Fix _SimpleMolecule atom names in roundtrip (#1928)

* Reproduce issue #1927

* Ensure atom name is stored in `_SimpleAtom` dicts

* Update release history

docs/releasehistory.md

@@ -6,20 +6,15 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-## Current development
-
-### API-breaking changes
-
-### Behavior changes
+## 0.16.4
 
 ### Bugfixes
 
-### New features
+- [PR #1928](https://github.com/openforcefield/openff-toolkit/pull/1928): Fixes a bug in which atom names were lost when adding `_SimpleMolecule` to a topology or serializing through a dictionary.
 
 ### Improved documentation and warnings
 - [PR #1925](https://github.com/openforcefield/openff-toolkit/pull/1925): Adds a FAQ entry describing how to send a prepared system to HPC resources.
 
-
 ## 0.16.3
 
 ### New features

openff/toolkit/_tests/test_mm_molecule.py

@@ -9,7 +9,7 @@
     dipeptide_residues_perceived as create_dipeptide,
 )
 from openff.toolkit._tests.utils import get_data_file_path, requires_rdkit
-from openff.toolkit.topology._mm_molecule import _SimpleMolecule
+from openff.toolkit.topology._mm_molecule import _SimpleAtom, _SimpleMolecule
 
 
 @pytest.fixture()
@@ -246,6 +246,26 @@ def test_generate_unique_atom_names(self, water):
         water.atom(1).name = "foo"
         assert water.has_unique_atom_names is False
 
+    def test_atom_names_roundtrip(self, water):
+        water.atom(0).name = "FOO"
+        water.atom(1).name = "BAR"
+        water.atom(2).name = "BAZ"
+
+        roundtrip = copy.deepcopy(water)
+
+        assert roundtrip.atom(0).name == "FOO"
+        assert roundtrip.atom(1).name == "BAR"
+        assert roundtrip.atom(2).name == "BAZ"
+
+
+class TestSimpleAtom:
+    def test_atom_name_in_dict(self):
+        atom = _SimpleAtom(atomic_number=7, name="FLAG")
+
+        assert atom.to_dict()["name"] == "FLAG"
+
+        assert copy.deepcopy(atom).name == "FLAG"
+
 
 class TestImpropers:
     @pytest.mark.parametrize(

openff/toolkit/_tests/test_topology.py

@@ -198,6 +198,22 @@ def test_from_molecule_nonlist(self):
 
             topology.add_molecules("CC.CCO")
 
+    def test_add_simple_molecule_atom_names(self):
+        """Reproduce issue #1927"""
+        simple = _SimpleMolecule.from_molecule(Molecule.from_smiles("C"))
+
+        for index, letter in enumerate("BLAHB"):
+            simple.atom(index).name = letter
+
+        topology = Topology()
+        topology.add_molecule(simple)
+
+        assert topology.atom(0).name == "B"
+        assert topology.atom(1).name == "L"
+        assert topology.atom(2).name == "A"
+        assert topology.atom(3).name == "H"
+        assert topology.atom(4).name == "B"
+
     def test_reinitialization_box_vectors(self):
         topology = Topology()
         assert Topology(topology).box_vectors is None

openff/toolkit/topology/_mm_molecule.py

@@ -627,6 +627,7 @@ def to_dict(self) -> dict[str, Union[dict, str, int]]:
         atom_dict: dict[str, Union[dict, str, int]] = dict()
         atom_dict["metadata"] = dict(self.metadata)
         atom_dict["atomic_number"] = self._atomic_number
+        atom_dict["name"] = self._name
 
         keys_to_skip = ["metadata", "molecule", "bonds"]
 
@@ -636,6 +637,7 @@ def to_dict(self) -> dict[str, Union[dict, str, int]]:
             if attr_name in keys_to_skip:
                 continue
             atom_dict[attr_name] = attr_val
+
         return atom_dict
 
     @classmethod