Implement viewer representations

aiidalab_widgets_base/computational_resources.py

@@ -159,7 +159,7 @@ def refresh(self, _=None):
         with self.hold_trait_notifications():
             self.code_select_dropdown.options = self._get_codes()
             if not self.code_select_dropdown.options:
-                self.output.value = f"No codes found for default calcjob plugin '{self.default_calc_job_plugin}'."
+                self.output.value = f"No codes found for default calcjob plugin {self.default_calc_job_plugin!r}."
                 self.code_select_dropdown.disabled = True
             else:
                 self.code_select_dropdown.disabled = False

aiidalab_widgets_base/elns.py

@@ -23,7 +23,7 @@ def connect_to_eln(eln_instance=None, **kwargs):
     except (FileNotFoundError, json.JSONDecodeError, KeyError):
         return (
             None,
-            f"Can't open '{ELN_CONFIG}' (ELN configuration file). Instance: {eln_instance}",
+            f"Can't open {ELN_CONFIG!r} (ELN configuration file). Instance: {eln_instance}",
         )
 
     # If no ELN instance was specified, trying the default one.
@@ -35,7 +35,7 @@ def connect_to_eln(eln_instance=None, **kwargs):
             eln_config = config[eln_instance]
             eln_type = eln_config.pop("eln_type", None)
         else:  # The selected instance is not present in the config.
-            return None, f"Didn't find configuration for the '{eln_instance}' instance."
+            return None, f"Didn't find configuration for the {eln_instance!r} instance."
 
         # If the ELN type cannot be identified - aborting.
         if not eln_type:
@@ -73,7 +73,7 @@ def __init__(self, path_to_root="../", **kwargs):
 
         if eln is None:
             url = f"{path_to_root}aiidalab-widgets-base/notebooks/eln_configure.ipynb"
-            error_message.value = f"""Warning! The access to ELN is not configured. Please follow <a href="{url}" target="_blank">the link</a> to configure it.</br> More details: {msg}"""
+            error_message.value = f"""Warning! The access to ELN is not configured. Please follow <a href={url!r} target="_blank">the link</a> to configure it.</br> More details: {msg!r}"""
             return
 
         tl.dlink((eln, "node"), (self, "node"))

aiidalab_widgets_base/nodes.py

@@ -308,7 +308,7 @@ def to_html_string(self):
         return f"""
             <table style="border-collapse:separate;border-spacing:15px;">
             <tr>
-                <td style="width:200px"> <a href="{self.link}" target="_blank">  <img src="{self.logo}"> </a></td>
+                <td style="width:200px"> <a href={self.link!r} target="_blank">  <img src={self.logo!r}> </a></td>
                 <td style="width:800px"> <p style="font-size:16px;">{self.description} </p></td>
             </tr>
             </table>

aiidalab_widgets_base/structures.py

@@ -1,5 +1,4 @@
 """Module to provide functionality to import structures."""
-
 import datetime
 import functools
 import io
@@ -14,7 +13,7 @@
 from aiida import engine, orm, plugins
 
 # Local imports
-from .data import LigandSelectorWidget
+from .data import FunctionalGroupSelectorWidget
 from .utils import StatusHTML, exceptions, get_ase_from_file, get_formula
 from .viewers import StructureDataViewer
 
@@ -85,7 +84,7 @@ def __init__(
             self.viewer = viewer
         else:
             self.viewer = StructureDataViewer(**kwargs)
-        tl.dlink((self, "structure_node"), (self.viewer, "structure"))
+        tl.dlink((self, "structure"), (self.viewer, "structure"))
 
         # Store button.
         self.btn_store = ipw.Button(description="Store in AiiDA", disabled=True)
@@ -184,6 +183,10 @@ def _structure_editors(self, editors):
             for i, editor in enumerate(editors):
                 editors_tab.set_title(i, editor.title)
                 tl.link((editor, "structure"), (self, "structure"))
+                if editor.has_trait("input_selection"):
+                    tl.dlink(
+                        (editor, "input_selection"), (self.viewer, "input_selection")
+                    )
                 if editor.has_trait("selection"):
                     tl.link((editor, "selection"), (self.viewer, "selection"))
                 if editor.has_trait("camera_orientation"):
@@ -336,6 +339,7 @@ def _structure_changed(self, change=None):
         This function enables/disables `btn_store` widget if structure is provided/set to None.
         Also, the function sets `structure_node` trait to the selected node type.
         """
+
         if not self.structure_set_by_undo:
             self.history.append(change["new"])
 
@@ -1051,7 +1055,7 @@ def disable_element(_=None):
                 self.element.disabled = True
 
         # Ligand selection.
-        self.ligand = LigandSelectorWidget()
+        self.ligand = FunctionalGroupSelectorWidget()
         self.ligand.observe(disable_element, names="value")
 
         # Add atom.
@@ -1262,6 +1266,8 @@ def translate_dr(self, _=None, atoms=None, selection=None):
             self.action_vector * self.displacement.value
         )
 
+        self.input_selection = None  # Clear selection.
+
         self.structure, self.input_selection = atoms, selection
 
     @_register_structure
@@ -1271,7 +1277,7 @@ def translate_dxdydz(self, _=None, atoms=None, selection=None):
 
         # The action.
         atoms.positions[self.selection] += np.array(self.str2vec(self.dxyz.value))
-
+        self.input_selection = None  # Clear selection.
         self.structure, self.input_selection = atoms, selection
 
     @_register_structure
@@ -1281,7 +1287,7 @@ def translate_to_xyz(self, _=None, atoms=None, selection=None):
         # The action.
         geo_center = np.average(self.structure[self.selection].get_positions(), axis=0)
         atoms.positions[self.selection] += self.str2vec(self.dxyz.value) - geo_center
-
+        self.input_selection = None  # Clear selection.
         self.structure, self.input_selection = atoms, selection
 
     @_register_structure
@@ -1295,6 +1301,7 @@ def rotate(self, _=None, atoms=None, selection=None):
         center = self.str2vec(self.point.value)
         rotated_subset.rotate(self.phi.value, v=vec, center=center, rotate_cell=False)
         atoms.positions[self.selection] = rotated_subset.positions
+        self.input_selection = None  # Clear selection.
 
         self.structure, self.input_selection = atoms, selection
 
@@ -1329,6 +1336,8 @@ def mirror(self, _=None, norm=None, point=None, atoms=None, selection=None):
         # Mirror atoms.
         atoms.positions[selection] -= 2 * projections
 
+        self.input_selection = None  # Clear selection.
+
         self.structure, self.input_selection = atoms, selection
 
     def mirror_3p(self, _=None):
@@ -1375,6 +1384,7 @@ def mod_element(self, _=None, atoms=None, selection=None):
             initial_ligand = self.ligand.rotate(
                 align_to=self.action_vector, remove_anchor=True
             )
+
             for idx in self.selection:
                 position = self.structure.positions[idx].copy()
                 lgnd = initial_ligand.copy()
@@ -1390,22 +1400,23 @@ def mod_element(self, _=None, atoms=None, selection=None):
     @_register_selection
     def copy_sel(self, _=None, atoms=None, selection=None):
         """Copy selected atoms and shift by 1.0 A along X-axis."""
+
         last_atom = atoms.get_global_number_of_atoms()
 
         # The action
         add_atoms = atoms[self.selection].copy()
         add_atoms.translate([1.0, 0, 0])
         atoms += add_atoms
 
-        new_selection = list(range(last_atom, last_atom + len(selection)))
-        self.structure, self.input_selection = atoms, new_selection
+        self.structure, self.input_selection = atoms, list(
+            range(last_atom, last_atom + len(selection))
+        )
 
     @_register_structure
     @_register_selection
     def add(self, _=None, atoms=None, selection=None):
         """Add atoms."""
         last_atom = atoms.get_global_number_of_atoms()
-
         if self.ligand.value == 0:
             initial_ligand = ase.Atoms([ase.Atom(self.element.value, [0, 0, 0])])
             rad = SYMBOL_RADIUS[self.element.value]
@@ -1431,6 +1442,8 @@ def add(self, _=None, atoms=None, selection=None):
 
         new_selection = list(range(last_atom, last_atom + len(selection) * len(lgnd)))
 
+        # The order of the traitlets below is important -
+        # we must be sure trait atoms is set before trait selection
         self.structure, self.input_selection = atoms, new_selection
 
     @_register_structure
@@ -1439,6 +1452,8 @@ def remove(self, _=None, atoms=None, selection=None):
         """Remove selected atoms."""
         del [atoms[selection]]
 
+        # The order of the traitlets below is important -
+        # we must be sure trait atoms is set before trait selection
         self.structure = atoms
         self.input_selection = None
         self.input_selection = []

aiidalab_widgets_base/utils/__init__.py

@@ -34,7 +34,7 @@ def predefine_settings(obj, **kwargs):
         if hasattr(obj, key):
             setattr(obj, key, value)
         else:
-            raise AttributeError(f"'{obj}' object has no attribute '{key}'")
+            raise AttributeError(f"{obj!r} object has no attribute {key!r}")
 
 
 def get_ase_from_file(fname, file_format=None):  # pylint: disable=redefined-builtin

aiidalab_widgets_base/utils/exceptions.py

@@ -3,5 +3,5 @@ class ListOrTuppleError(TypeError):
 
     def __init__(self, value):
         super().__init__(
-            f"The provided value '{value}' is not a list or a tupple, but a {type(value)}."
+            f"The provided value {value!r} is not a list or a tupple, but a {type(value)}."
         )