Enumerate input molecule with tautomers

docs/releasehistory.md

@@ -12,6 +12,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Behavior changes
 
+- [PR #17XX](https://github.com/openforcefield/openff-toolkit/pull/17XX): `Molecule.enumerate_tautomers` now includes the input molecule in the returned list.
+
 ### Bugfixes
 
 ### New features

openff/toolkit/_tests/test_molecule.py

@@ -2103,12 +2103,18 @@ def test_enumerating_tautomers(self, molecule_data, toolkit_class):
 
             tautomers = mol.enumerate_tautomers(toolkit_registry=toolkit)
 
-            assert len(tautomers) == molecule_data["tautomers"]
-            assert mol not in tautomers
-            # check that the molecules are not isomorphic of the input
+            assert len(tautomers) == molecule_data["tautomers"] + 1
+            assert mol in tautomers
+
+            # check that only one molecule (literally the input) is isomorphic of the input
+
+            number_isomorphic = 0
             for taut in tautomers:
                 assert taut.n_conformers == 0
-                assert mol.is_isomorphic_with(taut) is False
+                if mol.is_isomorphic_with(taut):
+                    number_isomorphic += 1
+
+            assert number_isomorphic == 1
 
         else:
             pytest.skip("Required toolkit is unavailable")
@@ -2132,8 +2138,8 @@ def test_enumerating_tautomers_options(self, toolkit_class):
             tautomers = mol.enumerate_tautomers(
                 max_states=tauts_no, toolkit_registry=toolkit
             )
-            assert len(tautomers) <= tauts_no
-            assert mol not in tautomers
+            assert len(tautomers) <= tauts_no + 1
+            assert mol in tautomers
 
     @pytest.mark.parametrize(
         "toolkit_class", [RDKitToolkitWrapper, OpenEyeToolkitWrapper]
@@ -2146,7 +2152,8 @@ def test_enumerating_no_tautomers(self, toolkit_class):
             mol = Molecule.from_smiles("CC", toolkit_registry=toolkit)
 
             tautomers = mol.enumerate_tautomers(toolkit_registry=toolkit)
-            assert tautomers == []
+            assert len(tautomers) == 1
+            assert tautomers[0] == mol
 
         else:
             pytest.skip("Required toolkit is unavailable")

openff/toolkit/topology/molecule.py

@@ -4144,8 +4144,11 @@ def to_file(self, file_path, file_format, toolkit_registry=GLOBAL_TOOLKIT_REGIST
         else:
             toolkit.to_file_obj(self, file_path, file_format)
 
+    # TODO: This should probably be a class method
     def enumerate_tautomers(
-        self, max_states=20, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY
+        self,
+        max_states=20,
+        toolkit_registry=GLOBAL_TOOLKIT_REGISTRY,
     ):
         """
         Enumerate the possible tautomers of the current molecule
@@ -4161,8 +4164,8 @@ def enumerate_tautomers(
 
         Returns
         -------
-        molecules: List[openff.toolkit.topology.Molecule]
-            A list of openff.toolkit.topology.Molecule instances not including the input molecule.
+        molecules: list[openff.toolkit.Molecule]
+            A list of openff.toolkit.Molecule instances including the input molecule.
         """
 
         if isinstance(toolkit_registry, ToolkitRegistry):

openff/toolkit/utils/openeye_wrapper.py

@@ -811,22 +811,24 @@ def _assign_aromaticity_and_stereo_from_3d(self, offmol):
         return offmol_w_stereo_and_aro
 
     def enumerate_protomers(
-        self, molecule: "Molecule", max_states: int = 10
-    ) -> List["Molecule"]:
+        self,
+        molecule: "Molecule",
+        max_states: int = 10,
+    ) -> list["Molecule"]:
         """
         Enumerate the formal charges of a molecule to generate different protomoers.
 
         Parameters
         ----------
-        molecule: openff.toolkit.topology.Molecule
+        molecule: openff.toolkit.Molecule
             The molecule whose state we should enumerate
 
         max_states: int optional, default=10,
             The maximum number of protomer states to be returned.
 
         Returns
         -------
-        molecules: List[openff.toolkit.topology.Molecule],
+        molecules: list[openff.toolkit.Molecule],
             A list of the protomers of the input molecules not including the input.
         """
 
@@ -912,8 +914,10 @@ def enumerate_stereoisomers(
         return molecules[:max_isomers]
 
     def enumerate_tautomers(
-        self, molecule: "Molecule", max_states: int = 20
-    ) -> List["Molecule"]:
+        self,
+        molecule: "Molecule",
+        max_states: int = 20,
+    ) -> list["Molecule"]:
         """
         Enumerate the possible tautomers of the current molecule
 
@@ -927,8 +931,8 @@ def enumerate_tautomers(
 
         Returns
         -------
-        molecules: List[openff.toolkit.topology.Molecule]
-            A list of openff.toolkit.topology.Molecule instances excluding the input molecule.
+        molecules: list[openff.toolkit.Molecule]
+            A list of openff.toolkit.Molecule instances excluding the input molecule.
         """
         from openeye import oequacpac
 
@@ -945,16 +949,13 @@ def enumerate_tautomers(
         tautomer_options.SetCarbonHybridization(False)
 
         for tautomer in oequacpac.OEEnumerateTautomers(oemol, tautomer_options):
-            # remove the input tautomer from the output
-            taut = self.from_openeye(
-                tautomer, allow_undefined_stereo=True, _cls=molecule.__class__
-            )
-            if taut != molecule:
-                tautomers.append(
-                    self.from_openeye(
-                        tautomer, allow_undefined_stereo=True, _cls=molecule.__class__
-                    )
+            tautomers.append(
+                self.from_openeye(
+                    tautomer,
+                    allow_undefined_stereo=True,
+                    _cls=molecule.__class__,
                 )
+            )
 
         return tautomers
 

openff/toolkit/utils/rdkit_wrapper.py

@@ -1339,23 +1339,25 @@ def enumerate_stereoisomers(
         return molecules
 
     def enumerate_tautomers(
-        self, molecule: "Molecule", max_states: int = 20
-    ) -> List["Molecule"]:
+        self,
+        molecule: "Molecule",
+        max_states: int = 20,
+    ) -> list["Molecule"]:
         """
         Enumerate the possible tautomers of the current molecule.
 
         Parameters
         ----------
-        molecule: openff.toolkit.topology.Molecule
+        molecule: openff.toolkit.Molecule
             The molecule whose state we should enumerate
 
         max_states: int optional, default=20
             The maximum amount of molecules that should be returned
 
         Returns
         -------
-        molecules: List[openff.toolkit.topology.Molecule]
-            A list of openff.toolkit.topology.Molecule instances not including the input molecule.
+        molecules: list[openff.toolkit.Molecule]
+            A list of openff.toolkit.Molecule instances including the input molecule.
         """
 
         from rdkit import Chem
@@ -1371,11 +1373,12 @@ def enumerate_tautomers(
         molecules = []
         for taut in tautomers:
             taut_hs = Chem.AddHs(taut)
-            mol = self.from_smiles(
-                Chem.MolToSmiles(taut_hs), allow_undefined_stereo=True
+            molecules.append(
+                self.from_smiles(
+                    Chem.MolToSmiles(taut_hs),
+                    allow_undefined_stereo=True,
+                )
             )
-            if mol != molecule:
-                molecules.append(mol)
 
         return molecules[:max_states]