Different methods of creating TopologyGroups give different results

[lilyminium]

Expected behavior

Creating a TopologyGroup with TopologyGroup.__init__ gives the same result as Universe.add_TopologyAttr.

Actual behavior

Properties such as type, guessed, order, are reshaped and become array values.

Code to reproduce the behavior

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

In [58]: import MDAnalysis as mda
In [59]: from MDAnalysis.tests.datafiles import PSF

In [60]: psf = mda.Universe(PSF)

In [61]: psf.bonds._bondtypes
Out[61]: array([None, None, None, ..., None, None, None], dtype=object)

In [62]: b = mda.core.topologyobjects.TopologyGroup(psf.bonds.indices, psf, type=None)
In [63]: b._bondtypes
Out[63]:
array([[None],
       [None],
       [None],
       ...,
       [None],
       [None],
       [None]], dtype=object)

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

[orbeckst]

This seems ... weird?

[richardjgowers]

I wrote this all a while ago, I think this was something to do with avoiding numpy crusing the datatype into bool (ie preserving the dtype=object which lets you have a numpy array of python objects (ie a list you can manipulate like a numpy array)). It's probably a bug, I can't remember what _bondtype even is any more :(