You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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
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, unlessforce_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
Current version of MDAnalysis
python -c "import MDAnalysis as mda; print(mda.__version__)"
)2.8.0-dev0
python -V
)?3.11
MacOS
The text was updated successfully, but these errors were encountered: