Easy way to add bond pair (#88)

Add `add_bond_pair` method

docs/source/bond.rst

@@ -1,6 +1,12 @@
 Bond
 ===============
-Use can control the bond using `avr.bond.settings`. For example, we delete the bond between Ca and Ti, and Ti and Ca.
+Use can control the bond using `avr.bond.settings`.
+
+
+Delete bond pair
+----------------
+
+For example, we delete the bond between Ca and Ti, and Ti and Ca.
 
 .. code-block:: python
 
@@ -11,6 +17,13 @@ Use can control the bond using `avr.bond.settings`. For example, we delete the b
     # change the maximum bond length between Ti and O
     viewer.avr.bond.settings['Ti-O']["max"] = 3.0
 
+Add bond pair
+-------------
+
+.. code-block:: python
+
+    # add the bond between Pt and Au
+    viewer.avr.bond.add_bond_pair('Pt', 'Au', max=3.2)
 
 Hydrogen bond
 -------------

src/weas_widget/base_class.py

@@ -116,7 +116,7 @@ def update(self, *args, **kwargs):
     def _mark_changed(self):
         """Set the changed flag to True, notify parent, and update widget if set."""
         self._changed = True
-        if self._parent:
+        if self._parent is not None:
             self._parent._mark_changed()
         else:
             if not (self._widget and self._key):

src/weas_widget/plugins/bond.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from ..base_class import WidgetWrapper, ChangeTrackingDict
 from weas_widget.data import default_bond_pairs
 
@@ -58,3 +59,41 @@ def get_default_settings(self):
                     "type": bond_line_type,
                 }
         return settings
+
+    def add_bond_pair(
+        self,
+        species1: str,
+        species2: str | None = None,
+        min: float = 0.0,
+        max: float = None,
+        color1: list | None = None,
+        color2: list | None = None,
+        type: int = 0,
+    ) -> None:
+        """Add a bond between two species."""
+
+        species2 = species1 if species2 is None else species2
+        if max is None:
+            max = (
+                self._widget.speciesSettings[species1]["radius"]
+                + self._widget.speciesSettings[species2]["radius"]
+            ) * 1.1
+        color1 = (
+            self._widget.speciesSettings[species1]["color"]
+            if color1 is None
+            else color1
+        )
+        color2 = (
+            self._widget.speciesSettings[species2]["color"]
+            if color2 is None
+            else color2
+        )
+        self.settings[f"{species1}-{species2}"] = {
+            "specie1": species1,
+            "specie2": species2,
+            "color1": color1,
+            "color2": color2,
+            "min": min,
+            "max": max,
+            "type": type,
+        }

tests/test_bond.py

@@ -0,0 +1,20 @@
+def test_add_bond():
+    from weas_widget import WeasWidget
+    from ase.build import bulk
+
+    atoms = bulk("Al", cubic=True)
+    atoms[0].symbol = "Cu"
+    viewer = WeasWidget(from_ase=atoms)
+    viewer.avr.show_bonded_atoms = True
+    viewer.avr.model_style = 1
+    viewer.avr.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
+    # add bonds
+    viewer.avr.bond.settings["Al-Cu"] = {
+        "specie1": "Al",
+        "specie2": "Cu",
+        "color1": viewer.avr.species.settings["Al"]["color"],
+        "color2": viewer.avr.species.settings["Cu"]["color"],
+        "min": 0,
+        "max": 3,
+    }
+    len(viewer.avr.bond.settings) == 1