mythos.energy.na1.nucleotide
============================

.. py:module:: mythos.energy.na1.nucleotide

.. autoapi-nested-parse::

   Extends `jax_md.rigid_body.RigidBody` for NA1 nucleotide.



Classes
-------

.. autoapisummary::

   mythos.energy.na1.nucleotide.HybridNucleotide


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

.. py:class:: HybridNucleotide

   Nucleotide rigid body with additional sites for NA1.

   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:: dna
      :type:  mythos.energy.dna2.nucleotide.Nucleotide


   .. py:attribute:: rna
      :type:  mythos.energy.rna2.nucleotide.Nucleotide


   .. py:method:: from_rigid_body(rigid_body: jax_md.rigid_body.RigidBody, dna_com_to_backbone_x: mythos.utils.types.Scalar, dna_com_to_backbone_y: mythos.utils.types.Scalar, dna_com_to_backbone_dna1: mythos.utils.types.Scalar, dna_com_to_hb: mythos.utils.types.Scalar, dna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_backbone_x: mythos.utils.types.Scalar, rna_com_to_backbone_y: mythos.utils.types.Scalar, rna_com_to_stacking: mythos.utils.types.Scalar, rna_com_to_hb: mythos.utils.types.Scalar, rna_p3_x: mythos.utils.types.Scalar, rna_p3_y: mythos.utils.types.Scalar, rna_p3_z: mythos.utils.types.Scalar, rna_p5_x: mythos.utils.types.Scalar, rna_p5_y: mythos.utils.types.Scalar, rna_p5_z: mythos.utils.types.Scalar, rna_pos_stack_3_a1: mythos.utils.types.Scalar, rna_pos_stack_3_a2: mythos.utils.types.Scalar, rna_pos_stack_5_a1: mythos.utils.types.Scalar, rna_pos_stack_5_a2: mythos.utils.types.Scalar) -> HybridNucleotide
      :staticmethod:


      Class method to precompute nucleotide sites from a rigid body.