jax_dna.energy.dna1.expected_stacking
=====================================

.. py:module:: jax_dna.energy.dna1.expected_stacking

.. autoapi-nested-parse::

   Stacking energy function for DNA1 model.



Classes
-------

.. autoapisummary::

   jax_dna.energy.dna1.expected_stacking.ExpectedStackingConfiguration
   jax_dna.energy.dna1.expected_stacking.ExpectedStacking


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

.. py:class:: ExpectedStackingConfiguration

   Bases: :py:obj:`jax_dna.energy.dna1.stacking.StackingConfiguration`


   Configuration for the expected stacking energy function.


   .. py:attribute:: sequence_constraints
      :type:  jax_dna.input.sequence_constraints.SequenceConstraints | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('eps_stack_base', 'eps_stack_kt_coeff', 'dr_low_stack', 'dr_high_stack', 'a_stack',...



.. py:class:: ExpectedStacking

   Bases: :py:obj:`jax_dna.energy.dna1.stacking.Stacking`


   Expected stacking energy function for DNA1 model.


   .. py:attribute:: params
      :type:  ExpectedStackingConfiguration


   .. py:method:: weight(i: int, j: int, seq: jax_dna.utils.types.Probabilistic_Sequence) -> float

      Computes the sequence-dependent weight for a bonded pair.



   .. py:method:: __call__(body: jax_dna.energy.base.BaseNucleotide, seq: jax_dna.utils.types.Probabilistic_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.