MoleditPy-linux 2.2.4__py3-none-any.whl → 2.2.6__py3-none-any.whl

moleditpy_linux/modules/align_plane_dialog.py

@@ -45,7 +45,6 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
         plane_names = {'xy': 'XY', 'xz': 'XZ', 'yz': 'YZ'}
         self.setWindowTitle(f"Align to {plane_names[self.plane]} Plane")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

moleditpy_linux/modules/alignment_dialog.py

@@ -47,7 +47,6 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         axis_names = {'x': 'X-axis', 'y': 'Y-axis', 'z': 'Z-axis'}
         self.setWindowTitle(f"Align to {axis_names[self.axis]}")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

moleditpy_linux/modules/angle_dialog.py

@@ -45,7 +45,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Adjust Angle")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
+  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

moleditpy_linux/modules/bond_length_dialog.py

@@ -38,7 +38,7 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Adjust Bond Length")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
+  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.2.4'
+VERSION = '2.2.6'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux/modules/constrained_optimization_dialog.py

@@ -123,7 +123,6 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.setWindowTitle("Constrained Optimization")
         self.setModal(False)
         self.resize(450, 500)
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)
         layout = QVBoxLayout(self)
 
         # 1. 説明

moleditpy_linux/modules/custom_interactor_style.py

@@ -42,6 +42,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         self._mouse_press_pos = None
 
         self.AddObserver("LeftButtonPressEvent", self.on_left_button_down)
+        #self.AddObserver("LeftButtonDoubleClickEvent", self.on_left_button_down)
         self.AddObserver("RightButtonPressEvent", self.on_right_button_down)
         self.AddObserver("MouseMoveEvent", self.on_mouse_move)
         self.AddObserver("LeftButtonReleaseEvent", self.on_left_button_up)
@@ -85,8 +86,12 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                 if 0 <= closest_atom_idx < mw.current_mol.GetNumAtoms():
                     atom = mw.current_mol.GetAtomWithIdx(int(closest_atom_idx))
                     if atom:
-                        atomic_num = atom.GetAtomicNum()
-                        vdw_radius = pt.GetRvdw(atomic_num)
+                        try:
+                            atomic_num = atom.GetAtomicNum()
+                            vdw_radius = pt.GetRvdw(atomic_num)
+                            if vdw_radius < 0.1: vdw_radius = 1.5
+                        except Exception:
+                            vdw_radius = 1.5
                         click_threshold = vdw_radius * 1.5
                         
                         if distances[closest_atom_idx] < click_threshold:
@@ -148,11 +153,11 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     move_group_dialog.update_display()
                     return
             else:
-                # 原子以外をクリック - 全選択を解除
-                move_group_dialog.group_atoms.clear()
-                move_group_dialog.selected_atoms.clear()
-                move_group_dialog.clear_atom_labels()
-                move_group_dialog.update_display()
+                # 原子以外をクリック
+                # 即座に解除せず、マウスイベントを追跡して回転かクリックかを判定する
+                self._mouse_press_pos = self.GetInteractor().GetEventPosition()
+                self._mouse_moved_during_drag = False
+
                 # カメラ回転を許可
                 super(CustomInteractorStyle, self).OnLeftButtonDown()
                 return
@@ -166,8 +171,9 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         # 測定モードが有効な場合の処理
         if mw.measurement_mode and mw.current_mol:
             click_pos = self.GetInteractor().GetEventPosition()
-            self._mouse_press_pos = click_pos  # マウスプレス位置を記録
-            self._mouse_moved_during_drag = False  # 移動フラグをリセット
+            # Note: We do NOT set _mouse_press_pos here initially.
+            # We only set it if we confirm it's a background click (see below).
+            self._mouse_moved_during_drag = False  # Reset drag flag
             
             picker = mw.plotter.picker
             
@@ -185,17 +191,24 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     # クリック閾値チェック
                     atom = mw.current_mol.GetAtomWithIdx(int(closest_atom_idx))
                     if atom:
-                        atomic_num = atom.GetAtomicNum()
-                        vdw_radius = pt.GetRvdw(atomic_num)
+                        try:
+                            atomic_num = atom.GetAtomicNum()
+                            vdw_radius = pt.GetRvdw(atomic_num)
+                            if vdw_radius < 0.1: vdw_radius = 1.5
+                        except Exception:
+                            vdw_radius = 1.5
                         click_threshold = vdw_radius * 1.5
 
                         if distances[closest_atom_idx] < click_threshold:
                             mw.handle_measurement_atom_selection(int(closest_atom_idx))
                             return  # 原子選択処理完了、カメラ回転は無効
             
+            
             # 測定モードで原子以外をクリックした場合は計測選択をクリア
-            # ただし、これは通常のカメラ回転も許可する
+            # ただし、回転操作（ドラッグ）の場合はクリアしないため、
+            # ここで _mouse_press_pos を記録し、Upイベントで判定する。
             self._is_dragging_atom = False
+            self._mouse_press_pos = click_pos 
             super().OnLeftButtonDown()
             return
         
@@ -219,8 +232,12 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     # RDKitのMolオブジェクトから原子を安全に取得
                     atom = mw.current_mol.GetAtomWithIdx(int(closest_atom_idx))
                     if atom:
-                        atomic_num = atom.GetAtomicNum()
-                        vdw_radius = pt.GetRvdw(atomic_num)
+                        try:
+                            atomic_num = atom.GetAtomicNum()
+                            vdw_radius = pt.GetRvdw(atomic_num)
+                            if vdw_radius < 0.1: vdw_radius = 1.5
+                        except Exception:
+                            vdw_radius = 1.5
                         click_threshold = vdw_radius * 1.5
 
                         if distances[closest_atom_idx] < click_threshold:
@@ -265,8 +282,12 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                 if 0 <= closest_atom_idx < mw.current_mol.GetNumAtoms():
                     atom = mw.current_mol.GetAtomWithIdx(int(closest_atom_idx))
                     if atom:
-                        atomic_num = atom.GetAtomicNum()
-                        vdw_radius = pt.GetRvdw(atomic_num)
+                        try:
+                            atomic_num = atom.GetAtomicNum()
+                            vdw_radius = pt.GetRvdw(atomic_num)
+                            if vdw_radius < 0.1: vdw_radius = 1.5
+                        except Exception:
+                            vdw_radius = 1.5
                         click_threshold = vdw_radius * 1.5
                         
                         if distances[closest_atom_idx] < click_threshold:
@@ -458,37 +479,23 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                         move_group_dialog.on_atom_picked(clicked_atom)
                     except Exception as e:
                         print(f"Error in toggle: {e}")
-            
-            # 状態をリセット（完全なクリーンアップ）
-            move_group_dialog._is_dragging_group_vtk = False
-            move_group_dialog._drag_start_pos = None
-            move_group_dialog._mouse_moved = False
-            if hasattr(move_group_dialog, '_initial_positions'):
-                delattr(move_group_dialog, '_initial_positions')
-            if hasattr(move_group_dialog, '_drag_atom_idx'):
-                delattr(move_group_dialog, '_drag_atom_idx')
-            
-            # CustomInteractorStyleの状態もクリア
-            self._is_dragging_atom = False
-            self.is_dragging = False
-            self._mouse_moved_during_drag = False
-            self._mouse_press_pos = None
-            
-            try:
-                mw.plotter.setCursor(Qt.CursorShape.ArrowCursor)
-            except Exception:
-                pass
-            return
+        
+        # Move Groupモードでの背景クリック判定（選択解除）
+        # グループドラッグでなく、マウス移動もなかった（＝回転操作でない）場合
+        # かつ、mouse_press_pos が記録されている（背景クリックで開始した）場合
+        if move_group_dialog and not getattr(move_group_dialog, '_is_dragging_group_vtk', False):
+            if not self._mouse_moved_during_drag and self._mouse_press_pos is not None:
+                # 背景クリック -> 選択解除
+                move_group_dialog.group_atoms.clear()
+                move_group_dialog.selected_atoms.clear()
+                move_group_dialog.clear_atom_labels()
+                move_group_dialog.update_display()
 
         # 計測モードで、マウスが動いていない場合（つまりクリック）の処理
+        # _mouse_press_pos が None でない = 背景をクリックしたことを意味する（Downイベントでそう設定したため）
         if mw.measurement_mode and not self._mouse_moved_during_drag and self._mouse_press_pos is not None:
-            click_pos = self.GetInteractor().GetEventPosition()
-            picker = mw.plotter.picker
-            picker.Pick(click_pos[0], click_pos[1], 0, mw.plotter.renderer)
-            
-            # 原子がクリックされていない場合は測定選択をクリア
-            if picker.GetActor() is not mw.atom_actor:
-                mw.clear_measurement_selection()
+             # 背景クリック -> 測定選択をクリア
+             mw.clear_measurement_selection()
 
         if self._is_dragging_atom:
             # カスタムドラッグの後始末
@@ -594,7 +601,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             # カメラ回転の後始末を親クラスに任せます
             super().OnLeftButtonUp()
 
-        # 状態をリセット（完全なクリーンアップ）
+        # 状態をリセット（完全なクリーンアップ） - すべてのチェックの後に実行
         self._is_dragging_atom = False
         self.is_dragging = False
         self._mouse_press_pos = None
@@ -602,12 +609,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         
         # Move Group関連の状態もクリア
         try:
-            move_group_dialog = None
-            for widget in QApplication.topLevelWidgets():
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
-                    move_group_dialog = widget
-                    break
-            
             if move_group_dialog:
                 move_group_dialog._is_dragging_group_vtk = False
                 move_group_dialog._drag_start_pos = None
@@ -619,12 +620,11 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         except Exception:
             pass
         
-        # ピックリセットは測定モードで実際に問題が発生した場合のみ行う
-        # （通常のドラッグ回転では行わない）
-        
         # ボタンを離した後のカーソル表示を最新の状態に更新
-        self.on_mouse_move(obj, event)
-
+        try:
+             mw.plotter.setCursor(Qt.CursorShape.ArrowCursor)
+        except Exception:
+             pass
         # 2Dビューにフォーカスを戻し、ショートカットキーなどが使えるようにする
         if mw and mw.view_2d:
             mw.view_2d.setFocus()

moleditpy_linux/modules/custom_qt_interactor.py

@@ -11,6 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 from pyvistaqt import QtInteractor
+import time
 
 
 class CustomQtInteractor(QtInteractor):
@@ -24,6 +25,7 @@ class CustomQtInteractor(QtInteractor):
         # the VTK interactor and causing unexpected behaviour in the 3D view.
         self._last_click_time = 0.0
         self._click_count = 0
+        self._ignore_next_release = False
 
     def wheelEvent(self, event):
         """
@@ -40,17 +42,58 @@ class CustomQtInteractor(QtInteractor):
         """
         Qtのマウスリリースイベントをオーバーライドし、
         3Dビューでの全ての操作完了後に2Dビューへフォーカスを戻す。
+        また、Ghost Release（対応するPressがないRelease）をフィルタリングする。
         """
+        if self._ignore_next_release:
+            self._ignore_next_release = False
+            event.accept()
+            return
+
         super().mouseReleaseEvent(event) # 親クラスのイベントを先に処理
         if self.main_window and hasattr(self.main_window, 'view_2d'):
             self.main_window.view_2d.setFocus()
 
+    def mousePressEvent(self, event):
+        """
+        Custom mouse press handling to track accumulated clicks and filter out
+        triple-clicks.
+        """
+        current_time = time.time()
+        # Reset count if too much time has passed (0.5s is standard double-click time)
+        if current_time - self._last_click_time > 0.5:
+            self._click_count = 0
+        
+        self._click_count += 1
+        self._last_click_time = current_time
+
+        # If this is the 3rd click (or more), swallow it to prevent
+        # the internal state desync that happens with rapid clicking sequences.
+        if self._click_count >= 3:
+            self._ignore_next_release = True
+            event.accept()
+            return
+
+        super().mousePressEvent(event)
+
     def mouseDoubleClickEvent(self, event):
         """Ignore mouse double-clicks on the 3D widget to avoid accidental actions.
 
         Swallow the double-click event so it doesn't trigger selection, editing,
         or camera jumps. We intentionally do not call the superclass handler.
+        Crucially, we also flag the NEXT release event to be swallowed, preventing
+        a "Ghost Release" (Release without Press) from reaching VTK.
         """
+        current_time = time.time()
+        self._last_click_time = current_time
+        # Set to 2 to ensure the next click counts as 3rd
+        if current_time - self._last_click_time < 0.5:
+             self._click_count = 2
+        else:
+             self._click_count = 2 # Force sync
+        
+        # We must ignore the release event that follows this double-click event
+        self._ignore_next_release = True
+        
         try:
             # Accept the event to mark it handled and prevent further processing.
             event.accept()

moleditpy_linux/modules/dialog3_d_picking_mixin.py

@@ -31,6 +31,11 @@ class Dialog3DPickingMixin:
             event.type() == QEvent.Type.MouseButtonPress and 
             event.button() == Qt.MouseButton.LeftButton):
             
+            # Start tracking for smart selection (click vs drag)
+            self._mouse_press_pos = event.pos()
+            self._mouse_moved = False
+
+            
             try:
                 # VTKイベント座標を取得（元のロジックと同じ）
                 interactor = self.main_window.plotter.interactor
@@ -48,8 +53,12 @@ class Dialog3DPickingMixin:
                         # クリック閾値チェック（元のロジックと同じ）
                         atom = self.mol.GetAtomWithIdx(int(closest_atom_idx))
                         if atom:
-                            atomic_num = atom.GetAtomicNum()
-                            vdw_radius = pt.GetRvdw(atomic_num)
+                            try:
+                                atomic_num = atom.GetAtomicNum()
+                                vdw_radius = pt.GetRvdw(atomic_num)
+                                if vdw_radius < 0.1: vdw_radius = 1.5
+                            except Exception:
+                                vdw_radius = 1.5
                             click_threshold = vdw_radius * 1.5
 
                             if distances[closest_atom_idx] < click_threshold:
@@ -63,15 +72,14 @@ class Dialog3DPickingMixin:
                                 except Exception:
                                     pass
                                 self.on_atom_picked(int(closest_atom_idx))
+                                
+                                # We picked an atom, so stop tracking for background click
+                                self._mouse_press_pos = None
                                 return True
                 
-                # 原子以外をクリックした場合は選択をクリア（Measurementモードと同じロジック）
-                if hasattr(self, 'clear_selection'):
-                    self.clear_selection()
-                # We did not actually pick an atom; do NOT consume the event here so
-                # the interactor and CustomInteractorStyle can handle camera rotation
-                # and other behaviors. Returning False (or calling the base
-                # implementation) allows normal processing to continue.
+                # 原子以外をクリックした場合
+                # 即時には解除せず、回転操作（ドラッグ）を許可する。
+                # 実際の解除は MouseButtonRelease イベントで行う。
                 return False
                     
             except Exception as e:
@@ -80,6 +88,31 @@ class Dialog3DPickingMixin:
                 # event pipeline continue so the UI remains responsive.
                 return False
 
+        # Add movement tracking for smart selection
+        elif (obj == self.main_window.plotter.interactor and 
+              event.type() == QEvent.Type.MouseMove):
+            if hasattr(self, '_mouse_press_pos') and self._mouse_press_pos is not None:
+                # Check if moved significantly
+                diff = event.pos() - self._mouse_press_pos
+                if diff.manhattanLength() > 3:
+                     self._mouse_moved = True
+
+        # Add release handling for smart selection
+        elif (obj == self.main_window.plotter.interactor and 
+              event.type() == QEvent.Type.MouseButtonRelease and 
+              event.button() == Qt.MouseButton.LeftButton):
+              
+            if hasattr(self, '_mouse_press_pos') and self._mouse_press_pos is not None:
+                if not getattr(self, '_mouse_moved', False):
+                    # Pure click (no drag) on background -> Clear selection
+                    if hasattr(self, 'clear_selection'):
+                        self.clear_selection()
+                
+                # Reset state
+                self._mouse_press_pos = None
+                self._mouse_moved = False
+
+
         return super().eventFilter(obj, event)
     
     def enable_picking(self):

moleditpy_linux/modules/dihedral_dialog.py

@@ -47,7 +47,7 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Adjust Dihedral Angle")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
+  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

moleditpy_linux/modules/main_window_app_state.py

@@ -596,8 +596,10 @@ class MainWindowAppState(object):
             json_data["last_successful_optimization_method"] = None
         
         # Plugin State Persistence (Phase 3)
+        # Start with preserved data from missing plugins
+        plugin_data = self._preserved_plugin_data.copy() if self._preserved_plugin_data else {}
+        
         if self.plugin_manager and self.plugin_manager.save_handlers:
-            plugin_data = {}
             for name, callback in self.plugin_manager.save_handlers.items():
                 try:
                     p_state = callback()
@@ -606,8 +608,8 @@ class MainWindowAppState(object):
                 except Exception as e:
                     print(f"Error saving state for plugin {name}: {e}")
             
-            if plugin_data:
-                json_data['plugins'] = plugin_data
+        if plugin_data:
+            json_data['plugins'] = plugin_data
 
         return json_data
 
@@ -629,14 +631,19 @@ class MainWindowAppState(object):
             self.last_successful_optimization_method = None
 
         # Plugin State Restoration (Phase 3)
-        if "plugins" in json_data and self.plugin_manager and self.plugin_manager.load_handlers:
+        self._preserved_plugin_data = {} # Reset preserved data on new load
+        if "plugins" in json_data:
             plugin_data = json_data["plugins"]
             for name, p_state in plugin_data.items():
-                if name in self.plugin_manager.load_handlers:
+                if self.plugin_manager and name in self.plugin_manager.load_handlers:
                     try:
                         self.plugin_manager.load_handlers[name](p_state)
                     except Exception as e:
                         print(f"Error loading state for plugin {name}: {e}")
+                else:
+                    # No handler found (plugin disabled or missing)
+                    # Preserve data so it's not lost on next save
+                    self._preserved_plugin_data[name] = p_state
 
 
         # 2D構造データの復元
@@ -697,7 +704,7 @@ class MainWindowAppState(object):
             for atom in self.data.atoms.values():
                 atom['item'].update_style()
         # 3D構造データの復元
-        if "3d_structure" in json_data:
+        if "3d_structure" in json_data and json_data["3d_structure"] is not None:
             structure_3d = json_data["3d_structure"]
 
             # 制約データの復元 (JSONはタプルをリストとして保存するので、タプルに再変換)

moleditpy_linux/modules/main_window_dialog_manager.py

@@ -263,7 +263,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = TranslationDialog(self.current_mol, self)
+        dialog = TranslationDialog(self.current_mol, self, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Translation applied."))
@@ -279,7 +279,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = MoveGroupDialog(self.current_mol, self)
+        dialog = MoveGroupDialog(self.current_mol, self, parent=self)
         self.active_3d_dialogs.append(dialog)
         dialog.show()
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Group transformation applied."))
@@ -302,7 +302,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = AlignPlaneDialog(self.current_mol, self, plane, preselected_atoms)
+        dialog = AlignPlaneDialog(self.current_mol, self, plane, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage(f"Atoms alignd to {plane.upper()} plane."))
@@ -325,7 +325,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
 
-        dialog = PlanarizeDialog(self.current_mol, self, preselected_atoms)
+        dialog = PlanarizeDialog(self.current_mol, self, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)
         dialog.show()
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Selection planarized to best-fit plane."))
@@ -348,7 +348,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = AlignmentDialog(self.current_mol, self, axis, preselected_atoms)
+        dialog = AlignmentDialog(self.current_mol, self, axis, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage(f"Atoms aligned to {axis.upper()}-axis."))
@@ -371,7 +371,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = BondLengthDialog(self.current_mol, self, preselected_atoms)
+        dialog = BondLengthDialog(self.current_mol, self, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Bond length adjusted."))
@@ -394,7 +394,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = AngleDialog(self.current_mol, self, preselected_atoms)
+        dialog = AngleDialog(self.current_mol, self, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Angle adjusted."))
@@ -417,7 +417,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = DihedralDialog(self.current_mol, self, preselected_atoms)
+        dialog = DihedralDialog(self.current_mol, self, preselected_atoms, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # execではなくshowを使用してモードレス表示
         dialog.accepted.connect(lambda: self.statusBar().showMessage("Dihedral angle adjusted."))
@@ -453,7 +453,7 @@ class MainWindowDialogManager(object):
             self.measurement_action.setChecked(False)
             self.toggle_measurement_mode(False)
         
-        dialog = ConstrainedOptimizationDialog(self.current_mol, self)
+        dialog = ConstrainedOptimizationDialog(self.current_mol, self, parent=self)
         self.active_3d_dialogs.append(dialog)  # 参照を保持
         dialog.show()  # モードレス表示
         dialog.finished.connect(lambda: self.remove_dialog_from_list(dialog))

moleditpy_linux/modules/main_window_edit_actions.py

@@ -1211,7 +1211,10 @@ class MainWindowEditActions(object):
                 
                 atom = mol.GetAtomWithIdx(idx)
                 # GetRvdw() はファンデルワールス半径を返す
-                vdw_radii.append(pt.GetRvdw(atom.GetAtomicNum()))
+                try:
+                    vdw_radii.append(pt.GetRvdw(atom.GetAtomicNum()))
+                except RuntimeError:
+                    vdw_radii.append(1.5)
 
             positions_np = np.array(positions)
             vdw_radii_np = np.array(vdw_radii)

moleditpy_linux/modules/main_window_main_init.py

@@ -264,6 +264,9 @@ class MainWindowMainInit(object):
         except Exception as e:
             print(f"Failed to initialize PluginManager: {e}")
             self.plugin_manager = None
+        
+        # ロードされていないプラグインのデータを保持する辞書
+        self._preserved_plugin_data = {}
 
         self.init_ui()
         self.init_worker_thread()
@@ -1832,6 +1835,14 @@ class MainWindowMainInit(object):
                       if not found_sub:
                           current_menu = current_menu.addMenu(part)
                  
+                 # If last action was NOT from a plugin, insert a separator
+                 actions = current_menu.actions()
+                 if actions:
+                     last_action = actions[-1]
+                     if not last_action.isSeparator() and last_action.data() != PLUGIN_ACTION_TAG:
+                          sep = current_menu.addSeparator()
+                          sep.setData(PLUGIN_ACTION_TAG)
+
                  # Add action
                  action_text = text if text else parts[-1]
                  action = QAction(action_text, self)

moleditpy_linux/modules/main_window_view_3d.py

@@ -219,7 +219,15 @@ class MainWindowView3d(object):
         if current_style == 'cpk':
             atom_scale = self.settings.get('cpk_atom_scale', 1.0)
             resolution = self.settings.get('cpk_resolution', 32)
-            rad = np.array([pt.GetRvdw(pt.GetAtomicNumber(s)) * atom_scale for s in sym])
+            # Safe VDW lookup to handle custom elements like 'Bq'
+            def get_safe_rvdw(s):
+                try:
+                    r = pt.GetRvdw(pt.GetAtomicNumber(s))
+                    return r if r > 0.1 else 1.5
+                except Exception:
+                    return 1.5
+
+            rad = np.array([get_safe_rvdw(s) * atom_scale for s in sym])
         elif current_style == 'wireframe':
             # Wireframeでは原子を描画しないので、この設定は実際には使用されない
             resolution = self.settings.get('wireframe_resolution', 6)

moleditpy_linux/modules/move_group_dialog.py

@@ -42,7 +42,6 @@ class MoveGroupDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Move Group")
         self.setModal(False)
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)
         self.resize(300,400)  # ウィンドウサイズを設定
         layout = QVBoxLayout(self)
         
@@ -195,9 +194,12 @@ class MoveGroupDialog(Dialog3DPickingMixin, QDialog):
                         if 0 <= closest_atom_idx < self.mol.GetNumAtoms():
                             atom = self.mol.GetAtomWithIdx(int(closest_atom_idx))
                             if atom:
-                                atomic_num = atom.GetAtomicNum()
-                                pt = Chem.GetPeriodicTable()
-                                vdw_radius = pt.GetRvdw(atomic_num)
+                                try:
+                                    atomic_num = atom.GetAtomicNum()
+                                    vdw_radius = pt.GetRvdw(atomic_num)
+                                    if vdw_radius < 0.1: vdw_radius = 1.5
+                                except Exception:
+                                    vdw_radius = 1.5
                                 click_threshold = vdw_radius * 1.5
                                 
                                 if distances[closest_atom_idx] < click_threshold:
@@ -349,7 +351,7 @@ class MoveGroupDialog(Dialog3DPickingMixin, QDialog):
                 return False
         
         # その他のイベントは親クラスに渡す
-        return False
+        return super().eventFilter(obj, event)
     
     def on_atom_picked(self, atom_idx):
         """原子がピックされたときに、その原子が属する連結成分全体を選択（複数グループ対応）"""

moleditpy_linux/modules/planarize_dialog.py

@@ -46,7 +46,6 @@ class PlanarizeDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Planarize")
         self.setModal(False)
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)
         layout = QVBoxLayout(self)
 
         instruction_label = QLabel("Click atoms in the 3D view to select them for planarization (minimum 3 required).")

moleditpy_linux/modules/plugin_interface.py

@@ -65,6 +65,24 @@ class PluginContext:
         """
         return self._manager.get_main_window()
 
+    @property
+    def current_molecule(self) -> Any:
+        """
+        Get or set the current molecule (RDKit Mol object).
+        """
+        mw = self._manager.get_main_window()
+        if mw:
+            return mw.current_mol
+        return None
+
+    @current_molecule.setter
+    def current_molecule(self, mol: Any):
+        mw = self._manager.get_main_window()
+        if mw:
+            mw.current_mol = mol
+            if hasattr(mw, 'draw_molecule_3d'):
+                 mw.draw_molecule_3d(mol)
+
     def add_export_action(self, label: str, callback: Callable):
         """
         Register a custom export action.

moleditpy_linux/modules/translation_dialog.py

@@ -31,7 +31,6 @@ class TranslationDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         self.setWindowTitle("Translation")
         self.setModal(False)  # モードレスにしてクリックを阻害しない
-        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy_linux-2.2.4.dist-info → moleditpy_linux-2.2.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.2.4
+Version: 2.2.6
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -706,7 +706,9 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 
-**MoleditPy** is a cross-platform, intuitive molecular editor built in Python. It provides a seamless workflow for drawing 2D molecular structures, visualizing them in 3D, and performing interactive geometric manipulations. Its powerful editing and export capabilities make it an ideal tool for preparing input files for DFT calculation software.
+[🇯🇵 日本語 (Japanese)](#japanese)
+
+**MoleditPy** is a **programmable** and cross-platform molecular editor built in Python. It streamlines the workflow from 2D drawing to 3D visualization, making it an **ideal tool for rapidly preparing input files for DFT calculations**. Designed as an **open platform**, it also allows users to freely extend its capabilities, writing custom Python scripts to manipulate molecular data, automate tasks, or integrate new cheminformatics algorithms seamlessly.
 
 **Author**: HiroYokoyama
 **License**: GPL-v3
@@ -715,7 +717,7 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 -----
 ![](img/icon.png)
 ![](img/screenshot.png)
------
+
 
 ## Overview
 
@@ -760,7 +762,14 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * Import structures from **MOL/SDF** files or **SMILES** strings.
       * Export 3D structures to **MOL** or **XYZ** formats, which are compatible with most DFT calculation software.
       * Export 2D and 3D views as high-resolution PNG images.
-  * **Plugin System:** Extend functionality with Python scripts. Place custom scripts in `~/.moleditpy/plugins` to add new features to the "Plugin" menu.
+      * Export 2D and 3D views as high-resolution PNG images.
+
+### 4. Programmable & Extensible
+
+  * **Python Plugin System:** Drop your Python scripts into the plugin folder, and they instantly become part of the application menu.
+  * **Downloadable Plugins:** Explore and download specialized plugins from the [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/).
+  * **Full API Access:** Plugins have direct access to the `MainWindow`, `RDKit` molecule objects, and `PyGraphics` items, allowing for limitless customization.
+  * **Rapid Prototyping:** Ideal for researchers who need to test new algorithms or workflow automations on the fly.
 
 ## Installation and Execution
 
@@ -822,9 +831,11 @@ This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**.
 
 -----
 
+<div id="japanese"></div>
+
 # MoleditPy — A Python Molecular Editor
 
-**MoleditPy**は、Pythonで構築されたクロスプラットフォームかつ直感的な分子エディターです。2Dでの分子描画から3D構造の可視化・編集、さらにはインタラクティブな幾何学的操作まで、シームレスなワークフローを提供します。その強力な編集機能とエクスポート機能により、**DFT計算ソフトウェアのインプット作成に最適なツール**です。
+**MoleditPy**は、Pythonで構築された**機能拡張が自由自在な**分子エディタープラットフォームです。2D描画から3Dへの変換により、**DFT計算用インプットの迅速な作成に最適なツール**であると同時に、**Pythonスクリプトを用いて必要な機能をユーザー自身が手軽に追加・開発できる**柔軟な環境を提供します。
 
 **作者**: HiroYokoyama
 **ライセンス**: GPL-v3
@@ -875,7 +886,14 @@ This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**.
       * **MOL/SDF**ファイルや**SMILES**文字列から構造をインポートできます。
       * 3D構造を**MOL**または**XYZ**形式でエクスポートでき、これらは多くのDFT計算ソフトウェアと互換性があります。
       * 2Dおよび3Dビューを高解像度のPNG画像としてエクスポートできます。
-  * **プラグインシステム:** Pythonスクリプトで機能を拡張できます。`~/.moleditpy/plugins` にスクリプトを配置することで、「Plugin」メニューに独自の機能を追加できます。
+      * 2Dおよび3Dビューを高解像度のPNG画像としてエクスポートできます。
+
+### 4. プログラマブルで拡張可能
+
+  * **Pythonプラグインシステム:** Pythonスクリプトをプラグインフォルダに入れるだけで、即座にアプリケーションメニューの一部として機能します。
+  * **プラグインのダウンロード:** [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/) から特化したプラグインを探索・ダウンロードできます。
+  * **フルAPIアクセス:** プラグインは `MainWindow`、`RDKit` 分子オブジェクト、`PyGraphics` アイテムに直接アクセスでき、無限のカスタマイズが可能です。
+  * **迅速なプロトタイピング:** 新しいアルゴリズムやワークフローの自動化をその場でテストしたい研究者に最適です。
 
 ## インストールと実行
 

{moleditpy_linux-2.2.4.dist-info → moleditpy_linux-2.2.6.dist-info}/RECORD

@@ -3,56 +3,57 @@ moleditpy_linux/__main__.py,sha256=bYu_h7lhc6PIl1-I_VI4_Q5MdBHmVrMiO4DYsy9jbiY,8
 moleditpy_linux/main.py,sha256=0D8_CXe4xdgqlu2TWoT2pi35K9y2b4ilFj6LWD9Qk7w,1178
 moleditpy_linux/modules/__init__.py,sha256=PFwvuEKXsgQlHTYL8oT5sTeo22gR0XmQcySp7kOTtqk,1396
 moleditpy_linux/modules/about_dialog.py,sha256=zkR-w0vtqLH1Y0baQaoTb0tYmVamT4ztEMBdIANKKvc,3693
-moleditpy_linux/modules/align_plane_dialog.py,sha256=A4sGfnpWSLM5v4g2ADUVmZnWtKEaQxeGQk7ZRLTRj58,11944
-moleditpy_linux/modules/alignment_dialog.py,sha256=lZOWo1Y7uKt31nxZAguNDHNZxKww_aLcg-JPilM2CPQ,11419
+moleditpy_linux/modules/align_plane_dialog.py,sha256=SEC32l8z2x1W1Sf1Gu001OQEtinuvqGuCGHRELmtU5s,11834
+moleditpy_linux/modules/alignment_dialog.py,sha256=CPubSJI52mNSXmWt7oKQ2un5lXnN8_K4Z-LMM7wWTxQ,11309
 moleditpy_linux/modules/analysis_window.py,sha256=zjP5ipSTpKw8oLr1eKdoxW8Bk1SslGlPqsVucD-x_5w,9403
-moleditpy_linux/modules/angle_dialog.py,sha256=ytuE5VqT0dskgob1x08B6VW06qnslgCdAs_dwS2ANgY,17837
+moleditpy_linux/modules/angle_dialog.py,sha256=uc2WbvSfRe892xoEirqpZ78pf2Smwzkinkso6zLWr0Y,17751
 moleditpy_linux/modules/atom_item.py,sha256=u8ge6B1M9sOGobfzg3tp1-EGXtEUmvdee7Fx6msg8Wk,15566
 moleditpy_linux/modules/bond_item.py,sha256=eVkEeKvM4igYI67DYxpey3FllqDyt_iWDo4VPYMhaPk,19137
-moleditpy_linux/modules/bond_length_dialog.py,sha256=k5x_DhK9Q8CSwouKhEo_kLRRdaYHDaK84KDNmuDNLvY,14868
+moleditpy_linux/modules/bond_length_dialog.py,sha256=6bFPGssnqlgINuqpxLv-OhjMH3_hspnaH8QtorAyu2M,14782
 moleditpy_linux/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy_linux/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy_linux/modules/constants.py,sha256=FZjG-RLZs_Xqn8D7MDAGKZAJY4G44Bh2Nm2qnDTFXm8,4702
-moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=IEdNVhFoNSEMeA5ABpUH9Q88-YzDXFloQM2gwnPwnHY,30150
-moleditpy_linux/modules/custom_interactor_style.py,sha256=NjsXE2a43IDNEanZBlcG9eR4ZIERT1MsQC6lbfesapQ,38453
-moleditpy_linux/modules/custom_qt_interactor.py,sha256=MFaTuDh-FPeFBS4303CqxsxmsOIOW4QXUz6USwI8PHQ,2451
-moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=2Sut0J5ltXMtrUJ9R3o1oZ4ysed27mdSIqLpWxmGdyM,5037
-moleditpy_linux/modules/dihedral_dialog.py,sha256=rgry7LqyX9JMAR7d82QSroTPoKT3xz18EgKN1GzYZx4,18088
+moleditpy_linux/modules/constants.py,sha256=_LJDuqJFfR_t_84zzl3p5dhK7C2LB-ZyFuBE4K0dUE4,4702
+moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=REsk4ePsqNmAGPMTS_jckeM7jexrU3krwun8sKqKUCs,30062
+moleditpy_linux/modules/custom_interactor_style.py,sha256=LDNODMJoNHGe1AUSrvqv6PdeJm-hpPmSpWINppnJLt0,38942
+moleditpy_linux/modules/custom_qt_interactor.py,sha256=vCZsDfRO-FtphD5cTP7Ps-5rpHZMIGloaoe6EaKzrsw,4139
+moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=z4udbkiX9PYmIGazPXsbftkk_oRRwZhcvlCqbyJzr24,6493
+moleditpy_linux/modules/dihedral_dialog.py,sha256=bOTDO6-b74vEDn_z6OyuBr5cRz3RnRj83PiaEBUyWJA,18002
 moleditpy_linux/modules/main_window.py,sha256=IL8dH3qPx2TkPgO7amuDgjlFoadh5J59xYUEVhlNZqA,36338
-moleditpy_linux/modules/main_window_app_state.py,sha256=DmBfzurTftUIkPZu8465YnxL8Hdx2vHYSbyWdB-kvjs,34757
+moleditpy_linux/modules/main_window_app_state.py,sha256=8YDcGNCSpLTO1NGL9tEvNkXpUcS7JW-uK7TdUGvEqnk,35189
 moleditpy_linux/modules/main_window_compute.py,sha256=ipIkhH_DONXDnPzh7xeym9X-Yfx8EhsvXYOdyxsAj4c,53347
-moleditpy_linux/modules/main_window_dialog_manager.py,sha256=9ZVy5-dlk8SjGU5R6NtbaVZuBQfVK5Nwrc633pEzjq8,19955
+moleditpy_linux/modules/main_window_dialog_manager.py,sha256=QR96LqHAPSOShXbc9cK-Ffq8a16JrXAoMKB0pHjESrQ,20072
 moleditpy_linux/modules/main_window_edit_3d.py,sha256=CUArB5wcsgq1C7LygAEC6URlbnn4RhRYDa5n-Y-etWI,19731
-moleditpy_linux/modules/main_window_edit_actions.py,sha256=-SDLoMQ7S-3u3eBUb-w7BU7OAsFkhQ9ZBjF3Y2jGgZc,64708
+moleditpy_linux/modules/main_window_edit_actions.py,sha256=yEc0Nw-VpN0P4e4neUu7pDuUHPGEcu6eFmwWFrSBIQ8,64815
 moleditpy_linux/modules/main_window_export.py,sha256=dSVfylsybDDboDuXU9Inotf6YkrKJwgBTqGYSfq1lRE,38241
-moleditpy_linux/modules/main_window_main_init.py,sha256=ZxScNJI-OVx_ki5C37fY4Dmm9IIm5eJWVwd7jIKu8ms,90606
+moleditpy_linux/modules/main_window_main_init.py,sha256=Shxs8_vVa7PhfhVZdHYtPniItLHKJ3i9wcamcVofvso,91172
 moleditpy_linux/modules/main_window_molecular_parsers.py,sha256=KR6vzuqc3nutOcorpYr0QOyX3MFBcxTwDhZX96VgJ9Q,48291
 moleditpy_linux/modules/main_window_project_io.py,sha256=TWwtuKDuvgcvPZ9IGmW8r1EJJOrgxrIJRnxe_f4C1oM,17149
 moleditpy_linux/modules/main_window_string_importers.py,sha256=v47wOd4RtjKYcF-aLP-mogGGdYTpTEo3dDyAu79_5MM,10782
 moleditpy_linux/modules/main_window_ui_manager.py,sha256=HofI6T9EvcSSzPbsdPqkYEEDoB6Hui1Uj2Ll-wwczGA,24016
-moleditpy_linux/modules/main_window_view_3d.py,sha256=6eN3_NdpNJrCzMSp17t9_Omm71MwfgqDC8A5DSYHhUo,73942
+moleditpy_linux/modules/main_window_view_3d.py,sha256=CxZxyJHl2isF7KtyVWSI9f8LVbvdZM5H9Gnhm_8ovBM,74227
 moleditpy_linux/modules/main_window_view_loaders.py,sha256=gklTMo27QnyJ8Gd0ampPdbm9d0Gi-oHWkIqQuGADHmI,14352
 moleditpy_linux/modules/mirror_dialog.py,sha256=c3v4qY6R4FAljzk4EPaDjL9ZdZMjLQSFLqDMXz2fBUk,4696
 moleditpy_linux/modules/molecular_data.py,sha256=8gE9ByYg3kSBfb1zANsyad_BVBTm6WOLF7NsZIYuG2E,13250
 moleditpy_linux/modules/molecule_scene.py,sha256=khdt7h9Mk_D1cMbYeHGtq7P9aFXo0xG-hcShU_H2Y-Q,95911
-moleditpy_linux/modules/move_group_dialog.py,sha256=65HVXTJSaQ9lp03XFhI1l7OzUsXmH_aqd8OgwjpjfGg,27174
+moleditpy_linux/modules/move_group_dialog.py,sha256=Fyuy3Uq1KsFsk9qR96r_FxPbAM_-zSfW2dsMQGv7btc,27276
 moleditpy_linux/modules/periodic_table_dialog.py,sha256=ItEZUts1XCietz9paY-spvbzxh6SXak3GnikwqkHZCw,4006
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