chore: remove TODO's

src/biotite/structure/bonds.pyx

@@ -1647,14 +1647,16 @@ def connect_via_residue_names(atoms, bint inter_residue=True,
                 res_names[curr_start_i], {}
             )
 
-        atom_names_in_res = atom_names[curr_start_i : next_start_i]
-
         # Check if we should use alternative atom names
+        atom_names_in_res = atom_names[curr_start_i : next_start_i]
         std_atom_ids = get_from_ccd(
             "chem_comp_atom", 
             res_names[curr_start_i], 
             "atom_id"
         ) 
+
+        # Only lookup alternative atom names if we cannot match
+        # all atoms using standard names
         if (atom_names_in_res is not None and \
             std_atom_ids is not None and \
             not set(atom_names_in_res).issubset(std_atom_ids)):
@@ -1666,25 +1668,16 @@ def connect_via_residue_names(atoms, bint inter_residue=True,
                 "alt_atom_id"
             ) 
             if set(atom_names_in_res).issubset(alt_atom_ids):
-                # Standardize atom IDs
+                # Residue uses alternative names; standardize them
                 mapping = dict(zip(alt_atom_ids, std_atom_ids))
-                mapped_atom_names_in_res = np.vectorize(
-                    mapping.get
-                )(atom_names_in_res)
-                atom_names_in_res = mapped_atom_names_in_res
-
-                # If we uncomment the line below, we modify the atom_name in-place
-                # And thus enforce standardized atom names (which may be an unexpected behavior)
-                # TODO: Is that a desired behavior?
-                # atoms.atom_name[curr_start_i : next_start_i] = atom_names_in_res
-
-            # TODO: How to handle cases that do not fit either mapping?
+                atom_names_in_res = [mapping.get(atom_name) for atom_name in atom_names_in_res]
 
         for (atom_name1, atom_name2), bond_type in bond_dict_for_res.items():
             atom_indices1 = np.where(atom_names_in_res == atom_name1)[0] \
                             .astype(np.int64, copy=False)
             atom_indices2 = np.where(atom_names_in_res == atom_name2)[0] \
                             .astype(np.int64, copy=False)
+
             # In rare cases the same atom name may appear multiple times
             # (e.g. in altlocs)
             # -> create all possible bond combinations

tests/structure/io/test_pdbx.py

@@ -224,22 +224,19 @@ def test_connect_via_residue_names_with_alt_atom_ids():
     )
     atoms = pdbx.get_structure(pdbx_file_with_no_alt_ids, model=1, include_bonds=True)
 
+    # ZY9 modified to have alternative atom IDs
     pdbx_file_with_alt_ids = pdbx.CIFFile.read(
         join(data_dir("structure"), "6q9t_with_alt_ids.cif")
     )
     atoms_with_alt_ids = pdbx.get_structure(
         pdbx_file_with_alt_ids, model=1, include_bonds=True
     )
 
-    # Assert bonds are the same
-    assert (
-        atoms_with_alt_ids[atoms_with_alt_ids.res_name == "ZY9"].bonds.as_array()
-        == atoms[atoms.res_name == "ZY9"].bonds.as_array()
-    ).all()
-
-    # zy9 = atoms.res_name == "ZY9"
+    # Ensure bonds are the same
+    assert (atoms_with_alt_ids.bonds.as_array() == atoms.bonds.as_array()).all()
 
-    print("Here.")
+    # Ensure atom names are the same (we mapped the alternative atom IDs to the standard atom IDs)
+    assert (atoms.atom_name == atoms_with_alt_ids.atom_name).all()
 
 
 def test_bond_sparsity():
@@ -923,7 +920,3 @@ def test_writing_and_reading_extra_fields(tmpdir):
     assert np.all(
         atoms.get_annotation("my_custom_annotation").astype(int) == custom_annotation
     )
-
-
-if __name__ == "__main__":
-    test_connect_via_residue_names_with_alt_atom_ids()