A variable in bonds parsing is printed in try/except while potentially undefined

[chmnk]

In

ccdutils/pdbeccdutils/core/ccd_reader.py

Line 333 in 38b7e24

except RuntimeError:

atom_2 is uninitialized if the failure happened while handling atom_1. So the except block fails, and since there is no except on top of it, the whole runtime fails.

for row in bonds:
    try:
        atom_1 = row["_chem_comp_bond.atom_id_1"]
        atom_1_id = atoms_ids.index(atom_1)
        atom_2 = row["_chem_comp_bond.atom_id_2"]
        atom_2_id = atoms_ids.index(atom_2)
        bond_order = helper.bond_pdb_order(row["_chem_comp_bond.value_order"])

        mol.AddBond(atom_1_id, atom_2_id, bond_order)
    except ValueError:
        errors.append(
            f"Error perceiving {atom_1} - {atom_2} bond in _chem_comp_bond"
        )
    except RuntimeError:
        errors.append(f"Duplicit bond {atom_1} - {atom_2}")