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Slicing trajectories

MDAnalysis trajectories can be indexed to return a :class:`~MDAnalysis.coordinates.base.Timestep`, or sliced to give a :class:`~MDAnalysis.coordinates.base.FrameIterator`.

.. ipython:: python
    :okwarning:

    import MDAnalysis as mda
    from MDAnalysis.tests.datafiles import PSF, DCD

    u = mda.Universe(PSF, DCD)
    u.trajectory[4]

Indexing a trajectory shifts the :class:`~MDAnalysis.core.universe.Universe` to point towards that particular frame, updating dynamic data such as Universe.atoms.positions.

Note

The trajectory frame is not read from the MD data. It is the internal index assigned by MDAnalysis.

.. ipython:: python

    u.trajectory.frame

Creating a :class:`~MDAnalysis.coordinates.base.FrameIterator` by slicing a trajectory does not shift the :class:`~MDAnalysis.core.universe.Universe` to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.

.. ipython:: python

    fiter = u.trajectory[10::10]
    frames = [ts.frame for ts in fiter]
    print(frames, u.trajectory.frame)

You can also create a sliced trajectory with boolean indexing and fancy indexing. Boolean indexing allows you to select only frames that meet a certain condition, by passing a :class:`~numpy.ndarray` with the same length as the original trajectory. Only frames that have a boolean value of True will be in the resulting :class:`~MDAnalysis.coordinates.base.FrameIterator`. For example, to select only the frames of the trajectory with an RMSD under 2 angstrom:

.. ipython:: python

    from MDAnalysis.analysis import rms

    protein = u.select_atoms('protein')
    rmsd = rms.RMSD(protein, protein).run()
    bools = rmsd.results.rmsd.T[-1] < 2
    print(bools)


.. ipython:: python
    :okwarning:

    fiter = u.trajectory[bools]
    print([ts.frame for ts in fiter])

You can also use fancy indexing to control the order of specific frames.

.. ipython:: python

    indices = [10, 2, 3, 9, 4, 55, 2]
    print([ts.frame for ts in u.trajectory[indices]])

You can even slice a :class:`~MDAnalysis.coordinates.base.FrameIterator` to create a new :class:`~MDAnalysis.coordinates.base.FrameIterator`.

.. ipython:: python

    print([ts.frame for ts in fiter[::3]])