mythos.observables.martini_utils
================================

.. py:module:: mythos.observables.martini_utils

.. autoapi-nested-parse::

   General utility functions for working with Martini observables.



Attributes
----------

.. autoapisummary::

   mythos.observables.martini_utils.NM_TO_ANGSTROMS


Functions
---------

.. autoapisummary::

   mythos.observables.martini_utils.universe_from_trajectory


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

.. py:data:: NM_TO_ANGSTROMS
   :value: 10.0


.. py:function:: universe_from_trajectory(topology: MDAnalysis.Universe, trajectory: mythos.simulators.io.SimulatorTrajectory) -> MDAnalysis.Universe

   Reconstruct an MDAnalysis Universe from a topology and SimulatorTrajectory.

   This is useful in cases where we want to work against a Universe object
   within an objective function. The topology of the system (e.g. as read by
   the tpr file) will typically be static and can be passed as a property of
   the observable, then have the trajectory embedded to produce a new Universe
   object. The SimulatorTrajectory stores positions in nm, MDAnalysis expects
   Angstroms.  Box dimensions are extended with 90 degree angles for MDAnalysis
   compatibility.