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Write _atom_site.occupancy in mmCIF output (Fix #331) #341

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Write _atom_site.occupancy in mmCIF output (Fix #331) #341

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4 changes: 4 additions & 0 deletions esm/utils/structure/molecular_complex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -870,6 +870,10 @@ def to_mmcif(self) -> str:
atom_array.atom_name = np.array(atom_names, dtype="U4")
atom_array.add_annotation("b_factor", dtype=float)
atom_array.b_factor = atom_bfactors
atom_array.add_annotation("occupancy", dtype=float)
atom_array.occupancy = np.ones(
n_atoms, dtype=np.float32
) # Necessary for BioPython MMCIFParser
atom_array.add_annotation("entity_id", dtype=int)
atom_array.entity_id = atom_entity_ids

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2 changes: 2 additions & 0 deletions esm/utils/structure/protein_chain.py
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Expand Up @@ -227,6 +227,7 @@ def atom_array(self) -> bs.AtomArray:
atom_name=residue_constants.atom_types[i],
element=residue_constants.atom_types[i][0],
b_factor=float(b_factor),
occupancy=1.0, # Necessary for BioPython MMCIFParser
)
atoms.append(atom)
return bs.array(atoms)
Expand Down Expand Up @@ -262,6 +263,7 @@ def atom_array_no_insertions(self) -> bs.AtomArray:
atom_name=residue_constants.atom_types[i],
element=residue_constants.atom_types[i][0],
b_factor=float(b_factor),
occupancy=1.0, # Necessary for BioPython MMCIFParser
)
atoms.append(atom)
return bs.array(atoms)
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