mythos.energy.dna1.fene
=======================

.. py:module:: mythos.energy.dna1.fene

.. autoapi-nested-parse::

   FENE energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.dna1.fene.FeneConfiguration
   mythos.energy.dna1.fene.Fene


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

.. py:class:: FeneConfiguration

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


   Configuration for the FENE energy function.


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



   .. py:attribute:: r0_backbone
      :type:  float | None
      :value: None



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



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



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



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('eps_backbone', 'r0_backbone', 'delta_backbone', 'fmax', '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:`mythos.energy.base.BaseEnergyFunction`


   FENE energy function for DNA1 model.


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


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

      Computes the FENE 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.