mythos.observables.rmse
=======================

.. py:module:: mythos.observables.rmse

.. autoapi-nested-parse::

   RMSE observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.rmse.ERR_SINGLE_TARGET_STATE_REQUIRED
   mythos.observables.rmse.ERR_TARGET_STATE_DIM
   mythos.observables.rmse.THREE_DIMENSIONS
   mythos.observables.rmse.N_DIMS_NUCLEOTIDES_POSITION


Classes
-------

.. autoapisummary::

   mythos.observables.rmse.RMSE


Functions
---------

.. autoapisummary::

   mythos.observables.rmse.svd_align
   mythos.observables.rmse.single_rmse


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

.. py:function:: svd_align(ref_coords: jax.numpy.ndarray, coords: jax.numpy.ndarray) -> tuple[jax.numpy.ndarray, jax.numpy.ndarray, jax.numpy.ndarray]

   Aligns a set of 3D coordinates to a reference configuration via SVD.


.. py:function:: single_rmse(target: jax_md.rigid_body.RigidBody, state_nts: mythos.energy.dna1.nucleotide.Nucleotide) -> mythos.utils.types.ARR_OR_SCALAR

   Computes the RMSE between a state and a target configuration.


.. py:data:: ERR_SINGLE_TARGET_STATE_REQUIRED
   :value: 'the target state must be a single conformation'


.. py:data:: ERR_TARGET_STATE_DIM
   :value: 'the target state must have center positions in (x, y, z) format'


.. py:data:: THREE_DIMENSIONS
   :value: 3


.. py:data:: N_DIMS_NUCLEOTIDES_POSITION
   :value: 2


.. py:class:: RMSE

   Bases: :py:obj:`mythos.observables.base.BaseObservable`


   Computes the RMSE with respect to a target configuration for each state.

   Args:
   - target_state: a rigid body specifying the target configuration


   .. py:attribute:: target_state
      :type:  jax_md.rigid_body.RigidBody


   .. py:method:: __post_init__() -> None

      Validate the input.



   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory) -> mythos.utils.types.ARR_OR_SCALAR

      Calculate the RMSE in Angstroms.

      :param trajectory: the trajectory to calculate the RMSE for
      :type trajectory: jd_traj.Trajectory

      :returns: the RMSE in Angstroms for each state, so expect a
                size of (n_states,)
      :rtype: jd_types.ARR_OR_SCALAR