Structure viewer for 0d hide the cell tab

aiidalab_widgets_base/structures.py

@@ -376,32 +376,6 @@ def __init__(
             children=[self.file_upload, supported_formats, self._status_message]
         )
 
-    def _validate_and_fix_ase_cell(self, ase_structure, vacuum_ang=10.0):
-        """
-        Checks if the ase Atoms object has a cell set,
-        otherwise sets it to bounding box plus specified "vacuum" space
-        """
-        if not ase_structure:
-            return None
-
-        cell = ase_structure.cell
-
-        # TODO: Since AiiDA 2.0, zero cell is possible if PBC=false
-        # so we should honor that here and do not put artificial cell
-        # around gas phase molecules.
-        if (
-            np.linalg.norm(cell[0]) < 0.1
-            or np.linalg.norm(cell[1]) < 0.1
-            or np.linalg.norm(cell[2]) < 0.1
-        ):
-            # if any of the cell vectors is too short, consider it faulty
-            # set cell as bounding box + vacuum_ang
-            bbox = np.ptp(ase_structure.positions, axis=0)
-            new_structure = ase_structure.copy()
-            new_structure.cell = bbox + vacuum_ang
-            return new_structure
-        return ase_structure
-
     def _on_file_upload(self, change=None):
         """When file upload button is pressed."""
         for fname, item in change["new"].items():
@@ -444,9 +418,9 @@ def _read_structure(self, fname, content):
                     return TrajectoryData(
                         structurelist=[
                             StructureData(
-                                ase=self._validate_and_fix_ase_cell(ase_struct)
+                                ase=ase_structure,
                             )
-                            for ase_struct in structures
+                            for ase_structure in structures
                         ]
                     )
                 else:
@@ -455,7 +429,7 @@ def _read_structure(self, fname, content):
                         """
                     return None
 
-            return self._validate_and_fix_ase_cell(structures[0])
+            return structures[0]
 
 
 class StructureExamplesWidget(ipw.VBox):
@@ -720,7 +694,6 @@ def _make_ase(self, species, positions, smiles):
         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()
         # We're attaching this info so that it
         # can be later stored as an extra on AiiDA Structure node.

aiidalab_widgets_base/viewers.py

@@ -169,47 +169,74 @@ def __init__(
         self._viewer.observe(self._on_atom_click, names="picked")
         self._viewer.stage.set_parameters(mouse_preset="pymol")
 
-        view_box = ipw.VBox([self._viewer])
+        self.view_box = ipw.VBox([self._viewer])
 
-        configuration_tabs_map = {
-            "Cell": self._cell_tab(),
-            "Selection": self._selection_tab(),
-            "Appearance": self._appearance_tab(),
-            "Download": self._download_tab(),
-        }
+        # Constructing configuration box
+        if configuration_tabs is None:
+            self._configuration_tabs = [
+                "Selection",
+                "Appearance",
+                "Lattice",
+                "Download",
+            ]
+        else:
+            self._configuration_tabs = configuration_tabs
 
-        if configure_view is not True:
+        # For backward compatibility, where the Lattice tab was called Cell.
+        if "Cell" in self._configuration_tabs:
             warnings.warn(
-                "`configure_view` is deprecated, please use `configuration_tabs` instead.",
+                "`Cell` tab is deprecated, please use `Lattice` instead. Will be removed in the version 3.0.0",
                 DeprecationWarning,
                 stacklevel=2,
             )
-            if not configure_view:
-                configuration_tabs.clear()
+            self._configuration_tabs.remove("Cell")
+            self._configuration_tabs.append("Lattice")
 
-        # Constructing configuration box
-        if configuration_tabs is None:
-            configuration_tabs = ["Selection", "Appearance", "Cell", "Download"]
-        if len(configuration_tabs) != 0:
-            self.configuration_box = ipw.Tab(
-                layout=ipw.Layout(flex="1 1 auto", width="auto")
+        if configure_view is not True:
+            warnings.warn(
+                "`configure_view` is deprecated, please use `configuration_tabs` instead. Will be removed in the version 3.0.0",
+                DeprecationWarning,
+                stacklevel=2,
             )
-            self.configuration_box.children = [
-                configuration_tabs_map[tab_title] for tab_title in configuration_tabs
-            ]
+            if not configure_view:
+                self._configuration_tabs.clear()
 
-            for i, title in enumerate(configuration_tabs):
-                self.configuration_box.set_title(i, title)
-            children = [ipw.HBox([view_box, self.configuration_box])]
-            view_box.layout = {"width": "60%"}
+        if len(self._configuration_tabs) != 0:
+            configuration_box = self._create_tabs(self._configuration_tabs)
+            children = [ipw.HBox([self.view_box, configuration_box])]
+            self.view_box.layout = {"width": "60%"}
         else:
-            children = [view_box]
+            children = [self.view_box]
 
         if "children" in kwargs:
+            warnings.warn(
+                "defining `children` is deprecated, will be removed in the version 3.0.0",
+                DeprecationWarning,
+                stacklevel=2,
+            )
             children += kwargs.pop("children")
 
         super().__init__(children, **kwargs)
 
+    def _create_tabs(self, configuration_tabs):
+        """Create tabs for configuration box."""
+        configuration_tabs_map = {
+            "Lattice": self._cell_tab(),
+            "Selection": self._selection_tab(),
+            "Appearance": self._appearance_tab(),
+            "Download": self._download_tab(),
+        }
+
+        configuration_box = ipw.Tab(layout=ipw.Layout(flex="1 1 auto", width="auto"))
+        configuration_box.children = [
+            configuration_tabs_map[tab_title] for tab_title in configuration_tabs
+        ]
+
+        for i, title in enumerate(self._configuration_tabs):
+            configuration_box.set_title(i, title)
+
+        return configuration_box
+
     def _selection_tab(self):
         """Defining the selection tab."""
 
@@ -317,7 +344,24 @@ def change_camera(change):
 
     @tl.observe("cell")
     def _observe_cell(self, _=None):
-        # Updtate the Cell and Periodicity.
+        # Update the widget layout view.
+        if not self.cell and "Lattice" in self._configuration_tabs:
+            self._configuration_tabs.remove("Lattice")
+
+        if self.cell and "Lattice" not in self._configuration_tabs:
+            self._configuration_tabs = ["Lattice"] + self._configuration_tabs
+
+        if len(self._configuration_tabs) != 0:
+            configuration_box = self._create_tabs(self._configuration_tabs)
+            self.children = [ipw.HBox([self.view_box, configuration_box])]
+            self.view_box.layout = {"width": "60%"}
+        else:
+            self.children = [self.view_box]
+
+        # Updtate the Lattice tab and Periodicity.
+
+        # For molecules, the cell is Cell([0, 0, 0]) and in the condition is still # `False``. That's why it is able to use `if self.cell` to cover both None and
+        # not cell defined cases.
         if self.cell:
             self.cell_a.value = "<i><b>a</b></i>: {:.4f} {:.4f} {:.4f}".format(
                 *self.cell.array[0]
@@ -363,22 +407,6 @@ def _observe_cell(self, _=None):
             self.periodicity.value = (
                 f"Periodicity: {periodicity_map[tuple(self.structure.pbc)]}"
             )
-        else:
-            self.cell_a.value = "<i><b>a</b></i>:"
-            self.cell_b.value = "<i><b>b</b></i>:"
-            self.cell_c.value = "<i><b>c</b></i>:"
-
-            self.cell_a_length.value = "|<i><b>a</b></i>|:"
-            self.cell_b_length.value = "|<i><b>b</b></i>|:"
-            self.cell_c_length.value = "|<i><b>c</b></i>|:"
-
-            self.cell_alpha.value = "&alpha;:"
-            self.cell_beta.value = "&beta;:"
-            self.cell_gamma.value = "&gamma;:"
-
-            self.cell_spacegroup.value = ""
-            self.cell_hall.value = ""
-            self.periodicity.value = ""
 
     def _cell_tab(self):
         self.cell_a = ipw.HTML()
@@ -397,8 +425,6 @@ def _cell_tab(self):
         self.cell_hall = ipw.HTML()
         self.periodicity = ipw.HTML()
 
-        self._observe_cell()
-
         return ipw.VBox(
             [
                 ipw.HTML("Length unit: angstrom (Å)"),
@@ -789,7 +815,9 @@ def __init__(self, structure=None, **kwargs):
 
     @tl.observe("supercell")
     def repeat(self, _=None):
-        if self.structure is not None:
+        # need to check if cell is defined, otherwise it will throw an error
+        # since it makes no sense to repeat a molecule
+        if self.structure is not None and self.cell:
             self.set_trait("displayed_structure", self.structure.repeat(self.supercell))
 
     @tl.validate("structure")
@@ -1096,7 +1124,8 @@ def add_info(indx, atom):
 
     @tl.observe("displayed_selection")
     def _observe_displayed_selection_2(self, _=None):
-        self.selection_info.value = self.create_selection_info()
+        if self.displayed_selection:
+            self.selection_info.value = self.create_selection_info()
 
 
 @register_viewer_widget("data.core.folder.FolderData.")

tests/conftest.py

@@ -203,6 +203,14 @@ def structure_data_object():
     return structure
 
 
+@pytest.fixture
+def molecule_ase_object():
+    """Return an ase molecule object."""
+    from ase.build import molecule
+
+    return molecule("H2O")
+
+
 @pytest.fixture
 def bands_data_object():
     BandsData = plugins.DataFactory("core.array.bands")  # noqa: N806

tests/test_viewers.py

@@ -104,3 +104,9 @@ def test_structure_data_viwer(structure_data_object):
     for fmt, out in format_cases:
         v.file_format.label = fmt
         assert v._prepare_payload() == out
+
+
+def test_structure_viewer_for_molecule(molecule_ase_object):
+    """Test the structure viewer widget for a molecule."""
+    v = viewers.StructureDataViewer(molecule_ase_object)
+    assert isinstance(v, viewers.StructureDataViewer)