Raise error when encountering empty InChi string (#1898)

* Raise error when encountering empty InChi string

* Fix test regex, lint/merge

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
 repos:
 - repo: https://github.com/psf/black
-  rev: 24.3.0
+  rev: 24.4.2
   hooks:
   - id: black
   - id: black-jupyter
@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.0.0
+  rev: 7.1.0
   hooks:
   - id: flake8
     files: ^openff|(^utilities/((?!deprecated).)*$)

openff/toolkit/_tests/test_toolkits.py

@@ -33,6 +33,7 @@
     ChargeMethodUnavailableError,
     ChemicalEnvironmentParsingError,
     ConformerGenerationError,
+    EmptyInChiError,
     InChIParseError,
     IncorrectNumConformersError,
     IncorrectNumConformersWarning,
@@ -842,6 +843,16 @@ def test_from_bad_inchi(self):
         with pytest.raises(InChIParseError, match="ksbfksfksfksbfks"):
             Molecule.from_inchi(inchi, toolkit_registry=toolkit)
 
+    def test_empty_inchi(self):
+        """Reproduce Issue #1897"""
+        with pytest.raises(
+            EmptyInChiError,
+            match="failed to generate",
+        ):
+            Molecule.from_mapped_smiles("[H:5][S:3]#[N+:2][S:1][H:4]").to_inchi(
+                toolkit_registry=OpenEyeToolkitWrapper()
+            )
+
     @pytest.mark.parametrize(
         "molecule",
         get_mini_drug_bank(
@@ -2321,6 +2332,16 @@ def test_non_standard_inchi_round_trip(self, molecule):
                 mol2, bond_order_matching=False, toolkit_registry=toolkit
             )
 
+    def test_empty_inchi(self):
+        """Reproduce Issue #1897"""
+        with pytest.raises(
+            EmptyInChiError,
+            match="failed to generate",
+        ):
+            Molecule.from_mapped_smiles("[H:5][S:3]#[N+:2][S:1][H:4]").to_inchi(
+                toolkit_registry=RDKitToolkitWrapper(),
+            )
+
     def test_smiles_charged(self):
         """Test RDKitWrapper functions for reading/writing charged SMILES"""
         toolkit_wrapper = RDKitToolkitWrapper()

openff/toolkit/utils/exceptions.py

@@ -135,6 +135,14 @@ class SmilesParsingError(OpenFFToolkitException):
     """
 
 
+class EmptyInChiError(OpenFFToolkitException):
+    """
+    This error is raised when a toolkit returns an empty InChi string, possibly due to bugs
+    in the underlying InChi code. For more context, see
+    https://github.com/openforcefield/openff-toolkit/issues/1897
+    """
+
+
 class NotAttachedToMoleculeError(OpenFFToolkitException):
     """Exception for when a component does not belong to a Molecule object, but is queried"""
 

openff/toolkit/utils/openeye_wrapper.py

@@ -39,6 +39,7 @@
     ChargeCalculationError,
     ChargeMethodUnavailableError,
     ConformerGenerationError,
+    EmptyInChiError,
     GAFFAtomTypeWarning,
     InChIParseError,
     InconsistentStereochemistryError,
@@ -1916,6 +1917,11 @@ def to_inchi(self, molecule: "Molecule", fixed_hydrogens: bool = False) -> str:
         else:
             inchi = oechem.OEMolToSTDInChI(oemol)
 
+        if len(inchi) == 0:
+            raise EmptyInChiError(
+                "OEChem failed to generate an InChI for the molecule."
+            )
+
         return inchi
 
     def to_inchikey(self, molecule: "Molecule", fixed_hydrogens: bool = False) -> str:

openff/toolkit/utils/rdkit_wrapper.py

@@ -30,6 +30,7 @@
     AmbiguousBondChemicalAssignment,
     ChargeMethodUnavailableError,
     ConformerGenerationError,
+    EmptyInChiError,
     InChIParseError,
     InvalidAromaticityModelError,
     MoleculeParseError,
@@ -2769,6 +2770,10 @@ def to_inchi(self, molecule: "Molecule", fixed_hydrogens: bool = False):
             inchi = Chem.MolToInchi(rdmol, options="-FixedH")
         else:
             inchi = Chem.MolToInchi(rdmol)
+
+        if len(inchi) == 0:
+            raise EmptyInChiError("RDKit failed to generate an InChI for the molecule.")
+
         return inchi
 
     def to_inchikey(self, molecule: "Molecule", fixed_hydrogens: bool = False) -> str:

utilities/test_plugins/custom_plugins/handler_plugins.py

@@ -1,7 +1,12 @@
 # noqa: INP001
-from openff.toolkit.typing.engines.smirnoff import ParameterHandler, ParameterIOHandler
-from openff.toolkit.typing.engines.smirnoff.parameters import ParameterAttribute, ParameterType, _NonbondedHandler
 from openff.toolkit import unit
+from openff.toolkit.typing.engines.smirnoff import ParameterHandler, ParameterIOHandler
+from openff.toolkit.typing.engines.smirnoff.parameters import (
+    ParameterAttribute,
+    ParameterType,
+    _NonbondedHandler,
+)
+
 
 class CustomHandler(ParameterHandler):
     _TAGNAME = "CustomHandler"
@@ -14,6 +19,7 @@ class WrongSubclass(list):
 class CustomIOHandler(ParameterIOHandler):
     _FORMAT = "JSON"
 
+
 class FOOBuckinghamHandler(_NonbondedHandler):
     """A custom parameter handler for buckingham interactions."""
 
@@ -23,18 +29,20 @@ class FOOBuckinghamType(ParameterType):
         _ELEMENT_NAME = "Atom"
 
         # Define unit as a Unit object
-        a = ParameterAttribute(default=None,
-                               unit=unit.kilojoule_per_mole,
-            )
+        a = ParameterAttribute(
+            default=None,
+            unit=unit.kilojoule_per_mole,
+        )
 
         # Define using a string
-        b = ParameterAttribute(default=None,
-                               unit="nanometer**-1",
-                               )
+        b = ParameterAttribute(
+            default=None,
+            unit="nanometer**-1",
+        )
 
         c = ParameterAttribute(
             default=None,
-            unit=unit.kilojoule_per_mole * unit.nanometer ** 6,
+            unit=unit.kilojoule_per_mole * unit.nanometer**6,
         )
 
     _TAGNAME = "FOOBuckingham"