Fix typos, tests

openff/toolkit/tests/test_topology.py

@@ -266,24 +266,22 @@ def test_get_atom(self, ethane_from_smiles):
         with pytest.raises(Exception) as context:
             topology_atom = topology.atom(8)
 
-    def test_topology_atom_element(self, toluene_from_sdf):
-        """Test getters of TopologyAtom element and atomic number"""
-        from mendeleev import element
-        from mendeleev.models import Element
-
+    def test_topology_atom_element_properties(self, toluene_from_sdf):
+        """
+        Test element-like getters of TopologyAtom atomic number. In 0.11.0, Atom.element
+        was removed and replaced with Atom.atomic_number and Atom.symbol.
+        """
         topology = Topology()
         topology.add_molecule(toluene_from_sdf)
 
-        first_element = topology.atom(0).element
-        eighth_element = topology.atom(7).element
-
-        # Check if types/instances are correct
-        assert isinstance(first_element, Element)
-        assert isinstance(eighth_element, Element)
+        first_atom = topology.atom(0)
+        eighth_atom = topology.atom(7)
 
-        # Make sure first is a carbon element and eighth is a hydrogen element
-        assert first_element.symbol == element(6).symbol
-        assert eighth_element.symbol == element(1).symbol
+        # These atoms are expected to be hydrogen and carbon, respectively
+        assert first_atom.symbol == "C"
+        assert first_atom.atomic_number == 6
+        assert eighth_atom.symbol == "H"
+        assert eighth_atom.atomic_number == 1
 
     def test_get_bond(self, ethane_from_smiles, ethene_from_smiles):
         """Test Topology.bond function (bond lookup from index)"""

openff/toolkit/topology/molecule.py

@@ -422,7 +422,7 @@ def atomic_number(self) -> int:
         """
         return self._atomic_number
 
-    @propert
+    @property
     def symbol(self) -> str:
         """
         Return the symbol implied by the atomic number of this atom
@@ -5539,7 +5539,7 @@ def _to_xyz_file(self, file_path):
             for j, atom_coords in enumerate(geometry.m_as(unit.angstrom)):
                 x, y, z = atom_coords
                 xyz_data.write(
-                    f"{SYMBOLS[self.atoms[j].atomic_number}       {x: .10f}   {y: .10f}   {z: .10f}\n"
+                    f"{SYMBOLS[self.atoms[j].atomic_number]}       {x: .10f}   {y: .10f}   {z: .10f}\n"
                 )
 
             # now we up the frame count

openff/toolkit/topology/topology.py

@@ -1420,7 +1420,9 @@ def from_openmm(cls, openmm_topology, unique_molecules=None):
         # Convert all openMM mols to graphs
         omm_topology_G = nx.Graph()
         for atom in openmm_topology.atoms():
-            omm_topology_G.add_node(atom.index, atomic_number=atom.atomic_number)
+            omm_topology_G.add_node(
+                atom.index, atomic_number=atom.element.atomic_number
+            )
         for bond in openmm_topology.bonds():
             omm_topology_G.add_edge(
                 bond.atom1.index, bond.atom2.index, bond_order=bond.order

openff/toolkit/utils/utils.py

@@ -273,7 +273,7 @@ def string_to_unit(unit_string):
     return unit.Unit(unit_string)
 
 
-def string_to_quantity(quantity_string) -> Union[str, unit.Quantity]:
+def string_to_quantity(quantity_string) -> Union[str, int, float, unit.Quantity]:
     """Attempt to parse a string into a unit.Quantity.
 
     Note that dimensionless floats and ints are returns as floats or ints, not Quantity objects.
@@ -291,9 +291,9 @@ def string_to_quantity(quantity_string) -> Union[str, unit.Quantity]:
     # TODO: Should intentionally unitless array-likes be Quantity objects
     #       or their raw representation?
     if (quantity.units == unit.dimensionless) and isinstance(quantity.m, (int, float)):
-        quantity = quantity.m
-
-    return quantity
+        return quantity.m
+    else:
+        return quantity
 
 
 def _string_to_quantity(quantity_string):