Outdated documentation for AMBER TRJReader

[lilyminium]

Expected behavior

mdanalysis/package/MDAnalysis/coordinates/TRJ.py

Lines 114 to 124 in e12958c

	.. rubric:: Limitations
	* Periodic boxes are only stored as box lengths A, B, C in an AMBER
	trajectory; the reader always assumes that these are orthorhombic
	boxes.
	* The trajectory does not contain time information so we simply set
	the time step to 1 ps (or the user could provide it as kwarg *dt*)
	* **No direct access of frames is implemented, only iteration through
	the trajectory.**

mdanalysis/package/MDAnalysis/coordinates/TRJ.py

Lines 208 to 209 in e12958c

	Functionality is currently limited to simple iteration over the
	trajectory.

I cannot directly access frames of the trajectory by indexing.

Actual behavior

I can directly access frames of the trajectory by indexing.

Code to reproduce the behavior

Show us how to reproduce the failiure. If you can, use trajectory files from the test data.

In [28]: import MDAnalysis as mda

In [29]: from MDAnalysis.tests.datafiles import PRM, TRJ

In [30]: trj = mda.Universe(PRM, TRJ)
/Users/lily/pydev/mdanalysis/package/MDAnalysis/topology/TOPParser.py:270: UserWarning: ATOMIC_NUMBER record not found, guessing atom elements based on their atom types
  warnings.warn(msg)

In [34]: trj.trajectory[2]
Out[34]: < Timestep 2 with unit cell dimensions [0. 0. 0. 0. 0. 0.] >

In [35]: t2 = trj.atoms.positions

In [36]: trj.trajectory[5]
Out[36]: < Timestep 5 with unit cell dimensions [0. 0. 0. 0. 0. 0.] >

In [37]: t5 = trj.atoms.positions

In [41]: np.array_equal(t2, t5)
Out[41]: False

Currently version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") 0.20.1
• Which version of Python (python -V)? 3.7.3
• Which operating system? MacOS

Just checking that I'm understanding this limitation correctly and can leave it out of the user guide.

[orbeckst]

The limitations are outdated. The reader creates offsets for random access.

(I think nowadays all our readers support some form of random access (since PR #1086, see #314 for discussion).)

[richardjgowers]

Yeah this looks like docs I forgot to update in the ascii offset push.

[IAlibay]

@lilyminium My understanding from this is that all that's needed here is just to clean up the docstring (and maybe add a test)?

I'm planning to do some work on the AMBER readers. Unless you were planning on picking this one up, I can make the changes whilst I'm dealing with that file.

[lilyminium]

@IAlibay Yes, I think it's just the documentation here. Please go ahead!