Click-to-measure atom selection for the Analysis-tab viewer (M-MEASURE)

quantui/app.py

@@ -204,6 +204,12 @@
 from quantui.app_history import (
     on_view_log as _hist_on_view_log,
 )
+from quantui.app_measurement import (
+    on_measure_clear as _measure_on_clear,
+)
+from quantui.app_measurement import (
+    on_measure_inbox_changed as _measure_on_inbox_changed,
+)
 from quantui.app_runflow import (
     calc_type_key as _run_calc_type_key,
 )
@@ -1219,6 +1225,15 @@ class QuantUIApp:
         _iso_wireframe_cb: Any
         _iso_resolution_dd: Any
         _last_result_dir: Any
+        _measure_inbox: Any
+        _measure_js_bridge: Any
+        _measure_readout: Any
+        _measure_clear_btn: Any
+        _measure_help_btn: Any
+        _measure_controls: Any
+        _measure_fallback_msg: Any
+        _measure_panel: Any
+        _measure_picks: Any
         _nmr_accordion: Any
         _nmr_output: Any
         _orb_accordion: Any
@@ -2258,6 +2273,14 @@ def _wire_callbacks(self) -> None:
         self._reorg_png_inbox.observe(
             self._safe_cb(self._on_reorg_png_captured), names="value"
         )
+        # Click-to-measure (M-MEASURE MEAS.2/3): a click in the Analysis-tab
+        # viewer posts an atom index into this inbox the same way the PNG
+        # buttons post a data URI.
+        self._measure_inbox.observe(
+            self._safe_cb(self._on_measure_inbox_changed), names="value"
+        )
+        self._measure_clear_btn.on_click(self._on_measure_clear)
+        self._measure_help_btn.on_click(self._on_measure_help)
         # Persist the grid choice so it survives a relaunch (ORBX.2).
         self._iso_resolution_dd.observe(
             self._safe_cb(self._on_iso_resolution_changed), names="value"
@@ -3199,6 +3222,12 @@ def _rerender_3d_views(self) -> None:
                     lighting=self._viz_lighting,
                     bgcolor=self._plotly_theme_colors()["scene_bgcolor"],
                 )
+                # M-MEASURE: same wiring as the post-calc render path — a
+                # backend-toggle switch is still a fresh viewer, so stale
+                # picks from the previous backend must not survive it.
+                from quantui.app_measurement import finalize_analysis_html
+
+                html = finalize_analysis_html(self, html, chosen)
                 self._set_html_output(self._analysis_mol_output, html)
                 self._update_analysis_backend_label(chosen)
 
@@ -3690,6 +3719,16 @@ def _on_orb_png_captured(self, change) -> None:
     def _on_reorg_png_captured(self, change) -> None:
         _exp_on_reorg_png_captured(self, change)
 
+    def _on_measure_inbox_changed(self, change) -> None:
+        _measure_on_inbox_changed(self, change)
+
+    def _on_measure_clear(self, btn=None) -> None:
+        _measure_on_clear(self, btn)
+
+    def _on_measure_help(self, btn) -> None:
+        _ = btn
+        self._show_help_topic("measure")
+
     def _on_iso_resolution_changed(self, change) -> None:
         """Persist the isosurface grid choice.
 

quantui/app_builders.py

@@ -10,6 +10,7 @@
 from IPython.display import HTML, display
 
 import quantui
+from quantui import app_measurement as _measure
 from quantui import molecule_library as _ml
 from quantui import theme as _theme
 from quantui.help_content import HELP_TOPICS
@@ -2426,6 +2427,68 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
     # box around it — the Output widget cannot shrink-wrap.
     app._analysis_mol_output = widgets.Output()
 
+    # ── Click-to-measure (M-MEASURE MEAS.2-.6) ──────────────────────────
+    # Hidden inbox for the click JS injected into the py3Dmol-rendered
+    # Analysis viewer (app_measurement.inject_click_js) — same JS->kernel
+    # "write into a hidden Textarea's DOM node, dispatch 'input'" trick
+    # ORBX.1's PNG capture uses, new inbox.
+    app._measure_inbox = widgets.Textarea(
+        value="", layout=layout_fn(width="1px", height="1px", visibility="hidden")
+    )
+    app._measure_inbox.add_class(_measure.MEASURE_INBOX_CLASS)
+    # Hidden Output that carries one-shot Javascript pushing highlight
+    # updates to the live viewer. Mirrors _iso_js_bridge.
+    app._measure_js_bridge = widgets.Output(
+        layout=layout_fn(width="0px", height="0px", visibility="hidden")
+    )
+    app._measure_readout = widgets.HTML(
+        value=_measure._readout_html(_measure._PLACEHOLDER_TEXT)
+    )
+    app._measure_clear_btn = widgets.Button(
+        description="Clear",
+        button_style="",
+        tooltip="Clear the picked atoms and their highlights",
+        layout=layout_fn(width="70px"),
+    )
+    app._measure_help_btn = widgets.Button(
+        description="?",
+        button_style="",
+        layout=layout_fn(width="28px", height="28px"),
+        tooltip="Click-to-measure bond length / angle / dihedral — opens Help tab",
+    )
+    app._measure_controls = widgets.VBox(
+        [
+            widgets.HBox(
+                [app._measure_readout],
+                layout=layout_fn(align_items="center"),
+            ),
+            widgets.HBox(
+                [app._measure_clear_btn, app._measure_help_btn],
+                layout=layout_fn(align_items="center", gap="6px", margin="2px 0 0"),
+            ),
+        ]
+    )
+    # DEC-009: the panel stays visible regardless of backend — only its
+    # content swaps (MEAS.6). Shown when the resolved backend can't support
+    # native clicking (plotlymol, or py3Dmol simply unavailable).
+    app._measure_fallback_msg = widgets.HTML(
+        value=(
+            f'<p style="color:{_theme.TEXT_SECONDARY};font-size:12px;margin:4px 0">'
+            "Click-to-measure needs the py3Dmol viewer — switch backends above "
+            "(or in Settings) to use it.</p>"
+        ),
+        layout=layout_fn(display="none"),
+    )
+    app._measure_panel = widgets.VBox(
+        [
+            app._measure_controls,
+            app._measure_fallback_msg,
+            app._measure_inbox,
+            app._measure_js_bridge,
+        ],
+        layout=layout_fn(margin="4px 0 8px"),
+    )
+
     # Analysis-tab backend toggle — mirrors the Calculate-tab `viz_backend_toggle`.
     # Created only when both backends are available (matches Calculate-tab
     # convention). Synchronized with the Calculate-tab toggle via
@@ -2490,6 +2553,7 @@ def _plot_export_row(prefix: str) -> widgets.HBox:
     ana_children = [
         app._analysis_context_lbl,
         app._analysis_mol_output,
+        app._measure_panel,
     ]
     if ana_backend_row is not None:
         ana_children.append(ana_backend_row)