SmilesWidget: Fix generation of 1- and 2-atom molecules (#489)

aiidalab_widgets_base/structures.py

@@ -724,7 +724,8 @@ def _make_ase(self, species, positions, smiles):
         from sklearn.decomposition import PCA
 
         # Get the principal axes and realign the molecule along z-axis.
-        positions = PCA(n_components=3).fit_transform(positions)
+        if len(species) > 2:
+            positions = PCA(n_components=3).fit_transform(positions)
         atoms = ase.Atoms(species, positions=positions, pbc=False)
         atoms.cell = np.ptp(atoms.positions, axis=0) + 10
         atoms.center()

tests/test_structures.py

@@ -142,6 +142,17 @@ def test_smiles_widget():
     assert isinstance(widget.structure, ase.Atoms)
     assert widget.structure.get_chemical_formula() == "CH4"
 
+    # Regression test that we can generate 1-atom and 2-atom molecules
+    widget.smiles.value = "[O]"
+    widget._on_button_pressed()
+    assert isinstance(widget.structure, ase.Atoms)
+    assert widget.structure.get_chemical_formula() == "O"
+
+    widget.smiles.value = "N#N"
+    widget._on_button_pressed()
+    assert isinstance(widget.structure, ase.Atoms)
+    assert widget.structure.get_chemical_formula() == "N2"
+
 
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_basic_cell_editor_widget(structure_data_object):