:py:mod:`RNADiscrepancy.rna`
============================

.. py:module:: RNADiscrepancy.rna

.. autodoc2-docstring:: RNADiscrepancy.rna
   :allowtitles:

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

Classes
~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`Atom <RNADiscrepancy.rna.Atom>`
     - .. autodoc2-docstring:: RNADiscrepancy.rna.Atom
          :summary:
   * - :py:obj:`Nucleotide <RNADiscrepancy.rna.Nucleotide>`
     -

API
~~~

.. py:class:: Atom(name, element, x, y, z, virtual=False)
   :canonical: RNADiscrepancy.rna.Atom

   .. autodoc2-docstring:: RNADiscrepancy.rna.Atom

   .. rubric:: Initialization

   .. autodoc2-docstring:: RNADiscrepancy.rna.Atom.__init__

   .. py:property:: position
      :canonical: RNADiscrepancy.rna.Atom.position

      .. autodoc2-docstring:: RNADiscrepancy.rna.Atom.position

   .. py:method:: distance(other)
      :canonical: RNADiscrepancy.rna.Atom.distance

      .. autodoc2-docstring:: RNADiscrepancy.rna.Atom.distance

   .. py:method:: __eq__(other)
      :canonical: RNADiscrepancy.rna.Atom.__eq__

   .. py:method:: __neq__(other)
      :canonical: RNADiscrepancy.rna.Atom.__neq__

      .. autodoc2-docstring:: RNADiscrepancy.rna.Atom.__neq__

   .. py:method:: __str__()
      :canonical: RNADiscrepancy.rna.Atom.__str__

   .. py:method:: __repr__()
      :canonical: RNADiscrepancy.rna.Atom.__repr__

.. py:class:: Nucleotide(name, atoms)
   :canonical: RNADiscrepancy.rna.Nucleotide

   Bases: :py:obj:`dict`

   .. py:property:: ribose_fulcrum
      :canonical: RNADiscrepancy.rna.Nucleotide.ribose_fulcrum

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.ribose_fulcrum

   .. py:property:: neighbors_fulcrum
      :canonical: RNADiscrepancy.rna.Nucleotide.neighbors_fulcrum

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.neighbors_fulcrum

   .. py:property:: heavy_atoms_residue
      :canonical: RNADiscrepancy.rna.Nucleotide.heavy_atoms_residue

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.heavy_atoms_residue

   .. py:property:: center_heavy_atoms_residue
      :canonical: RNADiscrepancy.rna.Nucleotide.center_heavy_atoms_residue

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.center_heavy_atoms_residue

   .. py:property:: rotation_matrix
      :canonical: RNADiscrepancy.rna.Nucleotide.rotation_matrix

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.rotation_matrix

   .. py:method:: add_virtual_atoms_from_ref()
      :canonical: RNADiscrepancy.rna.Nucleotide.add_virtual_atoms_from_ref

      .. autodoc2-docstring:: RNADiscrepancy.rna.Nucleotide.add_virtual_atoms_from_ref