mythos.energy.dna1.hydrogen_bonding
===================================

.. py:module:: mythos.energy.dna1.hydrogen_bonding

.. autoapi-nested-parse::

   Hydrogen bonding energy function for DNA1 model.



Attributes
----------

.. autoapisummary::

   mythos.energy.dna1.hydrogen_bonding.HB_WEIGHTS_SA


Classes
-------

.. autoapisummary::

   mythos.energy.dna1.hydrogen_bonding.HydrogenBondingConfiguration
   mythos.energy.dna1.hydrogen_bonding.HydrogenBonding


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

.. py:data:: HB_WEIGHTS_SA

.. py:class:: HydrogenBondingConfiguration

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


   Configuration for the hydrogen bonding energy function.


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



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



   .. py:attribute:: dr0_hb
      :type:  float | None
      :value: None



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



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



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



   .. py:attribute:: a_hb_1
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_1
      :type:  float | None
      :value: None



   .. py:attribute:: a_hb_2
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_2
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_2
      :type:  float | None
      :value: None



   .. py:attribute:: a_hb_3
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_3
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_3
      :type:  float | None
      :value: None



   .. py:attribute:: a_hb_4
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_4
      :type:  float | None
      :value: None



   .. py:attribute:: a_hb_7
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_7
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_7
      :type:  float | None
      :value: None



   .. py:attribute:: a_hb_8
      :type:  float | None
      :value: None



   .. py:attribute:: theta0_hb_8
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_star_hb_8
      :type:  float | None
      :value: None



   .. py:attribute:: ss_hb_weights
      :type:  numpy.ndarray | None
      :value: None



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



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



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



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



   .. py:attribute:: b_hb_1
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_1_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_hb_2
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_2_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_hb_3
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_3_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_hb_4
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_4_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_hb_7
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_7_c
      :type:  float | None
      :value: None



   .. py:attribute:: b_hb_8
      :type:  float | None
      :value: None



   .. py:attribute:: delta_theta_hb_8_c
      :type:  float | None
      :value: None



   .. py:attribute:: eps_hb_weights
      :type:  numpy.ndarray | None
      :value: None



   .. py:attribute:: pseq
      :type:  mythos.utils.types.Probabilistic_Sequence | None
      :value: None



   .. py:attribute:: pseq_constraints
      :type:  mythos.input.sequence_constraints.SequenceConstraints | None
      :value: None



   .. py:attribute:: required_params
      :type:  tuple[str]
      :value: ('eps_hb', 'a_hb', 'dr0_hb', 'dr_c_hb', 'dr_low_hb', 'dr_high_hb', 'a_hb_1', 'theta0_hb_1',...



   .. py:attribute:: dependent_params
      :type:  tuple[str]
      :value: ('b_low_hb', 'dr_c_low_hb', 'b_high_hb', 'dr_c_high_hb', 'b_hb_1', 'delta_theta_hb_1_c',...



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

      Initializes the dependent parameters in configuration.

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



.. py:class:: HydrogenBonding

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


   Hydrogen bonding energy function for DNA1 model.


   .. py:attribute:: params
      :type:  HydrogenBondingConfiguration


   .. py:method:: compute_v_hb(body_i: mythos.energy.base.BaseNucleotide, body_j: mythos.energy.base.BaseNucleotide, unbonded_neighbors: mythos.utils.types.Arr_Unbonded_Neighbors) -> mythos.utils.types.Arr_Unbonded_Neighbors

      Computes the sequence-independent energy for each unbonded pair.



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

      Computes the sequence-dependent weight for an unbonded pair.



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

      Computes the hydrogen bonding 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.