mythos.energy.dna2.base_functions
=================================

.. py:module:: mythos.energy.dna2.base_functions

.. autoapi-nested-parse::

   Base energy functions for DNA2 model.

   This function is based on the oxDNA2 model paper found here:
   https://ora.ox.ac.uk/objects/uuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcd/files/m7422ee58d9747bbd7af00d6435b570e6



Functions
---------

.. autoapisummary::

   mythos.energy.dna2.base_functions.f1
   mythos.energy.dna2.base_functions.f2
   mythos.energy.dna2.base_functions.f3
   mythos.energy.dna2.base_functions.f4
   mythos.energy.dna2.base_functions.f5
   mythos.energy.dna2.base_functions.f6


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

.. py:function:: f1(r: mythos.utils.types.ARR_OR_SCALAR, r_low: mythos.utils.types.Scalar, r_high: mythos.utils.types.Scalar, r_c_low: mythos.utils.types.Scalar, r_c_high: mythos.utils.types.Scalar, eps: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, r0: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, b_low: mythos.utils.types.Scalar, b_high: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   The radial part of the stacking and hydrogen-bonding potentials.

   This is based on equation 2.7 from the oxDNA paper.


.. py:function:: f2(r: mythos.utils.types.ARR_OR_SCALAR, r_low: mythos.utils.types.Scalar, r_high: mythos.utils.types.Scalar, r_c_low: mythos.utils.types.Scalar, r_c_high: mythos.utils.types.Scalar, k: mythos.utils.types.Scalar, r0: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, b_low: mythos.utils.types.Scalar, b_high: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   The radial part of the cross-stacking and coaxial stacking potentials.

   This is based on equation 2.8 from the oxDNA paper.


.. py:function:: f3(r: mythos.utils.types.ARR_OR_SCALAR, r_star: mythos.utils.types.Scalar, r_c: mythos.utils.types.Scalar, eps: mythos.utils.types.Scalar, sigma: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   The radial part of the excluded volume potential.

   This is based on equation 2.9 from the oxDNA paper.


.. py:function:: f4(theta: mythos.utils.types.ARR_OR_SCALAR, theta0: mythos.utils.types.Scalar, delta_theta_star: mythos.utils.types.Scalar, delta_theta_c: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   The angular modulation factor used in stacking, hydrogen-bonding, cross-stacking and coaxial stacking.

   This is based on equation 2.10 from the oxDNA paper.


.. py:function:: f5(x: mythos.utils.types.ARR_OR_SCALAR, x_star: mythos.utils.types.Scalar, x_c: mythos.utils.types.Scalar, a: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   Another modulating term which is used to impose right-handedness (effectively a one-sided modulation).

   This is based on equation 2.11 from the oxDNA paper.


.. py:function:: f6(theta: mythos.utils.types.ARR_OR_SCALAR, a: mythos.utils.types.Scalar, b: mythos.utils.types.Scalar) -> mythos.utils.types.ARR_OR_SCALAR

   Replaces a coaxial stacking potential in the DNA1 model.