jax_dna.energy.na1.fene
=======================

.. py:module:: jax_dna.energy.na1.fene

.. autoapi-nested-parse::

   FENE energy function for NA1 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.na1.fene.FeneConfiguration
   jax_dna.energy.na1.fene.Fene


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

.. py:class:: FeneConfiguration

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


   Configuration for the FENE energy function.


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



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



   .. py:attribute:: dna_r0_backbone
      :type:  float | None
      :value: None



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



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



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



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



   .. py:attribute:: rna_r0_backbone
      :type:  float | None
      :value: None



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



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



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



   .. py:attribute:: dna_config
      :type:  jax_dna.energy.dna1.FeneConfiguration | None
      :value: None



   .. py:attribute:: rna_config
      :type:  jax_dna.energy.dna1.FeneConfiguration | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('nt_type', 'dna_eps_backbone', 'dna_r0_backbone', 'dna_delta_backbone', 'dna_fmax', 'dna_finf',...



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: Fene

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


   FENE energy function for NA1 model.


   .. py:attribute:: params
      :type:  FeneConfiguration


   .. 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.