Remove openbabel dependency (#518)

* Add tests for invalid SMILES

aiidalab_widgets_base/structures.py

@@ -685,13 +685,6 @@ class SmilesWidget(ipw.VBox):
 
     def __init__(self, title=""):
         self.title = title
-
-        try:
-            from openbabel import openbabel  # noqa: F401
-            from openbabel import pybel  # noqa: F401
-        except ImportError:
-            self.disable_openbabel = True
-
         try:  # noqa: TC101
             from rdkit import Chem  # noqa: F401
             from rdkit.Chem import AllChem  # noqa: F401
@@ -735,30 +728,6 @@ def _make_ase(self, species, positions, smiles):
 
         return atoms
 
-    def _pybel_opt(self, smiles, steps):
-        """Optimize a molecule using force field and pybel (needed for complex SMILES)."""
-        from openbabel import openbabel as ob
-        from openbabel import pybel as pb
-
-        obconversion = ob.OBConversion()
-        obconversion.SetInFormat("smi")
-        obmol = ob.OBMol()
-        obconversion.ReadString(obmol, smiles)
-
-        pbmol = pb.Molecule(obmol)
-        pbmol.make3D(forcefield="uff", steps=50)
-
-        pbmol.localopt(forcefield="gaff", steps=200)
-        pbmol.localopt(forcefield="mmff94", steps=100)
-
-        f_f = pb._forcefields["uff"]
-        f_f.Setup(pbmol.OBMol)
-        f_f.ConjugateGradients(steps, 1.0e-9)
-        f_f.GetCoordinates(pbmol.OBMol)
-        species = [ase.data.chemical_symbols[atm.atomicnum] for atm in pbmol.atoms]
-        positions = np.asarray([atm.coords for atm in pbmol.atoms])
-        return self._make_ase(species, positions, smiles)
-
     def _rdkit_opt(self, smiles, steps):
         """Optimize a molecule using force field and rdkit (needed for complex SMILES)."""
         from rdkit import Chem
@@ -795,28 +764,20 @@ def _rdkit_opt(self, smiles, steps):
         return self._make_ase(species, positions, smiles)
 
     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}"
-
+        """Convert SMILES to ASE structure using RDKit"""
         try:
-            return self._rdkit_opt(canonical_smiles, steps)
+            canonical_smiles = self.canonicalize_smiles(smiles)
+            ase = self._rdkit_opt(canonical_smiles, steps)
         except ValueError as e:
             self.output.value = str(e)
-            if self.disable_openbabel:
-                return None
-            self.output.value += " Trying OpenBabel..."
-            return self._pybel_opt(smiles, steps)
+            return None
+        else:
+            if canonical_smiles != smiles:
+                self.output.value = f"Canonical SMILES: {canonical_smiles}"
+            return ase
 
     def _on_button_pressed(self, change=None):
-        """Convert SMILES to ase structure when button is pressed."""
+        """Convert SMILES to ASE structure when button is pressed."""
         self.output.value = ""
 
         if not self.smiles.value:
@@ -829,19 +790,25 @@ def _on_button_pressed(self, change=None):
         if self.output.value == spinner:
             self.output.value = ""
 
-    def canonicalize_smiles(self, smiles):
+    # https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system#Terminology
+    @staticmethod
+    def canonicalize_smiles(smiles: str) -> str:
+        """Canonicalize the SMILES code.
+
+        :raises ValueError: if SMILES is invalid or if canonicalization fails
+        """
         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
+            # Something is seriously wrong with the SMILES code
+            msg = "Invalid SMILES string"
+            raise ValueError(msg)
+
         canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
         if not canonical_smiles:
-            self.output.value = "RDkit ERROR: Could not canonicalize SMILES"
-            return None
+            msg = "SMILES canonicalization failed"
+            raise ValueError(msg)
         return canonical_smiles
 
     @tl.default("structure")

tests/test_structures.py

@@ -148,21 +148,32 @@ def test_smiles_widget():
     assert isinstance(widget.structure, ase.Atoms)
     assert widget.structure.get_chemical_formula() == "N2"
 
+    # Should not raise for invalid smiles
+    widget.smiles.value = "invalid"
+    widget._on_button_pressed()
+    assert widget.structure is None
+
 
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_smiles_canonicalization():
     """Test the SMILES canonicalization via RdKit."""
-    widget = awb.SmilesWidget()
+    canonicalize = awb.SmilesWidget.canonicalize_smiles
 
     # Should not change canonical smiles
-    assert widget.canonicalize_smiles("C") == "C"
+    assert canonicalize("C") == "C"
 
     # Should canonicalize this
-    canonical = widget.canonicalize_smiles("O=CC=C")
+    canonical = canonicalize("O=CC=C")
     assert canonical == "C=CC=O"
 
     # Should be idempotent
-    assert canonical == widget.canonicalize_smiles(canonical)
+    assert canonical == canonicalize(canonical)
+
+    # Should raise for invalid smiles
+    with pytest.raises(ValueError):
+        canonicalize("invalid")
+    # There is another failure mode when RDkit mol object is generated
+    # but the canonicalization fails. I do not know how to trigger it though.
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")