Improve some typing (#2000)

* Improve some typing

* Fix type annotation for OMMQuantity

* Revert formatting changes

* Restore support for py3.10

* Fix mypy errors

* Type annotate return of _SimpleMolecule bond and atom methods

* Type annotate arg of _SimpleMolecule bond and atom methods

* Make HierarchyScheme.identifier variadic

* Fix fstring in _detect_undefined_stereo

* Fixes to get mypy passing

* Hacks for Pint compatibility

* Molecule.to_rdkit(): support residue number strings that aren't decimal ints

* Update changelog

* More type hints and more formatting reversions

* fix missing annotation referent

* Apply suggestions from code review

* Replace typeignores with type annotation

* Add type annotation for is_isomorphic_with(**kwargs)

---------

Co-authored-by: Matthew W. Thompson <[email protected]>

Author: Yoshanuikabundi

docs/releasehistory.md

@@ -23,6 +23,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### Bugfixes
 
 - [PR #2052](https://github.com/openforcefield/openff-toolkit/pull/2052): Fixes bug where `Topology.from_pdb` couldn't load NH4+ ([Issue #2051](https://github.com/openforcefield/openff-toolkit/issues/2051))
+- [PR #2000](https://github.com/openforcefield/openff-toolkit/pull/2000): Assorted type annotation fixes
+- [PR #2000](https://github.com/openforcefield/openff-toolkit/pull/2000): `Molecule.to_rdkit()` no longer raises an exception when converting a molecule with non-decimal residue numbers to RDKit; instead, the RDKit residue number is simply silently left unset.
 
 ### Miscellaneous
 

openff/toolkit/_tests/test_toolkits.py

@@ -3508,6 +3508,26 @@ def test_to_rdkit_losing_aromaticity_(self):
         for offatom, rdatom in zip(mol.atoms, rdmol.GetAtoms()):
             assert offatom.is_aromatic is rdatom.GetIsAromatic()
 
+    def test_to_rdkit_str_resnum(self):
+        smiles = ("O")
+
+        mol = Molecule.from_smiles(smiles)
+
+        # Test an int, a string that can convert to an int, and a non-intable str
+        atom_resnums = [9998, "9999", "A000"]
+        # RDKit's default residue number is 0
+        expected_atom_resnums = [9998, 9999, 0]
+
+        for atom, resnum in zip(mol.atoms, atom_resnums):
+            atom.metadata["residue_number"] = resnum
+            atom.metadata["residue_name"] = "HOH"
+
+        rdmol = mol.to_rdkit()
+
+        # now make sure the residue number matches for each atom
+        for resnum, rdatom in zip(expected_atom_resnums, rdmol.GetAtoms()):
+            assert rdatom.GetPDBResidueInfo().GetResidueNumber() == resnum
+
     @pytest.mark.slow
     def test_max_substructure_matches_can_handle_large_molecule(self):
         """Test RDKitToolkitWrapper substructure search handles more than the default of maxMatches = 1000

openff/toolkit/topology/_mm_molecule.py

@@ -82,13 +82,13 @@ def n_bonds(self) -> int:
     def n_conformers(self) -> int:
         return 0 if self._conformers is None else len(self._conformers)
 
-    def atom(self, index):
+    def atom(self, index: int) -> "_SimpleAtom":
         return self.atoms[index]
 
     def atom_index(self, atom) -> int:
         return self.atoms.index(atom)
 
-    def bond(self, index):
+    def bond(self, index: int) -> "_SimpleBond":
         return self.bonds[index]
 
     def get_bond_between(self, atom1_index, atom2_index):
@@ -369,7 +369,8 @@ def from_dict(cls, molecule_dict):
             atom1_index = bond_dict["atom1_index"]
             atom2_index = bond_dict["atom2_index"]
             molecule.add_bond(
-                atom1=molecule.atom(atom1_index), atom2=molecule.atom(atom2_index)
+                atom1=molecule.atom(atom1_index),
+                atom2=molecule.atom(atom2_index)
             )
 
         conformers = molecule_dict.pop("conformers")