .. py:attribute:: rna_theta0_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: rna_delta_theta_star_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_6
      :type:  float | None
      :value: None



   .. py:attribute:: rna_theta0_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: rna_delta_theta_star_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_9
      :type:  float | None
      :value: None



   .. py:attribute:: rna_theta0_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: rna_delta_theta_star_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_10
      :type:  float | None
      :value: None



   .. py:attribute:: rna_neg_cos_phi1_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_1
      :type:  float | None
      :value: None



   .. py:attribute:: rna_neg_cos_phi2_star_stack
      :type:  float | None
      :value: None



   .. py:attribute:: rna_a_stack_2
      :type:  float | None
      :value: None



   .. py:attribute:: rna_ss_stack_weights
      :type:  numpy.ndarray | None
      :value: None



   .. py:attribute:: dna_config
      :type:  mythos.energy.dna1.StackingConfiguration | None
      :value: None



   .. py:attribute:: rna_config
      :type:  mythos.energy.rna2.StackingConfiguration | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('nt_type', 'kt', 'dna_eps_stack_base', 'dna_eps_stack_kt_coeff', 'dna_dr_low_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:`mythos.energy.base.BaseEnergyFunction`


   Stacking energy function for DNA1 model.


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


   .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar

      Compute the energy of the system given the nucleotide.