Keep orbital handles and atom annotations consistent through Undo

CHANGELOG.md

@@ -233,9 +233,12 @@ The experimental browser editor runs from a source checkout only (`chemvas --ui
 
 ### Fixed
 
-- Changing bond length now refreshes desktop orbital lobes and handle distances
-  using the existing renderer. The visible size agrees with saving and reopening
-  the drawing, including after Undo/Redo.
+- Changing bond length now refreshes desktop orbital lobes and visible
+  scale/rotate handles, including after Undo/Redo. Their size and positions
+  agree with saving and reopening the drawing.
+- Undoing an atom charge shortcut (`+`/`-`) or an atom-bound Mark-tool
+  addition now restores pre-existing atom annotations, including values
+  without drawn marks.
 - Fixed macOS Ctrl-click editing before the mark context menu, handle priority
   over marks, and excessive scrolling in the owner-candidate preview.
 - Qt borderless rectangle selection no longer acquires interior holes from

app/chemvas/ui/canvas/canvas_mark_scene_service.py

@@ -29,6 +29,7 @@
     ChangeAtomLabelCommand,
     DeleteSceneItemsCommand,
     RebindMarkCommand,
+    SetAtomAnnotationCommand,
 )
 from chemvas.ui.molecule.atom_label_access import atom_has_visible_label_for
 from chemvas.ui.scene.scene_item_access import remove_item_from_canvas_scene
@@ -70,6 +71,8 @@ def change_charge_for_atom(self, atom_id: int, delta: int) -> None:
         atom = self.canvas.model.atom_for_id(atom_id)
         if atom is None:
             return
+        before = self.canvas.model.atom_annotations.get(atom_id)
+        before = dict(before) if before is not None else None
         with (
             document_transaction(self.canvas, history_service=self.history),
             history_transaction_scope(self.history.operations),
@@ -99,7 +102,21 @@ def change_charge_for_atom(self, atom_id: int, delta: int) -> None:
                 command = AddSceneItemsCommand.from_items(
                     item_states=[mark_state_dict_for(self.canvas, item)], items=[item]
                 )
-            self.history.push(command)
+            self._push_atom_mark_edit(atom_id, before, command)
+
+    def _push_atom_mark_edit(
+        self,
+        atom_id: int,
+        before: dict[str, int] | None,
+        command: HistoryCommand,
+    ) -> None:
+        after = self.canvas.model.atom_annotations.get(atom_id)
+        # A loaded annotation need not have marks; mark replay alone would
+        # rebuild it from the marks and lose that value on Undo.
+        annotation = SetAtomAnnotationCommand(
+            atom_id, before, dict(after) if after is not None else None
+        )
+        self.history.push(CompositeCommand([annotation, command]))
 
     def reveal_unmarked_isolated_carbons(
         self, atom_ids: set[int]
@@ -221,9 +238,28 @@ def add_mark_for_atom(
         *,
         kind: str | None = None,
     ):
-        item = self._add_mark_for_atom(atom_id, click_pos, kind=kind, record=True)
-        if item is not None:
+        if (
+            self.canvas.model.atom_for_id(atom_id) is None
+            or self.scene_decoration_service is None
+        ):
+            return None
+        before = self.canvas.model.atom_annotations.get(atom_id)
+        before = dict(before) if before is not None else None
+        with (
+            document_transaction(self.canvas, history_service=self.history),
+            history_transaction_scope(self.history.operations),
+        ):
+            item = self._add_mark_for_atom(atom_id, click_pos, kind=kind, record=False)
+            if item is None:
+                return None
             self.sync_marks_for_atom(atom_id)
+            self._push_atom_mark_edit(
+                atom_id,
+                before,
+                AddSceneItemsCommand.from_items(
+                    item_states=[mark_state_dict_for(self.canvas, item)], items=[item]
+                ),
+            )
         return item
 
     def materialize_mark_for_atom(

app/chemvas/ui/history/history_commands.py

@@ -85,6 +85,12 @@ def restore_mark_ownership(
     ) -> None: ...
 
 
+class HistoryAtomAnnotationOperations(Protocol):
+    def restore_atom_annotation(
+        self, atom_id: int, annotation: dict[str, int] | None
+    ) -> None: ...
+
+
 class HistoryCalculationPlanOperations(Protocol):
     def set_calculation_plan(self, state: dict[str, object] | None) -> None: ...
 
@@ -295,6 +301,46 @@ def redo(self, operations: HistoryMarkOperations) -> None:
         self._apply(operations, undo=False)
 
 
+@dataclass
+class SetAtomAnnotationCommand(HistoryCommand):
+    """Exact annotation of one atom across a user mark edit.
+
+    Mark add/remove replay rebuilds the annotation from the marks alone, which
+    loses a loaded value that no mark represents. A charge edit lists this
+    command first so Undo applies the exact prior value after that rebuild.
+    """
+
+    history_transaction_snapshot_covers_state = True
+    history_transaction_owns_exact_state = True
+
+    atom_id: int
+    before: dict[str, int] | None
+    after: dict[str, int] | None
+
+    def _apply(
+        self,
+        operations: HistoryAtomAnnotationOperations,
+        state: dict[str, int] | None,
+        rollback_state: dict[str, int] | None,
+    ) -> None:
+        with history_command_transaction(
+            operations,
+            inverse=lambda: operations.restore_atom_annotation(
+                self.atom_id, rollback_state
+            ),
+            inverse_phase="restoring the prior atom annotation",
+        ):
+            operations.restore_atom_annotation(self.atom_id, state)
+
+    @override
+    def undo(self, operations: HistoryAtomAnnotationOperations) -> None:
+        self._apply(operations, self.before, self.after)
+
+    @override
+    def redo(self, operations: HistoryAtomAnnotationOperations) -> None:
+        self._apply(operations, self.after, self.before)
+
+
 @dataclass
 class UpdateSceneItemCommand(HistoryCommand):
     history_transaction_snapshot_covers_state = True
@@ -687,6 +733,7 @@ def redo(self, operations: HistoryAtomLabelOperations) -> None:
     "ChangeAtomLabelCommand",
     "DeleteSceneItemsCommand",
     "GroupSceneItemsCommand",
+    "HistoryAtomAnnotationOperations",
     "HistoryAtomLabelOperations",
     "HistoryCalculationPlanOperations",
     "HistoryGroupOperations",
@@ -695,6 +742,7 @@ def redo(self, operations: HistoryAtomLabelOperations) -> None:
     "HistorySceneItemOperations",
     "HistorySelectionGeometryOperations",
     "SetAnnotationSettingsCommand",
+    "SetAtomAnnotationCommand",
     "SetCalculationPlanCommand",
     "SetNoteTextCommand",
     "SetSceneGeometryCommand",

app/chemvas/ui/history/history_operations.py

@@ -46,6 +46,7 @@
     restore_scene_item,
 )
 from chemvas.ui.scene.scene_signal_blocking import blocked_scene_signals
+from chemvas.ui.selection.selection_info_access import emit_selection_info_for
 from chemvas.ui.transactions.document import DocumentSavepoint
 from chemvas.ui.transactions.scene_runtime import capture_scene_runtime
 from chemvas.ui.transactions.scene_runtime_restore import (
@@ -428,6 +429,17 @@ def restore_mark_ownership(
             else:
                 model_annotations.pop(atom_id, None)
 
+    def restore_atom_annotation(
+        self, atom_id: int, annotation: dict[str, int] | None
+    ) -> None:
+        if annotation is None:
+            self.__canvas.model.atom_annotations.pop(atom_id, None)
+        else:
+            self.__canvas.model.atom_annotations[atom_id] = dict(annotation)
+        # The selection formula readout reflects annotations; mark replay has
+        # already refreshed it from the value this replaces.
+        emit_selection_info_for(self.__canvas)
+
     def set_calculation_plan(self, state: dict[str, object] | None) -> None:
         set_calculation_plan_for(self.__canvas, state)
 

app/chemvas/ui/molecule/bond_length_graphics_refresh.py

@@ -223,6 +223,13 @@ def refresh_bond_length_graphics_for(canvas) -> None:
             )
             canvas.services.scene_decoration_build_service.set_mark_center(item, center)
     canvas.services.selection.update_selection_outline()
+    # Orbital handles sit at the lobes' bond-length distance; redraw any still
+    # shown. The selection-outline refresh keeps clearing unselected targets.
+    handle_state = canvas.runtime_state.handle_state
+    if handle_state.active_handles and any(
+        item is handle_state.target for item in canvas.runtime_state.orbital_items()
+    ):
+        canvas.services.handle_overlay_service.show_orbital_handles(handle_state.target)
 
 
 __all__ = ["refresh_bond_length_graphics_for"]

docs/REFERENCE.ko.md

@@ -166,7 +166,7 @@ Chemvas는 분자 모델, 주석, 화살표, 설정 정보를 사람이 읽기 
 - **결합 편집 (결합 위에 마우스 올림)**: 단일선 `1`, 이중선 `2`, 삼중선 `3`, 굵은선 `b`, 쐐기 `w`, 해시 `h`, 점선 `d`, 굵은 이중선 `Shift+B`, 점선 이중선 `Shift+D`, 이중선 위치 `l`/`c`/`r`, 벤젠 융합 `a`, 고리 융합 `4`~`8`
 - **변형 및 조작**: 좌우 반전 `Ctrl+Shift+H`, 상하 반전 `Ctrl+Shift+V`, 회전 `Alt+Up/Down`(15°) / `Alt+Left/Right`(1°), 미세 이동 `Shift+방향키`(10 pt)
 - **정렬 및 배치**: **Edit ▸ Align** (좌, 우, 상, 하, 중앙) 및 **Edit ▸ Distribute** (가로, 세로)
-- **일반**: 저장 `Ctrl+S`, 열기 `Ctrl+O`, 전체 선택 `Ctrl+A`, 그룹화 `Ctrl+G`, 그룹 해제 `Ctrl+Shift+G`, 실행 취소 `Ctrl+Z`, 다시 실행 `Ctrl+Y`, 삭제 `Delete`/`Backspace`
+- **일반**: 저장 `Ctrl+S`, 열기 `Ctrl+O`, 전체 선택 `Ctrl+A`, 그룹화 `Ctrl+G`, 그룹 해제 `Ctrl+Shift+G`, 실행 취소 `Ctrl+Z`, 다시 실행 (Edit ▸ Redo에 표시된 단축키 사용, 예: Linux `Ctrl+Shift+Z`), 삭제 `Delete`/`Backspace`
 
 ### 원자 라벨 단축키 표
 

docs/REFERENCE.md

@@ -166,7 +166,7 @@ Select tools from the canvas or edit hovered atoms/bonds with the shortcuts belo
 - **Bond Editing (hover over bond)**: Single `1`, Double `2`, Triple `3`, Bold `b`, Wedge `w`, Hash `h`, Dotted `d`, Bold double `Shift+B`, Dotted double `Shift+D`, double-bond alignment `l`/`c`/`r`, Benzene fusion `a`, Ring fusion `4`–`8`
 - **Transformations**: Flip Horizontal `Ctrl+Shift+H`, Flip Vertical `Ctrl+Shift+V`, Rotate `Alt+Up/Down` (15°) / `Alt+Left/Right` (1°), Nudge `Shift+Arrows` (10 pt)
 - **Alignment**: **Edit ▸ Align** (Left, Center, Right, Top, Middle, Bottom) and **Edit ▸ Distribute** (Horizontally, Vertically)
-- **General**: Save `Ctrl+S`, Open `Ctrl+O`, Select All `Ctrl+A`, Group `Ctrl+G`, Ungroup `Ctrl+Shift+G`, Undo `Ctrl+Z`, Redo `Ctrl+Y`, Delete `Delete`/`Backspace`
+- **General**: Save `Ctrl+S`, Open `Ctrl+O`, Select All `Ctrl+A`, Group `Ctrl+G`, Ungroup `Ctrl+Shift+G`, Undo `Ctrl+Z`, Redo (use shortcut displayed by Edit ▸ Redo, e.g. `Ctrl+Shift+Z` on Linux), Delete `Delete`/`Backspace`
 
 ### Atom-label hotkey map