Implement attribute setting for PeriodicSite to route through propert…

src/pymatgen/core/sites.py

@@ -86,6 +86,30 @@ def __getattr__(self, attr: str) -> Any:
             return props[attr]
         raise AttributeError(f"{attr=} not found on {type(self).__name__}")
 
+    def __setattr__(self, attr: str, value: Any) -> None:
+        # Override setattr doesn't play nicely with pickle,
+        # so we can't use self._properties
+        if attr in {"properties", "_properties", "coords"} or attr.startswith("_"):
+            # Avoid infinite recursion when setting properties or _properties
+            super().__setattr__(attr, value)
+        elif isinstance(getattr(type(self), attr, None), property):
+            # If the attribute is a property, set it using the property setter
+            getattr(type(self), attr).fset(self, value)  # type: ignore[union-attr]
+        elif attr in self.__dict__:
+            # If the attribute already exists on the instance, set it directly on the instance
+            super().__setattr__(attr, value)
+        else:
+            warnings.warn(
+                f"Setting attribute {attr} on {type(self).__name__} is deprecated and will be disallowed in a "
+                f"future version. Please set this attribute on the 'properties' dict instead, e.g. "
+                f"site.properties['{attr}'] = {value!r} or use the "
+                f"structure.add_site_property('{attr}', {value!r}) method to add this property to all sites.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            props = self.__dict__.setdefault("properties", {})
+            props[attr] = value
+
     def __getitem__(self, el: Element) -> float:
         """Get the occupancy for element."""
         return self.species[el]

src/pymatgen/core/structure.py

@@ -109,8 +109,8 @@ def __init__(
         self._species: Composition = species
         self.coords: NDArray = coords
         self.properties: dict = properties or {}
-        self.nn_distance: float = nn_distance
-        self.index: int = index
+        object.__setattr__(self, "nn_distance", nn_distance)
+        object.__setattr__(self, "index", index)
         self._label = label
 
     def __len__(self) -> Literal[3]:
@@ -174,9 +174,9 @@ def __init__(
         self._frac_coords = coords
         self._species = species
         self.properties = properties or {}
-        self.nn_distance = nn_distance
-        self.index = index
-        self.image = image
+        object.__setattr__(self, "nn_distance", nn_distance)
+        object.__setattr__(self, "index", index)
+        object.__setattr__(self, "image", image)
         self._label = label
 
     def __len__(self) -> Literal[4]:

tests/core/test_sites.py

@@ -240,6 +240,35 @@ def test_setters(self):
         site.coords = [1.5, 3.25, 5]
         assert_allclose(site.frac_coords, [0.015, 0.0325, 0.05])
 
+    def test_property_setattr_routes_to_properties(self):
+        """Setting an arbitrary attribute on a site should store it in site.properties,
+        not as a bare instance attribute, so it survives from_sites / get_sorted_structure."""
+
+        site = PeriodicSite("Fe", [0.25, 0.35, 0.45], self.lattice)
+
+        # Assignment via attribute syntax must land in .properties
+        site.magmom = 5
+        assert site.properties["magmom"] == 5, "magmom should be stored in site.properties, not as a bare attribute"
+
+        # Round-trip through from_sites must preserve it
+        reconstructed = PeriodicSite.from_dict(site.as_dict())
+        assert reconstructed.magmom == 5, "magmom lost after as_dict/from_dict round-trip"
+
+        # Survival through get_sorted_structure is the real footgun
+        from pymatgen.core import Structure
+
+        struct = Structure(
+            self.lattice,
+            ["Cr", "Fe"],
+            [[0, 0, 0], [0.5, 0.5, 0.5]],
+        )
+        struct.sites[0].magmom = -5
+        struct.sites[1].magmom = 5
+        sorted_struct = struct.get_sorted_structure()
+        assert all("magmom" in site.properties for site in sorted_struct.sites), (
+            "magmom lost on one or more sites after get_sorted_structure"
+        )
+
     def test_repr(self):
         assert repr(self.propertied_site) == "PeriodicSite: Fe2+ (2.5, 3.5, 4.5) [0.25, 0.35, 0.45]"
         assert repr(self.labeled_site) == "PeriodicSite: site label (Fe) (2.5, 3.5, 4.5) [0.25, 0.35, 0.45]"