Bug Report: channels_bto_only and update_bonded_to() undefined in bonded-to logic #1
Description
In the following code block:
if len(self.ge_lig_batch.channels_bto_only) > 0: self.ge_lig_batch.update_bonded_to() if len(self.ge_prot_batch.channels_bto_only) > 0: self.ge_prot_batch.update_bonded_to()
channels_bto_only is referenced but I couldn't find where it's defined or initialized in either ge_lig_batch or ge_prot_batch.
Similarly, the method update_bonded_to() is called, but does not appear to be defined in the corresponding class.
Expected behavior:
These attributes/methods should either:
be properly defined and initialized before use, or
be removed or replaced with the correct alternatives if deprecated.
Please clarify where channels_bto_only and update_bonded_to() are defined.
If they are deprecated or planned features, a short note in the code or docstring would be helpful.
Thanks for your work!