Getting UnboundLocalError in atoms.py

[aimura09]

Hi team,

Thanks for the amazing work!
I'm getting the following error because cancat_atoms is not defined as a local variable.

[rank0]:   File "/usr/envs/project/lib/python3.11/site-packages/biotite/structure/atoms.py", line 1372, in concatenate
[rank0]:     concat_atoms.coord = np.concatenate([element.coord for element in atoms], axis=-2)
[rank0]:     ^^^^^^^^^^^^
[rank0]: UnboundLocalError: cannot access local variable 'concat_atoms' where it is not associated with a value

Thanks!

[padix-key]

Hi. Thanks for the report. I think your code has still some error, because an unbound concat_atoms should only be possible, if the concatenated elements are neither AtomArray or AtomArrayStack. I created PR #857 to give a proper error in this case.

[nscorley]

In this case, wouldn't rather than checking strict object equality, using isinstance rather than == be the most elegant solution? This error arises in our codebase because we have a data type that inherits from AtomArray to add a handful of additional features. Thus it fails the strict equality (==) but an isinstance with inheritance checks would pass

[padix-key]

True, thanks for pointing out this oversight 👍. The PR now uses issubclass() instead.

[nscorley]

Terrific, thanks!