MoleditPy 2.2.5__tar.gz → 2.2.6__tar.gz

{moleditpy-2.2.5 → moleditpy-2.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.2.5
+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

{moleditpy-2.2.5 → moleditpy-2.2.6}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.2.5"
+version = "2.2.6"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.2.5 → moleditpy-2.2.6}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.2.5
+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

{moleditpy-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.2.5'
+VERSION = '2.2.6'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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-2.2.5 → moleditpy-2.2.6}/src/moleditpy/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