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Add an additional kwarg to parse_ccd_residue to remove atoms named 'O… #93

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Add an additional kwarg to parse_ccd_residue to remove atoms named 'O… #93

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7 changes: 7 additions & 0 deletions src/boltz/data/parse/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,7 @@ def parse_ccd_residue(
name: str,
ref_mol: Mol,
res_idx: int,
remove_oxt_atom: bool = False
) -> Optional[ParsedResidue]:
"""Parse an MMCIF ligand.

Expand Down Expand Up @@ -273,6 +274,11 @@ def parse_ccd_residue(
for i, atom in enumerate(ref_mol.GetAtoms()):
# Get atom name, charge, element and reference coordinates
atom_name = atom.GetProp("name")

# Drop OXT atoms for non-canonical amino acids.
if remove_oxt_atom and atom_name == 'OXT':
continue

charge = atom.GetFormalCharge()
element = atom.GetAtomicNum()
ref_coords = conformer.GetAtomPosition(atom.GetIdx())
Expand Down Expand Up @@ -385,6 +391,7 @@ def parse_polymer(
name=res_corrected,
ref_mol=ref_mol,
res_idx=res_idx,
remove_oxt_atom=True,
)
parsed.append(residue)
continue
Expand Down