jax_dna.energy.dna2.interactions
================================

.. py:module:: jax_dna.energy.dna2.interactions

.. autoapi-nested-parse::

   DNA2 interactions.

   These functions are based on the oxDNA2 model paper found here:
   https://arxiv.org/abs/1504.00821



Functions
---------

.. autoapisummary::

   jax_dna.energy.dna2.interactions.debye
   jax_dna.energy.dna2.interactions.coaxial_stacking


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

.. py:function:: debye(r: jax_dna.utils.types.ARR_OR_SCALAR, kappa: jax_dna.utils.types.Scalar, prefactor: jax_dna.utils.types.Scalar, smoothing_coeff: jax_dna.utils.types.Scalar, r_cut: jax_dna.utils.types.Scalar, r_high: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.ARR_OR_SCALAR

   Debye-huckel potential.


.. py:function:: coaxial_stacking(dr_stack: jax_dna.utils.types.ARR_OR_SCALAR, theta4: jax_dna.utils.types.ARR_OR_SCALAR, theta1: jax_dna.utils.types.ARR_OR_SCALAR, theta5: jax_dna.utils.types.ARR_OR_SCALAR, theta6: jax_dna.utils.types.ARR_OR_SCALAR, dr_low_coax: jax_dna.utils.types.Scalar, dr_high_coax: jax_dna.utils.types.Scalar, dr_c_low_coax: jax_dna.utils.types.Scalar, dr_c_high_coax: jax_dna.utils.types.Scalar, k_coax: jax_dna.utils.types.Scalar, dr0_coax: jax_dna.utils.types.Scalar, dr_c_coax: jax_dna.utils.types.Scalar, b_low_coax: jax_dna.utils.types.Scalar, b_high_coax: jax_dna.utils.types.Scalar, theta0_coax_4: jax_dna.utils.types.Scalar, delta_theta_star_coax_4: jax_dna.utils.types.Scalar, delta_theta_coax_4_c: jax_dna.utils.types.Scalar, a_coax_4: jax_dna.utils.types.Scalar, b_coax_4: jax_dna.utils.types.Scalar, theta0_coax_1: jax_dna.utils.types.Scalar, delta_theta_star_coax_1: jax_dna.utils.types.Scalar, delta_theta_coax_1_c: jax_dna.utils.types.Scalar, a_coax_1: jax_dna.utils.types.Scalar, b_coax_1: jax_dna.utils.types.Scalar, a_coax_1_f6: jax_dna.utils.types.Scalar, b_coax_1_f6: jax_dna.utils.types.Scalar, theta0_coax_5: jax_dna.utils.types.Scalar, delta_theta_star_coax_5: jax_dna.utils.types.Scalar, delta_theta_coax_5_c: jax_dna.utils.types.Scalar, a_coax_5: jax_dna.utils.types.Scalar, b_coax_5: jax_dna.utils.types.Scalar, theta0_coax_6: jax_dna.utils.types.Scalar, delta_theta_star_coax_6: jax_dna.utils.types.Scalar, delta_theta_coax_6_c: jax_dna.utils.types.Scalar, a_coax_6: jax_dna.utils.types.Scalar, b_coax_6: jax_dna.utils.types.Scalar) -> jax_dna.utils.types.Scalar

   Coaxial stacking energy.