Compute an average structure from a trajectory — MMTK User Guide 2.7.7 documentation

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# Compute an average structure from a trajectory

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    # This program reads a trajecory and calculates the average
    # configuration, which is then visualized. This is not a particularly
    # useful operation, but it illustrates the use of trajectories and
    # configuration variables.
    #
    # Note: In order to create the trajectory file "bala1.nc" which is
    #       read by this example, you must run the example
    #       MolecularDynamics/protein.py!
    #

    from MMTK import *
    from MMTK.Trajectory import Trajectory
    from MMTK.Visualization import view

    # Open the input trajectory.
    trajectory = Trajectory(None, 'bala1.nc')
    universe = trajectory.universe

    # Create a zeroed particle vector object.
    sum = ParticleVector(universe)

    # Loop over all steps and add the configurations to the sum.
    for configuration in trajectory.configuration:
        sum = sum + configuration

    # Divide by the number of steps.
    sum = sum/len(trajectory)

    # Visualize the average.
    view(universe, sum)

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