mythos.energy.na1.bonded_excluded_volume
========================================

.. py:module:: mythos.energy.na1.bonded_excluded_volume

.. autoapi-nested-parse::

   Bonded excluded volume energy for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolumeConfiguration
   mythos.energy.na1.bonded_excluded_volume.BondedExcludedVolume


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

.. py:class:: BondedExcludedVolumeConfiguration

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


   Configuration for the bonded excluded volume energy function.


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



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



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



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



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



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



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



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



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



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



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



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



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



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



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



   .. py:attribute:: dna_config
      :type:  mythos.energy.dna1.BondedExcludedVolumeConfiguration | None
      :value: None



   .. py:attribute:: rna_config
      :type:  mythos.energy.dna1.BondedExcludedVolumeConfiguration | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('nt_type', 'dna_eps_exc', 'dna_dr_star_base', 'dna_sigma_base', 'dna_sigma_back_base',...



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: BondedExcludedVolume

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


   Bonded excluded volume energy function for NA1 model.


   .. py:attribute:: params
      :type:  BondedExcludedVolumeConfiguration


   .. py:method:: compute_energy(nucleotide: mythos.energy.na1.nucleotide.HybridNucleotide) -> mythos.utils.types.Scalar

      Compute the energy of the system given the nucleotide.