Unclear Error When Using to_guess=['bonds'] with Existing Bonds in Topology

[yuxuanzhuang]

Expected Behavior

The to_guess=['bonds'] option should work correctly even when bonds are already present in the topology. If bonds exist, the function should either skip guessing or provide an appropriate message, unless force_guess is explicitly set.

Actual Behavior

When attempting to use the new guesser with bonds already present in the topology, an unclear error message occurs:

AttributeError: 'NoneType' object has no attribute 'level'

This error does not provide sufficient information about the underlying issue.

Code to reproduce the behavior

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import CONECT

u = mda.Universe(CONECT, to_guess=['bonds'])

> AttributeError: 'NoneType' object has no attribute 'level'

u = mda.Universe(CONECT, force_guess=['bonds'])
print(u.atoms.bonds)
> <TopologyGroup containing 1922 bonds>

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
  2.8.0-dev0
• Which version of Python (python -V)?
  3.11
• Which operating system?
  MacOS

[lilyminium]

Hmm, I think conceptually one should be able to guess bonds/angles/dihedrals etc. in the to_guess list, and have the behaviour differ from force_guess -- where MDA adds the guessed items additively with to_guess, and replaces existing bonds etc with force_guess. Thoughts? I prototyped something in #4761 but uncovered another bug in #4762