Skip to content

fix glycan O1 leaving-atom cleanup for standalone glycans #633

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
magnusbauer wants to merge 2 commits into
base: main
Choose a base branch
from
+6 −2
Open

fix glycan O1 leaving-atom cleanup for standalone glycans #633

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
908b859
Make glycan O1 leaving-atom cleanup bond-aware
magnusbauer Mar 11, 2026
088a217
Trigger CLA recheck
magnusbauer Mar 13, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion src/alphafold3/model/atom_layout/atom_layout.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -677,7 +677,7 @@ def get_link_drop_atoms(
*chemical_component_sets.GLYCAN_OTHER_LIGANDS,
*chemical_component_sets.GLYCAN_LINKING_LIGANDS,
}:
if 'O1' not in bonded_atoms:
if bonded_atoms and 'O1' not in bonded_atoms:
drop_atoms.update({'O1'})
return drop_atoms

Expand Down
6 changes: 5 additions & 1 deletion src/alphafold3/model/pipeline/structure_cleaning.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -166,9 +166,13 @@ def clean_structure(
*chemical_component_sets.GLYCAN_OTHER_LIGANDS,
*chemical_component_sets.GLYCAN_LINKING_LIGANDS,
}
# If only glycan ligands and no O1 atoms, we can do parallel drop.
# If only glycan ligands and no O1 atoms, we can do parallel drop. If there are no glycan bonds at all, keep O1.
has_any_glycan_bond = bool(
ligand_ligand_bonds.atom_name.size or polymer_ligand_bonds.atom_name.size
)
if (
only_glycan_ligands_for_leaving_atoms
and has_any_glycan_bond
and (not (ligand_ligand_bonds.atom_name == 'O1').any())
and (not (polymer_ligand_bonds.atom_name == 'O1').any())
):
Expand Down