mythos.observables.melting_temp
===============================

.. py:module:: mythos.observables.melting_temp

.. autoapi-nested-parse::

   Melting temperature observable.



Attributes
----------

.. autoapisummary::

   mythos.observables.melting_temp.TARGETS


Classes
-------

.. autoapisummary::

   mythos.observables.melting_temp.MeltingTemp


Functions
---------

.. autoapisummary::

   mythos.observables.melting_temp.jax_interp1d
   mythos.observables.melting_temp.compute_finf
   mythos.observables.melting_temp.find_melting_temp
   mythos.observables.melting_temp.compute_curve_width


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

.. py:data:: TARGETS

.. py:function:: jax_interp1d(x: jax.numpy.ndarray, y: jax.numpy.ndarray, x_new: float) -> jax.numpy.ndarray

   Simple linear interpolation function using JAX.

   :param x: Array of x coordinates
   :param y: Array of y coordinates
   :param x_new: Point(s) at which to interpolate

   :returns: Interpolated y value(s)


.. py:function:: compute_finf(ratio: jax.numpy.ndarray) -> jax.numpy.ndarray

   Finite size correction to bound:unbound ratio.


.. py:function:: find_melting_temp(temperatures: jax.numpy.ndarray, ratios: jax.numpy.ndarray) -> float

   Find the temperature at which the concentration of single strands = 0.5 * duplex concentration.

   :param temperatures: Array of temperature values
   :param ratios: Array of unbound:bound ratio values corresponding to each temperature
   :param target_ratio: The ratio value to find (default: 0.5)

   :returns: The interpolated temperature where ratio = target_ratio


.. py:function:: compute_curve_width(temperatures: jax.numpy.ndarray, ratios: jax.numpy.ndarray) -> float

   Find the width of the melting curve.

   defined as the temperature separation between unbound:bound ratio = 0.2 and
   unbound:bound ratio = 0.8

   :param temperatures: Array of temperature values
   :param ratios: Array of unbound:bound ratio values corresponding to each temperature

   :returns: The width of the interpolated temperature curve between 0.2 and 0.8


.. py:class:: MeltingTemp

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


   Computes the melting temperature of a duplex using umbrella sampling.

   The melting temperature is defined as the temperature at which the
   concentration of DNA duplexes is double that of the concentration of single
   strands.

   :param sim_temperature: float. the temperature at which the SimulatorTrajectory
                           was collected, in sim. units.
   :param temperature_range: a vector containing the temperatures to extrapolate
                             the SimulatorTrajectory data to (via histogram reweighting), in sim.
                             units.
   :param energy_config: Energy configurations.
   :param energy_fn_builder: Energy function builder.


   .. py:attribute:: sim_temperature
      :type:  float


   .. py:attribute:: temperature_range
      :type:  jax.numpy.ndarray


   .. py:attribute:: energy_fn
      :type:  collections.abc.Callable


   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory, bind_states: jax.numpy.ndarray, umbrella_weights: jax.numpy.ndarray, opt_params: mythos.utils.types.PyTree) -> float

      Calculate the melting temperature.

      :param trajectory: the trajectory to calculate the melting temperature for
      :type trajectory: jd_traj.Trajectory
      :param bind_states: an array of the sampled states of the "bond" order parameter
      :type bind_states: jnp.ndarray
      :param umbrella_weights: an N-dimensional array containing umbrella sampling weights
      :type umbrella_weights: jnp.ndarray
      :param opt_params: the parameters to optimize; use the current vals in building the energy functions

      :returns: the melting temperature in simulation units
      :rtype: float



   .. py:method:: get_extrap_ratios(trajectory: mythos.simulators.io.SimulatorTrajectory, bind_states: jax.numpy.ndarray, umbrella_weights: jax.numpy.ndarray, opt_params: mythos.utils.types.PyTree) -> float

      Calculate the bound:unbound ratios at the extrapolated temperatures.



   .. py:method:: get_melting_temperature(trajectory: mythos.simulators.io.SimulatorTrajectory, bind_states: jax.numpy.ndarray, umbrella_weights: jax.numpy.ndarray, opt_params: mythos.utils.types.PyTree) -> float

      Calculate the melting temperature.



   .. py:method:: get_melting_curve(trajectory: mythos.simulators.io.SimulatorTrajectory, bind_states: jax.numpy.ndarray, umbrella_weights: jax.numpy.ndarray, opt_params: mythos.utils.types.PyTree) -> tuple[jax.numpy.ndarray, jax.numpy.ndarray]

      Calculate the melting curve.



   .. py:method:: get_melting_curve_width(trajectory: mythos.simulators.io.SimulatorTrajectory, bind_states: jax.numpy.ndarray, umbrella_weights: jax.numpy.ndarray, opt_params: mythos.utils.types.PyTree) -> float

      Calculate the melting curve width.