mythos.energy.dna2.debye
========================

.. py:module:: mythos.energy.dna2.debye

.. autoapi-nested-parse::

   Debye-huckel function for DNA2 model.



Classes
-------

.. autoapisummary::

   mythos.energy.dna2.debye.DebyeConfiguration
   mythos.energy.dna2.debye.Debye


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

.. py:class:: DebyeConfiguration

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


   Configuration for the debye-huckel energy function.


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



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



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



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



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



   .. py:attribute:: half_charged_ends
      :type:  bool | None
      :value: None



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



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



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



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



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



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



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('q_eff', 'lambda_factor', 'prefactor_coeff', 'kt', 'salt_conc', 'half_charged_ends')



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: Debye

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


   Debye-huckel energy function for DNA2 model.


   .. py:attribute:: params
      :type:  DebyeConfiguration


   .. py:attribute:: is_end
      :type:  mythos.utils.types.Arr_Nucleotide_Int | None
      :value: None



   .. py:method:: __post_init__(topology: mythos.input.topology.Topology | None) -> None


   .. 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_Bonded_Neighbors

      Computes the debye-huckel 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.