Fix bug where atoms with alt loc 1 aren't parsed

atomium/files/pdbdict2pdb.py

@@ -58,8 +58,11 @@ def residue_dict_to_residue(residue_dict, molecule=False):
     instead of a :py:class:`.Residue`.
     :rtype: :py:class:`.Residue` or :py:class:`.Molecule`"""
 
-    atoms = [atom_dict_to_atom(atom) for atom in residue_dict["atoms"]
-     if atom["alt_loc"] is None or atom["alt_loc"] == "A"]
+    atoms = [
+     atom_dict_to_atom(atom) for atom in residue_dict["atoms"]
+      if atom["alt_loc"] is None or atom["alt_loc"] == "A"
+       or atom["alt_loc"] == "1"
+    ]
     MolClass = Molecule if molecule else Residue
     residue = MolClass(*atoms, name=residue_dict["name"])
     residue._id = residue_dict["id"]

tests/unit/files_tests/test_pdb_dict_to_pdb.py

@@ -120,6 +120,7 @@ def test_can_convert_residue_dict_to_residue(self, mock_atom, mock_res):
     @patch("atomium.files.pdbdict2pdb.Residue")
     @patch("atomium.files.pdbdict2pdb.atom_dict_to_atom")
     def test_can_convert_residue_dict_to_residue_alt_loc(self, mock_atom, mock_res):
+        self.atom_dicts[1]["alt_loc"] = "1"
         self.atom_dicts[2]["alt_loc"] = "A"
         self.atom_dicts[3]["alt_loc"] = "B"
         self.atom_dicts[2]["occupancy"] = 0.8
@@ -130,7 +131,7 @@ def test_can_convert_residue_dict_to_residue_alt_loc(self, mock_atom, mock_res):
         res_dict = {"id": "A12", "name": "VAL", "atoms": self.atom_dicts}
         returned_residue = residue_dict_to_residue(res_dict)
         mock_atom.assert_any_call({"alt_loc": None, "atom_id": 1, "occupancy": 1})
-        mock_atom.assert_any_call({"alt_loc": None, "atom_id": 2, "occupancy": 1})
+        mock_atom.assert_any_call({"alt_loc": "1", "atom_id": 2, "occupancy": 1})
         mock_atom.assert_any_call({"alt_loc": "A", "atom_id": 3, "occupancy": 0.8})
         self.assertEqual(mock_atom.call_count, 3)
         self.assertIs(returned_residue, residue)