Correctly deal with the names of atoms

[GardevoirX]

The minimal possible Universe of MDAnalysis is

u = mda.Universe.empty(0)

which doesn't contain any atom or atom name, element, or type, but is still a valid Universe.

We shall be able to handle this case, in particular the case where no atom identifier (name, element, or type) is available.

[Luthaf]

Is this about supporting empty structures? I'm not sure how relevant this is, but I guess we can do something about it (although it is not limited to MDA)

[GardevoirX]

This wants to support the case where atoms don't have names (name, type, or element) since in MDAnalysis this is a valid case, and under this case we want to assign the atoms with names like "X"

[Luthaf]

Ah, ok. That works as well (your initial example seemed to show an empty structure)

[ceriottm]

I think we may want to throw an error, TBH. I mean, it'd be an OK response from the point of view of chemiscope. "Sorry we expect actual atoms, please modify your universe to include atom type information"