mythos.energy.dna2.nucleotide
=============================

.. py:module:: mythos.energy.dna2.nucleotide

.. autoapi-nested-parse::

   Extends `jax_md.rigid_body.RigidBody` for DNA2 nucleotide.



Classes
-------

.. autoapisummary::

   mythos.energy.dna2.nucleotide.Nucleotide


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

.. py:class:: Nucleotide

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


   Nucleotide rigid body with additional sites for DNA2.

   This class is inteneded to be used as a dataclass for a nucleotide rigid body
   as a `rigid_body_transform_fn` in `jax_md.energy.ComposedEnergyFunction`.


   .. py:attribute:: center
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: orientation
      :type:  mythos.utils.types.Arr_Nucleotide_3 | jax_md.rigid_body.Quaternion


   .. py:attribute:: stack_sites
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: back_sites
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: back_sites_dna1
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: base_sites
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: back_base_vectors
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: base_normals
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:attribute:: cross_prods
      :type:  mythos.utils.types.Arr_Nucleotide_3


   .. py:method:: from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, com_to_backbone_x: mythos.utils.types.Scalar, com_to_backbone_y: mythos.utils.types.Scalar, com_to_backbone_dna1: mythos.utils.types.Scalar, com_to_hb: mythos.utils.types.Scalar, com_to_stacking: mythos.utils.types.Scalar) -> Nucleotide
      :staticmethod:


      Class method to precompute nucleotide sites from a rigid body.