Support hydrogen bond

docs/source/bond.rst

@@ -5,8 +5,24 @@ Use can control the bond using `avr.bond.settings`. For example, we delete the b
 .. code-block:: python
 
     # delete the bond between Ca and Ti
-    del viewer1.avr.bond.settings['[Ti, Ca]']
+    del viewer.avr.bond.settings['Ti-Ca']
     # change the bond color between Ti and O
-    viewer1.avr.bond.settings['[Ti, O]'].update({"color": "red"})
+    viewer.avr.bond.settings['Ti-O'].update({"color": "red"})
     # change the maximum bond length between Ti and O
-    viewer1.avr.bond.settings['[Ti, O]']["max"] = 3.0
+    viewer.avr.bond.settings['Ti-O']["max"] = 3.0
+
+
+Hydrogen bond
+-------------
+The hydrogen bond can be controlled using `avr.bond.show_hydrogen_bonds`:
+
+.. code-block:: python
+
+    # set hydrogen bond length parameters for H-O
+    viewer.avr.bond.settings['H-O']["min"] = 1.5
+    viewer.avr.bond.settings['H-O']["max"] = 2.5
+    # show hydrogen bonds
+    viewer.avr.bond.show_hydrogen_bonds = True
+
+.. image:: _static/images/example-bond-hydrogen-bond.png
+   :width: 6cm

docs/source/highlight.rst

@@ -0,0 +1,31 @@
+Highlight atoms
+===============
+
+One can highlight the atoms using the following shapes:
+
+- sphere
+- box
+- cross
+
+One can see the highlight setting:
+
+.. code-block:: python
+
+    viewer.avr.highlight.settings
+
+The default settings has `selection` and `fixed` items, which are used to highlight the selected atoms and fixed atoms, respectively.
+
+Add highlight item
+-------------------
+One can add one highlight item with the following code:
+
+.. code-block:: python
+
+    # highlight the first two atoms with a cross, e.g., show the atoms which are fixed
+    viewer.avr.highlight.settings['my_highlight'] = {"shape": "cross", "indices": [0, 1], color: "black"}
+    viewer.avr.draw()
+    viewer
+
+
+.. image:: ../_static/images/example-highlight.png
+   :width: 4cm

docs/source/index.rst

@@ -31,6 +31,7 @@ A widget to visualize and interact with atomic structures in Jupyter Notebook. I
    isosurface
    vector_field
    lattice_plane
+   highlight
    mesh_primitive
    search_operator
    selection

js/widget.js

@@ -47,11 +47,12 @@ function render({ model, el }) {
             _showCell: model.get("showCell"),
             _showBondedAtoms: model.get("showBondedAtoms"),
             _hideLongBonds: model.get("hideLongBonds"),
+            _showHydrogenBonds: model.get("showHydrogenBonds"),
             _boundary: model.get("boundary"),
             _currentFrame: model.get("currentFrame"),
         };
         editor = new weas.WEAS({ domElement, atoms, viewerConfig, guiConfig });
-        // window.editor = editor; // for debugging
+        window.editor = editor; // for debugging
         editor.avr.selectedAtomsIndices = model.get("selectedAtomsIndices");
         // editor.avr.atomScales = model.get("atomScales");
         // editor.avr.modelSticks = model.get("modelSticks");
@@ -61,6 +62,9 @@ function render({ model, el }) {
         // bond settings
         // console.log("bondSettings: ", model.get("bondSettings"));
         editor.avr.bondManager.fromSettings(model.get("bondSettings"));
+        // highlight settings
+        // console.log("highlightSettings: ", model.get("highlightSettings"));
+        editor.avr.highlightManager.fromSettings(model.get("highlightSettings"));
         // volumetric data
         editor.avr.isosurfaceManager.volumetricData = createVolumeData(model.get("volumetricData"), atoms.cell);
         console.log("isosettings: ", model.get("isoSettings"));
@@ -221,14 +225,17 @@ function render({ model, el }) {
     model.on("change:cameraZoom", () => {
         const cameraZoom = model.get("cameraZoom");
         editor.tjs.camera.updateZoom(cameraZoom);
+        editor.tjs.render();
     });
     model.on("change:cameraPosition", () => {
         const cameraPosition = model.get("cameraPosition");
         editor.tjs.camera.updatePosition(cameraPosition[0], cameraPosition[1], cameraPosition[2]);
+        editor.tjs.render();
     });
     model.on("change:cameraLookAt", () => {
         const cameraLookAt = model.get("cameraLookAt");
         editor.tjs.controls.target.set(cameraLookAt[0], cameraLookAt[1], cameraLookAt[2]);
+        editor.tjs.controls.update();
         editor.tjs.render();
     });
 }

package.json

@@ -7,7 +7,7 @@
 	"dependencies": {
 		"dat.gui": "^0.7.9",
 		"three": "^0.161.0",
-		"weas": ">=0.1.25"
+		"weas": ">=0.1.26"
 	},
 	"devDependencies": {
 		"esbuild": "^0.20.0"

src/weas_widget/atoms_viewer.py

@@ -4,6 +4,7 @@
 from .plugins.lattice_plane import LatticePlane
 from .plugins.bond import BondManager
 from .plugins.species import SpeciesManager
+from .plugins.highlight import HighlightManager
 from copy import deepcopy
 
 
@@ -20,6 +21,7 @@ class AtomsViewer(WidgetWrapper):
         "show_cell": "showCell",
         "show_bonded_atoms": "showBondedAtoms",
         "hide_long_bonds": "hideLongBonds",
+        "show_hydrogen_bonds": "showHydrogenBonds",
         "atom_label_type": "atomLabelType",
         "material_type": "materialType",
         "model_sticks": "modelSticks",
@@ -29,7 +31,16 @@ class AtomsViewer(WidgetWrapper):
         "phonon_setting": "phonon",
     }
 
-    _extra_allowed_attrs = ["species", "vf", "iso", "lp", "atoms", "bond", "color_type"]
+    _extra_allowed_attrs = [
+        "species",
+        "vf",
+        "iso",
+        "lp",
+        "atoms",
+        "bond",
+        "highlight",
+        "color_type",
+    ]
 
     def __init__(self, _widget):
 
@@ -40,6 +51,7 @@ def __init__(self, _widget):
         setattr(self, "lp", LatticePlane(_widget))
         setattr(self, "bond", BondManager(_widget))
         setattr(self, "species", SpeciesManager(_widget))
+        setattr(self, "highlight", HighlightManager(_widget))
 
     @property
     def atoms(self):
@@ -61,6 +73,8 @@ def atoms(self, atoms):
         self.bond.update_atoms()
         # vector field
         self.vf.update_atoms()
+        # highlight
+        self.highlight.update_atoms()
 
     def draw(self):
         """Redraw the widget."""

src/weas_widget/base_widget.py

@@ -32,6 +32,7 @@ class BaseWidget(anywidget.AnyWidget):
     atomLabelType = tl.Unicode("None").tag(sync=True)
     showCell = tl.Bool(True).tag(sync=True)
     showBondedAtoms = tl.Bool(False).tag(sync=True)
+    showHydrogenBonds = tl.Bool(False).tag(sync=True)
     hideLongBonds = tl.Bool(True).tag(sync=True)
     atomScales = tl.List([]).tag(sync=True)
     modelSticks = tl.List([]).tag(sync=True)
@@ -66,6 +67,8 @@ class BaseWidget(anywidget.AnyWidget):
     bondSettings = tl.Dict({}).tag(sync=True)
     # phonon
     phonon = tl.Dict({}).tag(sync=True)
+    # highlight
+    highlightSettings = tl.Dict({}).tag(sync=True)
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)

src/weas_widget/plugins/bond.py

@@ -34,12 +34,27 @@ def get_default_settings(self):
             for species2, data2 in species_dict.items():
                 if (data1["element"], data2["element"]) not in default_bond_pairs:
                     continue
-                settings[f"[{species1}, {species2}]"] = {
+                bond_type = default_bond_pairs[(data1["element"], data2["element"])][2]
+                min = 0
+                max = (data1["radius"] + data2["radius"]) * 1.1
+                color1 = data1["color"]
+                color2 = data2["color"]
+                if bond_type == 1:
+                    min = max + 0.4
+                    max = min + 1
+                    color1 = "#808080"
+                    color2 = "#808080"
+                    bond_line_type = 1
+                else:
+                    bond_line_type = 0
+
+                settings[f"{species1}-{species2}"] = {
                     "species1": species1,
                     "species2": species2,
-                    "color1": data1["color"],
-                    "color2": data2["color"],
-                    "min": 0,
-                    "max": (data1["radius"] + data2["radius"]) * 1.1,
+                    "color1": color1,
+                    "color2": color2,
+                    "min": min,
+                    "max": max,
+                    "type": bond_line_type,
                 }
         return settings

src/weas_widget/plugins/highlight.py

@@ -0,0 +1,41 @@
+from ..base_class import WidgetWrapper, ChangeTrackingDict
+
+
+class HighlightManager(WidgetWrapper):
+
+    catalog = "highlight"
+
+    _attribute_map = {}
+
+    _extra_allowed_attrs = ["_settings", "settings"]
+
+    def __init__(self, _widget):
+        super().__init__(_widget)
+        self._settings = ChangeTrackingDict(
+            widget=self._widget, key="highlightSettings"
+        )
+
+    @property
+    def settings(self):
+        return self._settings
+
+    @settings.setter
+    def settings(self, value):
+        self._settings = ChangeTrackingDict(
+            value, widget=self._widget, key="highlightSettings"
+        )
+
+    def update_atoms(self):
+        self.settings = self.get_default_settings()
+
+    def get_default_settings(self):
+        settings = {
+            "selection": {
+                "indices": [],
+                "scale": 1.1,
+                "color": "yellow",
+                "type": "sphere",
+            },
+            "fixed": {"indices": [], "scale": 1.1, "color": "black", "type": "cross"},
+        }
+        return settings