Assembling a trajectory step by step — MMTK User Guide 2.7.7 documentation

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# Assembling a trajectory step by step

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    # "Manual" creation of a trajectory using the snapshot generator.
    #

    from MMTK import *
    from MMTK.Proteins import Protein
    from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput

    # Construct system
    universe = InfiniteUniverse()
    universe.protein = Protein('bala1')

    # Transformation to be applied between the steps
    transformation = Rotation(Vector(0.,0.,1.), 1.*Units.deg)

    # Create trajectory
    trajectory = Trajectory(universe, "rotation.nc", "w", "A rotating molecule")

    # Create the snapshot generator
    snapshot = SnapshotGenerator(universe,
                                 actions = [TrajectoryOutput(trajectory,
                                                             ["all"], 0, None, 1)])

    # Perform rotations and write the configurations
    snapshot()
    for i in range(20):
        universe.protein.applyTransformation(transformation)
        snapshot()

    # Close trajectory
    trajectory.close()

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