O1 atom incorrectly dropped from non-linking saccharides/glycans

[Jonas-Wilhelm]

When filter_leaving_atoms=True, the clean_structure function drops the O1 atom from all glycans, including non-linking saccharides (GLYCAN_OTHER_LIGANDS). For linking saccharides, O1 is the hydroxyl group that can be replaced by a glycosidic bond, so treating it as a leaving atom is correct. But for non-linking saccharides, O1 should not be removed.

The issue appears in two places: structure_cleaning.py (line 177) and atom_layout.py (line 676).

In both cases, GLYCAN_OTHER_LIGANDS should probably be excluded so that only GLYCAN_LINKING_LIGANDS trigger O1 removal.

[Augustin-Zidek]

Thanks for reporting. This has also been reported in #633, we are working on a fix.