Merge branch 'master' into fix/do-not-except-if-computer-test-fails

aiidalab_widgets_base/structures.py

@@ -772,7 +772,10 @@ def _rdkit_opt(self, smiles, steps):
             return None
         mol = Chem.AddHs(mol)
 
-        AllChem.EmbedMolecule(mol, maxAttempts=20, randomSeed=42)
+        conf_id = AllChem.EmbedMolecule(mol, maxAttempts=20, randomSeed=42)
+        if conf_id < 0:
+            self.output.value = "RDKit ERROR: Could not generate conformer"
+            return None
         if AllChem.UFFHasAllMoleculeParams(mol):
             AllChem.UFFOptimizeMolecule(mol, maxIters=steps)
         else:
@@ -785,8 +788,18 @@ def _rdkit_opt(self, smiles, steps):
 
     def _mol_from_smiles(self, smiles, steps=1000):
         """Convert SMILES to ase structure try rdkit then pybel"""
+
+        # Canonicalize the SMILES code
+        # https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system#Terminology
+        canonical_smiles = self.canonicalize_smiles(smiles)
+        if not canonical_smiles:
+            return None
+
+        if canonical_smiles != smiles:
+            self.output.value = f"Canonical SMILES: {canonical_smiles}"
+
         try:
-            return self._rdkit_opt(smiles, steps)
+            return self._rdkit_opt(canonical_smiles, steps)
         except ValueError as e:
             self.output.value = str(e)
             if self.disable_openbabel:
@@ -802,11 +815,27 @@ def _on_button_pressed(self, change=None):
             return
         spinner = f"Screening possible conformers {self.SPINNER}"  # font-size:20em;
         self.output.value = spinner
+
         self.structure = self._mol_from_smiles(self.smiles.value)
         # Don't overwrite possible error/warning messages
         if self.output.value == spinner:
             self.output.value = ""
 
+    def canonicalize_smiles(self, smiles):
+        from rdkit import Chem
+
+        mol = Chem.MolFromSmiles(smiles, sanitize=True)
+        if mol is None:
+            # Something is seriously wrong with the SMILES code,
+            # just return None and don't attempt anything else.
+            self.output.value = "RDkit ERROR: Invalid SMILES string"
+            return None
+        canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
+        if not canonical_smiles:
+            self.output.value = "RDkit ERROR: Could not canonicalize SMILES"
+            return None
+        return canonical_smiles
+
     @tl.default("structure")
     def _default_structure(self):
         return None

tests/test_structures.py

@@ -149,6 +149,27 @@ def test_smiles_widget():
     assert widget.structure.get_chemical_formula() == "N2"
 
 
+@pytest.mark.usefixtures("aiida_profile_clean")
+def test_smiles_canonicalization():
+    """Test the SMILES canonicalization via RdKit."""
+    widget = awb.SmilesWidget()
+
+    # Should not change canonical smiles
+    assert widget.canonicalize_smiles("C") == "C"
+
+    # Should canonicalize this
+    canonical = widget.canonicalize_smiles("O=CC=C")
+    assert canonical == "C=CC=O"
+
+    # Should be idempotent
+    assert canonical == widget.canonicalize_smiles(canonical)
+
+    # Regression test for https://github.com/aiidalab/aiidalab-widgets-base/issues/505
+    # Throwing in this non-canonical string should not raise
+    nasty_smiles = "C=CC1=C(C2=CC=C(C3=CC=CC=C3)C=C2)C=C(C=C)C(C4=CC=C(C(C=C5)=CC=C5C(C=C6C=C)=C(C=C)C=C6C7=CC=C(C(C=C8)=CC=C8C(C=C9C=C)=C(C=C)C=C9C%10=CC=CC=C%10)C=C7)C=C4)=C1"
+    widget._rdkit_opt(nasty_smiles, steps=1)
+
+
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_basic_cell_editor_widget(structure_data_object):
     """Test the `BasicCellEditor`."""