Universe() should either work as Universe.empty() or raise an exception

[Luthaf]

Expected behavior

import MDAnalysis as mda
u = mda.Universe()
print(u)

Prints something sensible.

Actual behavior

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-f7a893c68ed4> in <module>
----> 1 print(u)

~/code/mdanalysis/package/MDAnalysis/core/universe.py in __repr__(self)
    775
    776         return "<Universe with {n_atoms} atoms>".format(
--> 777             n_atoms=len(self.atoms))
    778
    779     def __getstate__(self):

TypeError: object of type 'NoneType' has no len()

Currently version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)"): 0.20.2-dev0
• Which version of Python (python -V)? Python 3.7.6
• Which operating system? macOS 10.14.5

[Luthaf]

After looking a bit more at the docs, it looks like I should use mda.Universe.empty() instead to create a Universe. Then maybe calling mda.Universe() with no argument should fail?

[orbeckst]

Honestly, since we have Universe.empty() it is not clear to me why Universe() cannot (semantically) do the same thing — I concede that this would be pythonic behavior.

(There's a good chance that this is simply due to history and the fact that for the longest time empty universes weren't possible. I am also not sure if there are insurmountable technical difficulties.)

[richardjgowers]

@Luthaf thanks for the report. Because there's C allocation going on, and resizing is a pain, even an empty Universe needs to know its size.

It might actually be that you want to pass in the Topology object, which is the thing that a Parser (our reader of everything but coordinates/velocities/forces/dimensions) spits out?

[Luthaf]

It might actually be that you want to pass in the Topology object, which is the thing that a Parser (our reader of everything but coordinates/velocities/forces/dimensions) spits out?

I ended up using Universe.empty() and working with that without issue.

What I wanted to do initially was to create an Universe/a Topology without reading a file, instead adding atoms/coordinates directly from Python. So I created an universe with Universe.empty(n_atoms); and then set the different properties I wanted.