Slicing trajectoriesΒΆ
MDAnalysis trajectories can be indexed to return a Timestep, or sliced to give a FrameIterator.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import PSF, DCD
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-2-2f9c58525a71> in <module>
----> 1 from MDAnalysis.tests.datafiles import PSF, DCD
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysis/tests/datafiles.py in <module>
41
42 try:
---> 43 from MDAnalysisTests.datafiles import *
44 except ImportError:
45 print("*** ERROR ***")
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysisTests/__init__.py in <module>
124 try:
125 import matplotlib
--> 126 matplotlib.use('agg', warn=False)
127 except ImportError:
128 pass
TypeError: use() got an unexpected keyword argument 'warn'
In [3]: u = mda.Universe(PSF, DCD)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-3-62bb8796b82b> in <module>
----> 1 u = mda.Universe(PSF, DCD)
NameError: name 'PSF' is not defined
In [4]: u.trajectory[4]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-4-4fbf22aeeae3> in <module>
----> 1 u.trajectory[4]
NameError: name 'u' is not defined
Indexing a trajectory shifts the 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.
In [5]: u.trajectory.frame
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-5-c0cd53eaa961> in <module>
----> 1 u.trajectory.frame
NameError: name 'u' is not defined
Creating a FrameIterator by slicing a trajectory does not shift the Universe to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.
In [6]: fiter = u.trajectory[10::10]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-6-5a015cdf7981> in <module>
----> 1 fiter = u.trajectory[10::10]
NameError: name 'u' is not defined
In [7]: frames = [ts.frame for ts in fiter]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-7-acc03d2ea4ba> in <module>
----> 1 frames = [ts.frame for ts in fiter]
NameError: name 'fiter' is not defined
In [8]: print(frames, u.trajectory.frame)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-8-ecffb9803e98> in <module>
----> 1 print(frames, u.trajectory.frame)
NameError: name 'frames' is not defined
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 ndarray with the same length as the original trajectory. Only frames that have a boolean value of True will be in the resulting FrameIterator. For example, to select only the frames of the trajectory with an RMSD under 2 angstrom:
In [9]: from MDAnalysis.analysis import rms
In [10]: protein = u.select_atoms('protein')
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-10-61a96949b257> in <module>
----> 1 protein = u.select_atoms('protein')
NameError: name 'u' is not defined
In [11]: rmsd = rms.RMSD(protein, protein).run()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-11-380cb8765aff> in <module>
----> 1 rmsd = rms.RMSD(protein, protein).run()
NameError: name 'protein' is not defined
In [12]: bools = rmsd.rmsd.T[-1] < 2
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-12-c242f2746f79> in <module>
----> 1 bools = rmsd.rmsd.T[-1] < 2
NameError: name 'rmsd' is not defined
In [13]: print(bools)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-13-2ca3ea69cb7f> in <module>
----> 1 print(bools)
NameError: name 'bools' is not defined
In [14]: fiter = u.trajectory[bools]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-14-9f7be376a205> in <module>
----> 1 fiter = u.trajectory[bools]
NameError: name 'u' is not defined
In [15]: print([ts.frame for ts in fiter])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-15-0e02b73dc35f> in <module>
----> 1 print([ts.frame for ts in fiter])
NameError: name 'fiter' is not defined
You can also use fancy indexing to control the order of specific frames.
In [16]: indices = [10, 2, 3, 9, 4, 55, 2]
In [17]: print([ts.frame for ts in u.trajectory[indices]])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-17-973dccb4f0d4> in <module>
----> 1 print([ts.frame for ts in u.trajectory[indices]])
NameError: name 'u' is not defined
You can even slice a FrameIterator to create a new FrameIterator.
In [18]: print([ts.frame for ts in fiter[::3]])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-18-781b4e57c055> in <module>
----> 1 print([ts.frame for ts in fiter[::3]])
NameError: name 'fiter' is not defined