jax_dna.energy.na1.debye
========================

.. py:module:: jax_dna.energy.na1.debye

.. autoapi-nested-parse::

   Debye-huckel function for NA2 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.na1.debye.DebyeConfiguration
   jax_dna.energy.na1.debye.Debye


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

.. py:class:: DebyeConfiguration

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


   Configuration for the debye-huckel energy function.


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



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



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



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



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



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



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



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



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



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



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



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



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



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



   .. py:attribute:: dna_config
      :type:  jax_dna.energy.dna2.DebyeConfiguration | None
      :value: None



   .. py:attribute:: rna_config
      :type:  jax_dna.energy.dna2.DebyeConfiguration | None
      :value: None



   .. py:attribute:: drh_config
      :type:  jax_dna.energy.dna2.DebyeConfiguration | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('nt_type', 'is_end', 'half_charged_ends', 'kt', 'salt_conc', 'dna_q_eff', 'dna_lambda_factor',...



   .. 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:`jax_dna.energy.base.BaseEnergyFunction`


   Debye-huckel energy function for NA1 model.


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


   .. py:method:: __call__(body: jax_dna.energy.na1.nucleotide.HybridNucleotide, seq: jax_dna.utils.types.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.