mythos.energy.dna1.stacking
===========================

.. py:module:: mythos.energy.dna1.stacking

.. autoapi-nested-parse::

   Stacking energy function for DNA1 model.



Attributes
----------

.. autoapisummary::

   mythos.energy.dna1.stacking.STACK_WEIGHTS_SA


Classes
-------

.. autoapisummary::

   mythos.energy.dna1.stacking.StackingConfiguration
   mythos.energy.dna1.stacking.Stacking


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

.. py:data:: STACK_WEIGHTS_SA

.. py:class:: StackingConfiguration

   Bases: :py:obj:`mythos.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_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_stack_4
      :type:  float | None
      :value: None



   .. py:attribute:: a_stack_4
      :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:: 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:: pseq
      :type:  mythos.utils.types.Probabilistic_Sequence | None
      :value: None



   .. py:attribute:: pseq_constraints
      :type:  mythos.input.sequence_constraints.SequenceConstraints | None
      :value: None



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



   .. py:attribute:: ss_stack_weights
      :type:  numpy.ndarray | None
      :value: 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_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_stack_4_c
      :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_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:attribute:: dependent_params
      :type:  tuple[str]
      :value: ('b_low_stack', 'dr_c_low_stack', 'b_high_stack', 'dr_c_high_stack', 'b_stack_4',...



   .. 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_v_stack(stack_sites: mythos.utils.types.Arr_Nucleotide_3, back_sites: mythos.utils.types.Arr_Nucleotide_3, base_normals: mythos.utils.types.Arr_Nucleotide_3, cross_prods: mythos.utils.types.Arr_Nucleotide_3, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) -> mythos.utils.types.Arr_Bonded_Neighbors

      Computes the sequence-independent energy for each bonded pair.



   .. py:method:: pseq_weights(i: int, j: int, seq: mythos.utils.types.Probabilistic_Sequence) -> float

      Computes the probabilistic sequence-dependent weight for a bonded pair.



   .. py:method:: pairwise_energies(body: mythos.energy.base.BaseNucleotide, seq: mythos.utils.types.Discrete_Sequence, bonded_neighbors: mythos.utils.types.Arr_Bonded_Neighbors_2) -> mythos.utils.types.Arr_Bonded_Neighbors

      Computes the stacking energy for each bonded pair.



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

      Compute the energy of the system given the nucleotide.