mythos.energy.dna1.bonded_excluded_volume
=========================================

.. py:module:: mythos.energy.dna1.bonded_excluded_volume

.. autoapi-nested-parse::

   Bonded excluded volume energy for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.dna1.bonded_excluded_volume.BondedExcludedVolumeConfiguration
   mythos.energy.dna1.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:: eps_exc
      :type:  float | None
      :value: None



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



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



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



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



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



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



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



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



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



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



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



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



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('eps_exc', 'dr_star_base', 'sigma_base', 'sigma_back_base', 'sigma_base_back',...



   .. py:attribute:: dependent_params
      :type:  tuple[str]
      :value: ('b_base', 'dr_c_base', 'b_back_base', 'dr_c_back_base', 'b_base_back', 'dr_c_base_back')



   .. 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 DNA1 model.


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


   .. 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 excluded volume 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.