mythos.observables.martini_utils

General utility functions for working with Martini observables.

Attributes

NM_TO_ANGSTROMS

Functions

universe_from_trajectory(→ MDAnalysis.Universe)

Reconstruct an MDAnalysis Universe from a topology and SimulatorTrajectory.

Module Contents

mythos.observables.martini_utils.NM_TO_ANGSTROMS = 10.0

mythos.observables.martini_utils.universe_from_trajectory(topology: MDAnalysis.Universe, trajectory: mythos.simulators.io.SimulatorTrajectory) → MDAnalysis.Universe[source]

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.