analysis.rms.RMSD broken

[orbeckst]

Expected behaviour

I should be able to set a RMSD analysis with MDAnalysis.analysis.rms.RMSD

Actual behaviour

Raises NameError.

Analysis

It seems that recently _process_selection() was renamed to process_selection() in 46f915b --- @jdetle seems to have forgotten to also rename references.

Even worse: There are no unit tests for the RMSD class! There's a test TestRMSD but it does not test the RMSD class but the rmsd() function. We should

• fix rms.RMSD
• rename TestRMSD to Testrmsdfunc (or just Testrms --- it all looks ugly?)
• add a test TestRMSD for rms.RMSD

Stack Trace

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-6-be62615c3dd7> in <module>()
----> 1 R = RMSD(u, select="protein and name CA")

/nfs/homes2/oliver/Library/python/mdanalysis/package/MDAnalysis/analysis/rms.pyc in __init__(self, traj, reference, select, groupselections, filename, mass_weighted, tol_mass, ref_frame)
    339         else:
    340             self.reference = reference
--> 341         self.select = _process_selection(select)
    342         if groupselections is not None:
    343             self.groupselections = [_process_selection(s) for s in groupselections]

NameError: global name '_process_selection' is not defined

Code to reproduce the behaviour

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
from MDAnalysis.analysis.rms import RMSD
u = mda.Universe(PSF, DCD)
R = RMSD(u, select="protein and name CA")

Currently version of MDAnalysis:

(run python -c "import MDAnalysis as mda; print(mda.__version__)")
0.15.1-dev0

[orbeckst]

(By the way, not having tests for rms.RMSD is probably my own fault...)

[jdetle]

I broke it, someone else didn't cover the code, let's just call it a draw...

[orbeckst]

Sounds fair ;-)