mythos.energy.dna1.unbonded_excluded_volume
===========================================

.. py:module:: mythos.energy.dna1.unbonded_excluded_volume

.. autoapi-nested-parse::

   Unbonded excluded volume energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolumeConfiguration
   mythos.energy.dna1.unbonded_excluded_volume.UnbondedExcludedVolume


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

.. py:class:: UnbondedExcludedVolumeConfiguration

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


   Configuration for the unbonded 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:: dr_star_back_base
      :type:  float | None
      :value: None



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



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



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



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



   .. py:attribute:: sigma_backbone
      :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:: b_backbone
      :type:  float | None
      :value: None



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



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



   .. 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() -> UnbondedExcludedVolumeConfiguration

      Initializes the dependent parameters in configuration.

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



.. py:class:: UnbondedExcludedVolume

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


   Unbonded excluded volume energy function for DNA1 model.


   .. py:attribute:: params
      :type:  UnbondedExcludedVolumeConfiguration


   .. py:method:: pairwise_energies(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors_2) -> mythos.utils.types.Arr_Bonded_Neighbors

      Computes the excluded volume energy for each unbonded pair.



   .. py:method:: compute_energy(nucleotide: mythos.energy.base.BaseNucleotide) -> mythos.utils.types.Scalar

      Compute the energy of the system given the nucleotide.