MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_main_init.py

@@ -0,0 +1,2100 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+"""
+main_window_main_init.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowMainInit
+"""
+
+
+import math
+import os
+import json 
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+from rdkit import Chem
+try:
+    pass
+except Exception:
+    pass
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QApplication, QWidget, QVBoxLayout, QHBoxLayout,
+    QPushButton, QSplitter, QToolBar, QSizePolicy, QLabel, QToolButton, QMenu, QMessageBox, QFileDialog
+)
+
+from PyQt6.QtGui import (
+    QPen, QBrush, QColor, QPainter, QAction, QActionGroup, QFont, QPolygonF,
+    QKeySequence, 
+    QPixmap, QIcon, QShortcut, QDesktopServices
+)
+
+
+from PyQt6.QtCore import (
+    Qt, QPointF, QRectF, QLineF, QUrl, QTimer
+)
+import platform
+try:
+    import winreg
+except Exception:
+    winreg = None
+
+try:
+    from .plugin_manager import PluginManager
+except Exception:
+    from modules.plugin_manager import PluginManager
+
+
+def detect_system_dark_mode():
+    """Return True if the OS prefers dark app theme, False if light, or None if unknown.
+
+    This is a best-effort, cross-platform check supporting Windows (registry),
+    macOS (defaults read), and GNOME/GTK-based Linux (gsettings). Return
+    None if no reliable information is available.
+    """
+    # Delegate detailed OS detection to `detect_system_theme` and map
+    # 'dark' -> True, 'light' -> False. This avoids duplicating the
+    # registry and subprocess calls in two places.
+    theme = detect_system_theme()
+    if theme == 'dark':
+        return True
+    if theme == 'light':
+        return False
+    return None
+
+def detect_system_theme():
+    """OSの優先テーマ設定を 'dark', 'light', または None として返す。
+
+    This is a best-effort, cross-platform check.
+    """
+    try:
+        # Windows: AppsUseLightTheme (0 = dark, 1 = light)
+        if platform.system() == 'Windows' and winreg is not None:
+            try:
+                with winreg.OpenKey(winreg.HKEY_CURRENT_USER,
+                                    r'Software\Microsoft\Windows\CurrentVersion\Themes\Personalize') as k:
+                    val, _ = winreg.QueryValueEx(k, 'AppsUseLightTheme')
+                    return 'dark' if int(val) == 0 else 'light'
+            except Exception:
+                pass
+
+        # macOS: 'defaults read -g AppleInterfaceStyle'
+        if platform.system() == 'Darwin':
+            return 'light'
+            '''
+            try:
+                # 'defaults read ...' が成功すればダークモード
+                p = subprocess.run(
+                    ['defaults', 'read', '-g', 'AppleInterfaceStyle'],
+                    capture_output=True, text=True, check=True, encoding='utf-8'
+                )
+                if p.stdout.strip().lower() == 'dark':
+                    return 'dark'
+                
+            except subprocess.CalledProcessError:
+                # コマンド失敗 (キーが存在しない) = ライトモード
+                return 'light'
+            except Exception:
+                # その他のエラー
+                pass
+            '''
+
+        # Linux / GNOME: try color-scheme gsetting; fallback to gtk-theme detection
+        if platform.system() == 'Linux':
+            try:
+                p = subprocess.run(['gsettings', 'get', 'org.gnome.desktop.interface', 'color-scheme'], capture_output=True, text=True)
+                if p.returncode == 0:
+                    out = p.stdout.strip().strip("'\n ")
+                    if 'dark' in out.lower():
+                        return 'dark'
+                    if 'light' in out.lower():
+                        return 'light'
+            except Exception:
+                pass
+
+            try:
+                p = subprocess.run(['gsettings', 'get', 'org.gnome.desktop.interface', 'gtk-theme'], capture_output=True, text=True)
+                if p.returncode == 0 and '-dark' in p.stdout.lower():
+                    return 'dark'
+            except Exception:
+                pass
+    except Exception:
+        pass
+    return None
+
+
+# Use centralized Open Babel availability from package-level __init__
+# Use per-package modules availability (local __init__).
+try:
+    from . import OBABEL_AVAILABLE
+except Exception:
+    from modules import OBABEL_AVAILABLE
+# Only import pybel on demand — `moleditpy` itself doesn't expose `pybel`.
+if OBABEL_AVAILABLE:
+    try:
+        from openbabel import pybel
+    except Exception:
+        # If import fails here, disable OBABEL locally; avoid raising
+        pybel = None
+        OBABEL_AVAILABLE = False
+        print("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
+else:
+    pybel = None
+    
+# Optional SIP helper: on some PyQt6 builds sip.isdeleted is available and
+# allows safely detecting C++ wrapper objects that have been deleted. Import
+# it once at module import time and expose a small, robust wrapper so callers
+# can avoid re-importing sip repeatedly and so we centralize exception
+# handling (this reduces crash risk during teardown and deletion operations).
+try:
+    import sip as _sip  # type: ignore
+    _sip_isdeleted = getattr(_sip, 'isdeleted', None)
+except Exception:
+    _sip = None
+    _sip_isdeleted = None
+
+try:
+    # package relative imports (preferred when running as `python -m moleditpy`)
+    from .constants import NUM_DASHES, VERSION
+    from .molecular_data import MolecularData
+    from .molecule_scene import MoleculeScene
+    from .zoomable_view import ZoomableView
+    from .color_settings_dialog import ColorSettingsDialog
+    from .settings_dialog import SettingsDialog
+    from .custom_qt_interactor import CustomQtInteractor
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import NUM_DASHES, VERSION
+    from modules.molecular_data import MolecularData
+    from modules.molecule_scene import MoleculeScene
+    from modules.zoomable_view import ZoomableView
+    from modules.color_settings_dialog import ColorSettingsDialog
+    from modules.settings_dialog import SettingsDialog
+    from modules.custom_qt_interactor import CustomQtInteractor
+
+    
+
+# --- クラス定義 ---
+class MainWindowMainInit(object):
+    """ main_window.py から分離された機能クラス """
+
+    # __init__ は main_window.py からコピーされます
+
+
+    def __init__(self, initial_file=None):
+        # This helper is not used as a mixin in this project; initialization
+        # happens on the `MainWindow` instance. Avoid calling super() here
+        # because we initialize the `QMainWindow` base class in
+        # `MainWindow.__init__` directly.
+        self.setAcceptDrops(True)
+        self.settings_dir = os.path.join(os.path.expanduser('~'), '.moleditpy')
+        self.settings_file = os.path.join(self.settings_dir, 'settings.json')
+        self.settings = {}
+        self.load_settings()
+        self.initial_settings = self.settings.copy()
+        self.setWindowTitle("MoleditPy Ver. " + VERSION); self.setGeometry(100, 100, 1400, 800)
+        self.data = MolecularData(); self.current_mol = None
+        self.current_3d_style = 'ball_and_stick'
+        self.show_chiral_labels = False
+        self.atom_info_display_mode = None  # 'id', 'coords', 'symbol', or None
+        self.current_atom_info_labels = None  # 現在の原子情報ラベル
+        self.is_3d_edit_mode = False
+        self.dragged_atom_info = None
+        self.atom_actor = None 
+        self.is_2d_editable = True
+        self.is_xyz_derived = False  # XYZ由来の分子かどうかのフラグ
+        # Chemical check flags: whether a chemical/sanitization check was attempted and whether it failed
+        self.chem_check_tried = False
+        self.chem_check_failed = False
+        # 3D最適化のデフォルト手法
+        self.optimization_method = self.settings.get('optimization_method', 'MMFF_RDKIT')
+        self.axes_actor = None
+        self.axes_widget = None
+        self._template_dialog = None  # テンプレートダイアログの参照
+        self.undo_stack = []
+        self.redo_stack = []
+        self.constraints_3d = []
+        self.mode_actions = {} 
+        
+        # 保存状態を追跡する変数
+        self.has_unsaved_changes = False
+        # 設定ファイルのディスク書き込みを遅延するフラグ
+        # True に設定された場合、設定はメモリ上で更新され、アプリ終了時にまとめて保存されます。
+        self.settings_dirty = True
+        self.current_file_path = None  # 現在開いているファイルのパス
+        self.initialization_complete = False  # 初期化完了フラグ
+        # Token to invalidate pending implicit-hydrogen UI updates
+        self._ih_update_counter = 0
+        
+        # 測定機能用の変数
+        self.measurement_mode = False
+        self.selected_atoms_for_measurement = []
+        self.measurement_labels = []  # (atom_idx, label_text) のタプルのリスト
+        self.measurement_text_actor = None
+        self.measurement_label_items_2d = []  # 2Dビューの測定ラベルアイテム
+        self.atom_id_to_rdkit_idx_map = {}  # 2D原子IDから3D RDKit原子インデックスへのマッピング
+        
+        # 3D原子選択用の変数
+        self.selected_atoms_3d = set()
+        self.atom_selection_mode = False
+        self.selected_atom_actors = []
+        
+        # 3D編集用の原子選択状態 (3Dビューで選択された原子のインデックス)
+        self.selected_atoms_3d = set()
+        
+        # 3D編集ダイアログの参照を保持
+        self.active_3d_dialogs = []
+        
+
+        # プラグインマネージャーの初期化
+        try:
+            self.plugin_manager = PluginManager()
+        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()
+        self._setup_3d_picker() 
+
+        # --- RDKit初回実行コストの事前読み込み（ウォームアップ）---
+        try:
+            # Create a molecule with a variety of common atoms to ensure
+            # the valence/H-count machinery is fully initialized.
+            warmup_smiles = "OC(N)C(S)P"
+            warmup_mol = Chem.MolFromSmiles(warmup_smiles)
+            if warmup_mol:
+                for atom in warmup_mol.GetAtoms():
+                    atom.GetNumImplicitHs()
+        except Exception as e:
+            print(f"RDKit warm-up failed: {e}")
+
+        self.reset_undo_stack()
+        self.scene.selectionChanged.connect(self.update_edit_menu_actions)
+        QApplication.clipboard().dataChanged.connect(self.update_edit_menu_actions)
+
+        self.update_edit_menu_actions()
+
+        if initial_file:
+            self.load_command_line_file(initial_file)
+        
+        QTimer.singleShot(0, self.apply_initial_settings)
+        # カメラ初期化フラグ（初回描画時のみリセットを許可する）
+        self._camera_initialized = False
+        
+        # 初期メニューテキストと状態を設定
+        self.update_atom_id_menu_text()
+        self.update_atom_id_menu_state()
+        
+        
+        # 初期化完了を設定
+        self.initialization_complete = True
+        self.update_window_title()  # 初期化完了後にタイトルを更新
+        # Ensure initial keyboard/mouse focus is placed on the 2D view
+        # when opening a file or starting the application. This avoids
+        # accidental focus landing on toolbar/buttons (e.g. Optimize 2D).
+        try:
+            QTimer.singleShot(0, self.view_2d.setFocus)
+        except Exception:
+            pass
+
+
+
+    def init_ui(self):
+        # 1. 現在のスクリプトがあるディレクトリのパスを取得
+        script_dir = os.path.dirname(os.path.abspath(__file__))
+        
+        # 2. 'assets'フォルダ内のアイコンファイルへのフルパスを構築
+        icon_path = os.path.join(script_dir, 'assets', 'icon.png')
+        
+        # 3. ファイルパスから直接QIconオブジェクトを作成
+        if os.path.exists(icon_path): # ファイルが存在するか確認
+            app_icon = QIcon(icon_path)
+            
+            # 4. ウィンドウにアイコンを設定
+            self.setWindowIcon(app_icon)
+        else:
+            print(f"警告: アイコンファイルが見つかりません: {icon_path}")
+
+
+
+        self.splitter = QSplitter(Qt.Orientation.Horizontal)
+        # スプリッターハンドルを太くして視認性を向上
+        self.splitter.setHandleWidth(8)
+        # スプリッターハンドルのスタイルを改善
+        self.splitter.setStyleSheet("""
+            QSplitter::handle {
+                background-color: #ccc;
+                border: 1px solid #999;
+                border-radius: 4px;
+                margin: 2px;
+            }
+            QSplitter::handle:hover {
+                background-color: #aaa;
+            }
+            QSplitter::handle:pressed {
+                background-color: #888;
+            }
+        """)
+        self.setCentralWidget(self.splitter)
+
+        left_pane=QWidget()
+        left_pane.setAcceptDrops(True)
+        left_layout=QVBoxLayout(left_pane)
+
+        self.scene=MoleculeScene(self.data,self)
+        self.scene.setSceneRect(-4000,-4000,4000,4000)
+        self.scene.setBackgroundBrush(QColor("#FFFFFF"))
+
+        self.view_2d=ZoomableView(self.scene, self)
+        self.view_2d.setRenderHint(QPainter.RenderHint.Antialiasing)
+        self.view_2d.setSizePolicy(
+            QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding
+        )
+        left_layout.addWidget(self.view_2d, 1)
+
+        self.view_2d.scale(0.75, 0.75)
+
+        # --- 左パネルのボタンレイアウト ---
+        left_buttons_layout = QHBoxLayout()
+        self.cleanup_button = QPushButton("Clean Up 2D")
+        self.cleanup_button.clicked.connect(self.clean_up_2d_structure)
+        left_buttons_layout.addWidget(self.cleanup_button)
+
+        self.convert_button = QPushButton("Convert 2D to 3D")
+        self.convert_button.clicked.connect(self.trigger_conversion)
+        # Allow right-click to open a temporary conversion-mode menu
+        try:
+            self.convert_button.setContextMenuPolicy(Qt.ContextMenuPolicy.CustomContextMenu)
+            self.convert_button.customContextMenuRequested.connect(self.show_convert_menu)
+        except Exception:
+            pass
+        left_buttons_layout.addWidget(self.convert_button)
+        
+        left_layout.addLayout(left_buttons_layout)
+        self.splitter.addWidget(left_pane)
+
+        # --- 右パネルとボタンレイアウト ---
+        right_pane = QWidget()
+        # 1. 右パネル全体は「垂直」レイアウトにする
+        right_layout = QVBoxLayout(right_pane)
+        self.plotter = CustomQtInteractor(right_pane, main_window=self, lighting='none')
+        self.plotter.setAcceptDrops(False)
+        self.plotter.setSizePolicy(
+            QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding
+        )
+        self.plotter.setContextMenuPolicy(Qt.ContextMenuPolicy.NoContextMenu)
+        
+        # 2. 垂直レイアウトに3Dビューを追加
+        right_layout.addWidget(self.plotter, 1)
+        #self.plotter.installEventFilter(self)
+        # 3. ボタンをまとめるための「水平」レイアウトを作成
+        right_buttons_layout = QHBoxLayout()
+
+        # 3D最適化ボタン
+        self.optimize_3d_button = QPushButton("Optimize 3D")
+        self.optimize_3d_button.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
+        self.optimize_3d_button.clicked.connect(self.optimize_3d_structure)
+        self.optimize_3d_button.setEnabled(False)
+        # 初期状態は_enable_3d_features(False)で統一的に設定
+        # Allow right-click to open a temporary optimization-method menu
+        try:
+            self.optimize_3d_button.setContextMenuPolicy(Qt.ContextMenuPolicy.CustomContextMenu)
+            self.optimize_3d_button.customContextMenuRequested.connect(self.show_optimize_menu)
+        except Exception:
+            pass
+            pass
+        right_buttons_layout.addWidget(self.optimize_3d_button)
+
+        # エクスポートボタン (メニュー付き)
+        self.export_button = QToolButton()
+        self.export_button.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
+        self.export_button.setText("Export 3D")
+        self.export_button.setPopupMode(QToolButton.ToolButtonPopupMode.InstantPopup)
+        self.export_button.setEnabled(False) # 初期状態は無効
+
+        export_menu = QMenu(self)
+        export_mol_action = QAction("Export as MOL...", self)
+        export_mol_action.triggered.connect(self.save_3d_as_mol)
+        export_menu.addAction(export_mol_action)
+
+        export_xyz_action = QAction("Export as XYZ...", self)
+        export_xyz_action.triggered.connect(self.save_as_xyz)
+        export_menu.addAction(export_xyz_action)
+
+        export_png_action = QAction("Export as PNG...", self)
+        export_png_action.triggered.connect(self.export_3d_png)
+        export_menu.addAction(export_png_action)
+
+        self.export_button.setMenu(export_menu)
+        right_buttons_layout.addWidget(self.export_button)
+
+        # 4. 水平のボタンレイアウトを、全体の垂直レイアウトに追加
+        right_layout.addLayout(right_buttons_layout)
+        self.splitter.addWidget(right_pane)
+        
+        # スプリッターのサイズ変更をモニターして、フィードバックを提供
+        self.splitter.splitterMoved.connect(self.on_splitter_moved)
+        
+        self.splitter.setSizes([600, 600])
+        
+        # スプリッターハンドルにツールチップを設定
+        QTimer.singleShot(100, self.setup_splitter_tooltip)
+
+        # ステータスバーを左右に分離するための設定
+        self.status_bar = self.statusBar()
+        self.formula_label = QLabel("")  # 右側に表示するラベルを作成
+        # 右端に余白を追加して見栄えを調整
+        self.formula_label.setStyleSheet("padding-right: 8px;")
+        # ラベルを右側に常時表示ウィジェットとして追加
+        self.status_bar.addPermanentWidget(self.formula_label)
+
+        #self.view_2d.fitInView(self.scene.sceneRect(), Qt.AspectRatioMode.KeepAspectRatio)
+
+        # Top/main toolbar (keep 3D Edit controls on the right end of this toolbar)
+        toolbar = QToolBar("Main Toolbar")
+        self.addToolBar(toolbar)
+        # Keep a reference to the main toolbar for later updates
+        self.toolbar = toolbar
+
+        # Now that toolbar exists, initialize menu bar (which might add toolbar actions from plugins)
+        # self.init_menu_bar() - Moved down
+
+        # Templates toolbar: place it directly below the main toolbar (second row at the top)
+        # Use addToolBarBreak to ensure this toolbar appears on the next row under the main toolbar.
+        # Some older PyQt/PySide versions may not have addToolBarBreak; fall back silently in that case.
+        try:
+            # Insert a toolbar break in the Top toolbar area to force the next toolbar onto a new row
+            self.addToolBarBreak(Qt.ToolBarArea.TopToolBarArea)
+        except Exception:
+            # If addToolBarBreak isn't available, continue without raising; placement may still work depending on the platform.
+            pass
+
+        toolbar_bottom = QToolBar("Templates Toolbar")
+        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, toolbar_bottom)
+        self.toolbar_bottom = toolbar_bottom
+
+        # Plugin Toolbar (Third Row)
+        try:
+            self.addToolBarBreak(Qt.ToolBarArea.TopToolBarArea)
+        except Exception:
+            pass
+
+        self.plugin_toolbar = QToolBar("Plugin Toolbar")
+        self.addToolBar(Qt.ToolBarArea.TopToolBarArea, self.plugin_toolbar)
+        self.plugin_toolbar.hide()
+        
+        # Initialize menu bar (and populate toolbars) AFTER all toolbars are created
+        self.init_menu_bar()
+
+        self.tool_group = QActionGroup(self)
+        self.tool_group.setExclusive(True)
+
+        actions_data = [
+            ("Select", 'select', 'Space'), ("C", 'atom_C', 'c'), ("H", 'atom_H', 'h'), ("B", 'atom_B', 'b'),
+            ("N", 'atom_N', 'n'), ("O", 'atom_O', 'o'), ("S", 'atom_S', 's'), ("Si", 'atom_Si', 'Shift+S'), ("P", 'atom_P', 'p'), 
+            ("F", 'atom_F', 'f'), ("Cl", 'atom_Cl', 'Shift+C'), ("Br", 'atom_Br', 'Shift+B'), ("I", 'atom_I', 'i'), 
+            ("Other...", 'atom_other', '')
+        ]
+
+        for text, mode, shortcut_text in actions_data:
+            if text == "C": toolbar.addSeparator()
+            
+            action = QAction(text, self, checkable=(mode != 'atom_other'))
+            if shortcut_text: action.setToolTip(f"{text} ({shortcut_text})")
+
+            if mode == 'atom_other':
+                action.triggered.connect(self.open_periodic_table_dialog)
+                self.other_atom_action = action
+            else:
+                action.triggered.connect(lambda c, m=mode: self.set_mode(m))
+                self.mode_actions[mode] = action
+
+            toolbar.addAction(action)
+            if mode != 'atom_other': self.tool_group.addAction(action)
+            
+            if text == "Select":
+                select_action = action
+        
+        toolbar.addSeparator()
+
+        # --- アイコン前景色を決めるヘルパー（ダーク/ライトモード対応） ---
+        # Use module-level detector `detect_system_dark_mode()` so tests and other
+        # modules can reuse the logic.
+
+
+        def _icon_foreground_color():
+            """Return a QColor for icon foreground.
+
+            NOTE: choose icon foreground to contrast against the background
+            (i.e., white on dark backgrounds, black on light backgrounds). This
+            matches common conventions. Priority: explicit setting in
+            'icon_foreground' -> OS theme preference -> configured 3D
+            theme preference -> configured 3D background -> application palette.
+            """
+            try:
+                fg_hex = self.settings.get('icon_foreground')
+                if fg_hex:
+                    c = QColor(fg_hex)
+                    if c.isValid():
+                        return c
+            except Exception:
+                pass
+
+            # 1) Prefer the system/OS dark-mode preference if available.
+            try:
+                os_pref = detect_system_dark_mode()
+                # Standard mapping: dark -> white, light -> black
+                if os_pref is not None:
+                    return QColor('#FFFFFF') if os_pref else QColor('#000000')
+            except Exception:
+                pass
+
+            try:
+                # Keep background_color as a fallback: if system preference isn't
+                # available we'll use the configured 3D view background from settings.
+                bg_hex = self.settings.get('background_color')
+                if bg_hex:
+                    bg = QColor(bg_hex)
+                    if bg.isValid():
+                        lum = 0.2126 * bg.redF() + 0.7152 * bg.greenF() + 0.0722 * bg.blueF()
+                        # Return white on dark (lum<0.5), black on light
+                        return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
+            except Exception:
+                pass
+
+            try:
+                pal = QApplication.palette()
+                # palette.window() returns a QBrush; call color()
+                window_bg = pal.window().color()
+                lum = 0.2126 * window_bg.redF() + 0.7152 * window_bg.greenF() + 0.0722 * window_bg.blueF()
+                # Palette-based mapping: white on dark palette background
+                return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
+            except Exception:
+                return QColor('#000000')
+
+        # --- 結合ボタンのアイコンを生成するヘルパー関数 ---
+        def create_bond_icon(bond_type, size=32):
+            fg = _icon_foreground_color()
+            pixmap = QPixmap(size, size)
+            pixmap.fill(Qt.GlobalColor.transparent)
+            painter = QPainter(pixmap)
+            painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+
+            p1 = QPointF(6, size / 2)
+            p2 = QPointF(size - 6, size / 2)
+            line = QLineF(p1, p2)
+
+            pen = QPen(fg, 2)
+            painter.setPen(pen)
+            painter.setBrush(QBrush(fg))
+
+            if bond_type == 'single':
+                painter.drawLine(line)
+            elif bond_type == 'double':
+                v = line.unitVector().normalVector()
+                offset = QPointF(v.dx(), v.dy()) * 2.5
+                painter.drawLine(line.translated(offset))
+                painter.drawLine(line.translated(-offset))
+            elif bond_type == 'triple':
+                v = line.unitVector().normalVector()
+                offset = QPointF(v.dx(), v.dy()) * 3.0
+                painter.drawLine(line)
+                painter.drawLine(line.translated(offset))
+                painter.drawLine(line.translated(-offset))
+            elif bond_type == 'wedge':
+                vec = line.unitVector()
+                normal = vec.normalVector()
+                offset = QPointF(normal.dx(), normal.dy()) * 5.0
+                poly = QPolygonF([p1, p2 + offset, p2 - offset])
+                painter.drawPolygon(poly)
+            elif bond_type == 'dash':
+                vec = line.unitVector()
+                normal = vec.normalVector()
+
+                num_dashes = NUM_DASHES
+                for i in range(num_dashes + 1):
+                    t = i / num_dashes
+                    start_pt = p1 * (1 - t) + p2 * t
+                    width = 10 * t
+                    offset = QPointF(normal.dx(), normal.dy()) * width / 2.0
+                    painter.setPen(QPen(fg, 1.5))
+                    painter.drawLine(start_pt - offset, start_pt + offset)
+
+            elif bond_type == 'ez_toggle':
+                # アイコン下部に二重結合を描画
+                p1 = QPointF(6, size * 0.75)
+                p2 = QPointF(size - 6, size * 0.75)
+                line = QLineF(p1, p2)
+                v = line.unitVector().normalVector()
+                offset = QPointF(v.dx(), v.dy()) * 2.0
+                painter.setPen(QPen(fg, 2))
+                painter.drawLine(line.translated(offset))
+                painter.drawLine(line.translated(-offset))
+                # 上部に "Z⇌E" のテキストを描画
+                painter.setPen(QPen(fg, 1))
+                font = painter.font()
+                font.setPointSize(10)
+                font.setBold(True)
+                painter.setFont(font)
+                text_rect = QRectF(0, 0, size, size * 0.6)
+                # U+21CC は右向きと左向きのハープーンが重なった記号 (⇌)
+                painter.drawText(text_rect, Qt.AlignmentFlag.AlignCenter, "Z⇌E")
+
+            painter.end()
+            return QIcon(pixmap)
+
+        # --- 結合ボタンをツールバーに追加 ---
+        bond_actions_data = [
+            ("Single Bond", 'bond_1_0', '1', 'single'),
+            ("Double Bond", 'bond_2_0', '2', 'double'),
+            ("Triple Bond", 'bond_3_0', '3', 'triple'),
+            ("Wedge Bond", 'bond_1_1', 'W', 'wedge'),
+            ("Dash Bond", 'bond_1_2', 'D', 'dash'),
+            ("Toggle E/Z", 'bond_2_5', 'E/Z', 'ez_toggle'),
+        ]
+
+        for text, mode, shortcut_text, icon_type in bond_actions_data:
+            action = QAction(self)
+            action.setIcon(create_bond_icon(icon_type))
+            action.setToolTip(f"{text} ({shortcut_text})")
+            action.setCheckable(True)
+            action.triggered.connect(lambda checked, m=mode: self.set_mode(m))
+            self.mode_actions[mode] = action
+            toolbar.addAction(action)
+            self.tool_group.addAction(action)
+        
+        toolbar.addSeparator()
+
+        charge_plus_action = QAction("+ Charge", self, checkable=True)
+        charge_plus_action.setToolTip("Increase Atom Charge (+)")
+        charge_plus_action.triggered.connect(lambda c, m='charge_plus': self.set_mode(m))
+        self.mode_actions['charge_plus'] = charge_plus_action
+        toolbar.addAction(charge_plus_action)
+        self.tool_group.addAction(charge_plus_action)
+
+        charge_minus_action = QAction("- Charge", self, checkable=True)
+        charge_minus_action.setToolTip("Decrease Atom Charge (-)")
+        charge_minus_action.triggered.connect(lambda c, m='charge_minus': self.set_mode(m))
+        self.mode_actions['charge_minus'] = charge_minus_action
+        toolbar.addAction(charge_minus_action)
+        self.tool_group.addAction(charge_minus_action)
+
+        radical_action = QAction("Radical", self, checkable=True)
+        radical_action.setToolTip("Toggle Radical (0/1/2) (.)")
+        radical_action.triggered.connect(lambda c, m='radical': self.set_mode(m))
+        self.mode_actions['radical'] = radical_action
+        toolbar.addAction(radical_action)
+        self.tool_group.addAction(radical_action)
+
+        # We will show template controls in the bottom toolbar to improve layout.
+        # Add a small label to the bottom toolbar instead of the main toolbar.
+        toolbar_bottom.addWidget(QLabel(" Templates:"))
+        
+        # --- アイコンを生成するヘルパー関数 ---
+        def create_template_icon(n, is_benzene=False):
+            size = 32
+            fg = _icon_foreground_color()
+            pixmap = QPixmap(size, size)
+            pixmap.fill(Qt.GlobalColor.transparent)
+            painter = QPainter(pixmap)
+            painter.setRenderHint(QPainter.RenderHint.Antialiasing)
+            painter.setPen(QPen(fg, 2))
+
+            center = QPointF(size / 2, size / 2)
+            radius = size / 2 - 4 # アイコンの余白
+
+            points = []
+            angle_step = 2 * math.pi / n
+            # ポリゴンが直立するように開始角度を調整
+            start_angle = -math.pi / 2 if n % 2 != 0 else -math.pi / 2 - angle_step / 2
+
+            for i in range(n):
+                angle = start_angle + i * angle_step
+                x = center.x() + radius * math.cos(angle)
+                y = center.y() + radius * math.sin(angle)
+                points.append(QPointF(x, y))
+
+            painter.drawPolygon(QPolygonF(points))
+
+            if is_benzene:
+                painter.drawEllipse(center, radius * 0.6, radius * 0.6)
+
+            if n in [7, 8, 9]:
+                font = QFont("Arial", 10, QFont.Weight.Bold)
+                painter.setFont(font)
+                painter.setPen(QPen(fg, 1))
+                painter.drawText(QRectF(0, 0, size, size), Qt.AlignmentFlag.AlignCenter, str(n))
+
+            painter.end()
+            return QIcon(pixmap)
+
+        # --- ヘルパー関数を使ってアイコン付きボタンを作成 ---
+        templates = [("Benzene", "template_benzene", 6)] + [(f"{i}-Ring", f"template_{i}", i) for i in range(3, 10)]
+        for text, mode, n in templates:
+            action = QAction(self) # テキストなしでアクションを作成
+            action.setCheckable(True)
+
+            is_benzene = (text == "Benzene")
+            icon = create_template_icon(n, is_benzene=is_benzene)
+            action.setIcon(icon) # アイコンを設定
+
+            if text == "Benzene":
+                action.setToolTip(f"{text} Template (4)")
+            else:
+                action.setToolTip(f"{text} Template")
+
+            action.triggered.connect(lambda c, m=mode: self.set_mode(m))
+            self.mode_actions[mode] = action
+            # Add template actions to the bottom toolbar so templates are on the second line
+            toolbar_bottom.addAction(action)
+            self.tool_group.addAction(action)
+
+        # Add USER button for user templates (placed in bottom toolbar)
+        user_template_action = QAction("USER", self)
+        user_template_action.setCheckable(True)
+        user_template_action.setToolTip("Open User Templates Dialog")
+        user_template_action.triggered.connect(self.open_template_dialog_and_activate)
+        self.mode_actions['template_user'] = user_template_action
+        toolbar_bottom.addAction(user_template_action)
+        self.tool_group.addAction(user_template_action)
+
+        # 初期モードを'select'から'atom_C'（炭素原子描画モード）に変更
+        self.set_mode('atom_C')
+        # 対応するツールバーの'C'ボタンを選択状態にする
+        if 'atom_C' in self.mode_actions:
+            self.mode_actions['atom_C'].setChecked(True)
+
+        # スペーサーを追加して、次のウィジェットを右端に配置する (keep on top toolbar)
+        spacer = QWidget()
+        spacer.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
+        toolbar.addWidget(spacer)
+
+        # 測定機能ボタンを追加（"3D Select"に変更）
+        self.measurement_action = QAction("3D Select", self, checkable=True)
+        self.measurement_action.setToolTip("Enable distance, angle, and dihedral measurement in 3D view")
+        # 初期状態でも有効にする
+        self.measurement_action.triggered.connect(self.toggle_measurement_mode)
+        toolbar.addAction(self.measurement_action)
+
+        self.edit_3d_action = QAction("3D Drag", self, checkable=True)
+        self.edit_3d_action.setToolTip("Toggle 3D atom dragging mode (Hold Alt for temporary mode)")
+        # 初期状態でも有効にする
+        self.edit_3d_action.toggled.connect(self.toggle_3d_edit_mode)
+        toolbar.addAction(self.edit_3d_action)
+
+        # 3Dスタイル変更ボタンとメニューを作成
+
+        self.style_button = QToolButton()
+        self.style_button.setText("3D Style")
+        self.style_button.setPopupMode(QToolButton.ToolButtonPopupMode.InstantPopup)
+        toolbar.addWidget(self.style_button)
+
+        style_menu = QMenu(self)
+        self.style_button.setMenu(style_menu)
+
+        style_group = QActionGroup(self)
+        style_group.setExclusive(True)
+
+        # Ball & Stick アクション
+        bs_action = QAction("Ball & Stick", self, checkable=True)
+        bs_action.setChecked(True)
+        bs_action.triggered.connect(lambda: self.set_3d_style('ball_and_stick'))
+        style_menu.addAction(bs_action)
+        style_group.addAction(bs_action)
+
+        # CPK アクション
+        cpk_action = QAction("CPK (Space-filling)", self, checkable=True)
+        cpk_action.triggered.connect(lambda: self.set_3d_style('cpk'))
+        style_menu.addAction(cpk_action)
+        style_group.addAction(cpk_action)
+
+        # Wireframe アクション
+        wireframe_action = QAction("Wireframe", self, checkable=True)
+        wireframe_action.triggered.connect(lambda: self.set_3d_style('wireframe'))
+        style_menu.addAction(wireframe_action)
+        style_group.addAction(wireframe_action)
+
+        # Stick アクション
+        stick_action = QAction("Stick", self, checkable=True)
+        stick_action.triggered.connect(lambda: self.set_3d_style('stick'))
+        style_menu.addAction(stick_action)
+        style_group.addAction(stick_action)
+
+        quit_shortcut = QShortcut(QKeySequence("Ctrl+Q"), self)
+        quit_shortcut.activated.connect(self.close)
+
+        self.view_2d.setFocus()
+
+
+
+    def init_menu_bar(self):
+        menu_bar = self.menuBar()
+        
+        file_menu = menu_bar.addMenu("&File")
+        
+        # === プロジェクト操作 ===
+        new_action = QAction("&New", self)
+        new_action.setShortcut("Ctrl+N")
+        new_action.triggered.connect(self.clear_all)
+        file_menu.addAction(new_action)
+        
+        load_project_action = QAction("&Open Project...", self)
+        load_project_action.setShortcut("Ctrl+O")
+        load_project_action.triggered.connect(self.open_project_file)
+        file_menu.addAction(load_project_action)
+        
+        save_action = QAction("&Save Project", self)
+        save_action.setShortcut("Ctrl+S")
+        save_action.triggered.connect(self.save_project)
+        file_menu.addAction(save_action)
+        
+        save_as_action = QAction("Save Project &As...", self)
+        save_as_action.setShortcut("Ctrl+Shift+S")
+        save_as_action.triggered.connect(self.save_project_as)
+        file_menu.addAction(save_as_action)
+        
+        save_template_action = QAction("Save 2D as Template...", self)
+        save_template_action.triggered.connect(self.save_2d_as_template)
+        file_menu.addAction(save_template_action)
+        
+        file_menu.addSeparator()
+        
+        
+        # === インポート ===
+        self.import_menu = file_menu.addMenu("Import")
+        
+        load_mol_action = QAction("MOL/SDF File...", self)
+        load_mol_action.triggered.connect(self.load_mol_file)
+        self.import_menu.addAction(load_mol_action)
+        
+        import_smiles_action = QAction("SMILES...", self)
+        import_smiles_action.triggered.connect(self.import_smiles_dialog)
+        self.import_menu.addAction(import_smiles_action)
+        
+        import_inchi_action = QAction("InChI...", self)
+        import_inchi_action.triggered.connect(self.import_inchi_dialog)
+        self.import_menu.addAction(import_inchi_action)
+        
+        self.import_menu.addSeparator()
+        
+        load_3d_mol_action = QAction("3D MOL/SDF (3D View Only)...", self)
+        load_3d_mol_action.triggered.connect(self.load_mol_file_for_3d_viewing)
+        self.import_menu.addAction(load_3d_mol_action)
+        
+        load_3d_xyz_action = QAction("3D XYZ (3D View Only)...", self)
+        load_3d_xyz_action.triggered.connect(self.load_xyz_for_3d_viewing)
+        self.import_menu.addAction(load_3d_xyz_action)
+        
+        # === エクスポート ===
+        export_menu = file_menu.addMenu("Export")
+        
+        # プロジェクト形式エクスポート
+        export_pmeraw_action = QAction("PME Raw Format...", self)
+        export_pmeraw_action.triggered.connect(self.save_raw_data)
+        export_menu.addAction(export_pmeraw_action)
+        
+        export_menu.addSeparator()
+        
+        # 2D エクスポート
+        export_2d_menu = export_menu.addMenu("2D Formats")
+        save_mol_action = QAction("MOL File...", self)
+        save_mol_action.triggered.connect(self.save_as_mol)
+        export_2d_menu.addAction(save_mol_action)
+        
+        export_2d_png_action = QAction("PNG Image...", self)
+        export_2d_png_action.triggered.connect(self.export_2d_png)
+        export_2d_menu.addAction(export_2d_png_action)
+
+        export_2d_svg_action = QAction("SVG Image...", self)
+        export_2d_svg_action.triggered.connect(self.export_2d_svg)
+        export_2d_menu.addAction(export_2d_svg_action)
+        
+        # 3D エクスポート
+        export_3d_menu = export_menu.addMenu("3D Formats")
+        save_3d_mol_action = QAction("MOL File...", self)
+        save_3d_mol_action.triggered.connect(self.save_3d_as_mol)
+        export_3d_menu.addAction(save_3d_mol_action)
+        
+        save_xyz_action = QAction("XYZ File...", self)
+        save_xyz_action.triggered.connect(self.save_as_xyz)
+        export_3d_menu.addAction(save_xyz_action)
+        
+        export_3d_png_action = QAction("PNG Image...", self)
+        export_3d_png_action.triggered.connect(self.export_3d_png)
+        export_3d_menu.addAction(export_3d_png_action)
+        
+        export_3d_menu.addSeparator()
+        
+        export_stl_action = QAction("STL File...", self)
+        export_stl_action.triggered.connect(self.export_stl)
+        export_3d_menu.addAction(export_stl_action)
+        
+        export_obj_action = QAction("OBJ/MTL (with colors)...", self)
+        export_obj_action.triggered.connect(self.export_obj_mtl)
+        export_3d_menu.addAction(export_obj_action)
+        
+        file_menu.addSeparator()
+        quit_action = QAction("Quit", self)
+        quit_action.triggered.connect(self.close)
+        file_menu.addAction(quit_action)
+        
+        edit_menu = menu_bar.addMenu("&Edit")
+        self.undo_action = QAction("Undo", self); self.undo_action.setShortcut(QKeySequence.StandardKey.Undo)
+        self.undo_action.triggered.connect(self.undo); edit_menu.addAction(self.undo_action)
+        
+        self.redo_action = QAction("Redo", self); self.redo_action.setShortcut(QKeySequence.StandardKey.Redo)
+        self.redo_action.triggered.connect(self.redo); edit_menu.addAction(self.redo_action)
+        
+        edit_menu.addSeparator()
+
+        self.cut_action = QAction("Cut", self)
+        self.cut_action.setShortcut(QKeySequence.StandardKey.Cut)
+        self.cut_action.triggered.connect(self.cut_selection)
+        edit_menu.addAction(self.cut_action)
+
+        self.copy_action = QAction("Copy", self)
+        self.copy_action.setShortcut(QKeySequence.StandardKey.Copy)
+        self.copy_action.triggered.connect(self.copy_selection)
+        edit_menu.addAction(self.copy_action)
+        
+        self.paste_action = QAction("Paste", self)
+        self.paste_action.setShortcut(QKeySequence.StandardKey.Paste)
+        self.paste_action.triggered.connect(self.paste_from_clipboard)
+        edit_menu.addAction(self.paste_action)
+
+        edit_menu.addSeparator()
+
+        add_hydrogen_action = QAction("Add Hydrogens", self)
+        add_hydrogen_action.setToolTip("Add explicit hydrogens based on RDKit implicit counts")
+        add_hydrogen_action.triggered.connect(self.add_hydrogen_atoms)
+        edit_menu.addAction(add_hydrogen_action)
+    
+        remove_hydrogen_action = QAction("Remove Hydrogens", self)
+        remove_hydrogen_action.triggered.connect(self.remove_hydrogen_atoms)
+        edit_menu.addAction(remove_hydrogen_action)
+
+        edit_menu.addSeparator()
+
+        rotate_2d_action = QAction("Rotate 2D...", self)
+        rotate_2d_action.triggered.connect(self.open_rotate_2d_dialog)
+        edit_menu.addAction(rotate_2d_action)
+
+        edit_menu.addSeparator()
+
+        optimize_2d_action = QAction("Clean Up 2D", self)
+        optimize_2d_action.setShortcut(QKeySequence("Ctrl+J"))
+        optimize_2d_action.triggered.connect(self.clean_up_2d_structure)
+        edit_menu.addAction(optimize_2d_action)
+        
+        convert_3d_action = QAction("Convert 2D to 3D", self)
+        convert_3d_action.setShortcut(QKeySequence("Ctrl+K"))
+        convert_3d_action.triggered.connect(self.trigger_conversion)
+        edit_menu.addAction(convert_3d_action)
+
+        optimize_3d_action = QAction("Optimize 3D", self)
+        optimize_3d_action.setShortcut(QKeySequence("Ctrl+L")) 
+        optimize_3d_action.triggered.connect(self.optimize_3d_structure)
+        edit_menu.addAction(optimize_3d_action)
+
+        # Note: 3D Optimization Settings moved to Settings -> "3D Optimization Settings"
+        # to avoid duplicating the same submenu in both Edit and Settings.
+
+        # Note: Open Babel-based optimization menu entries were intentionally
+        # removed above. Open Babel (pybel) is still available for conversion
+        # fallback elsewhere in the code, so we don't disable menu items here.
+
+        edit_menu.addSeparator()
+        
+        select_all_action = QAction("Select All", self); select_all_action.setShortcut(QKeySequence.StandardKey.SelectAll)
+        select_all_action.triggered.connect(self.select_all); edit_menu.addAction(select_all_action)
+        
+        clear_all_action = QAction("Clear All", self)
+        clear_all_action.setShortcut(QKeySequence("Ctrl+Shift+C"))
+        clear_all_action.triggered.connect(self.clear_all); edit_menu.addAction(clear_all_action)
+
+        view_menu = menu_bar.addMenu("&View")
+
+        zoom_in_action = QAction("Zoom In", self)
+        zoom_in_action.setShortcut(QKeySequence.StandardKey.ZoomIn) # Ctrl +
+        zoom_in_action.triggered.connect(self.zoom_in)
+        view_menu.addAction(zoom_in_action)
+
+        zoom_out_action = QAction("Zoom Out", self)
+        zoom_out_action.setShortcut(QKeySequence.StandardKey.ZoomOut) # Ctrl -
+        zoom_out_action.triggered.connect(self.zoom_out)
+        view_menu.addAction(zoom_out_action)
+
+        reset_zoom_action = QAction("Reset Zoom", self)
+        reset_zoom_action.setShortcut(QKeySequence("Ctrl+0"))
+        reset_zoom_action.triggered.connect(self.reset_zoom)
+        view_menu.addAction(reset_zoom_action)
+        
+        fit_action = QAction("Fit to View", self)
+        fit_action.setShortcut(QKeySequence("Ctrl+9"))
+        fit_action.triggered.connect(self.fit_to_view)
+        view_menu.addAction(fit_action)
+
+        view_menu.addSeparator()
+
+        reset_3d_view_action = QAction("Reset 3D View", self)
+        reset_3d_view_action.triggered.connect(lambda: self.plotter.reset_camera() if hasattr(self, 'plotter') else None)
+        reset_3d_view_action.setShortcut(QKeySequence("Ctrl+R"))
+        view_menu.addAction(reset_3d_view_action)
+        
+        view_menu.addSeparator()
+
+        # Panel Layout submenu
+        layout_menu = view_menu.addMenu("Panel Layout")
+        
+        equal_panels_action = QAction("Equal Panels (50:50)", self)
+        equal_panels_action.setShortcut(QKeySequence("Ctrl+1"))
+        equal_panels_action.triggered.connect(lambda: self.set_panel_layout(50, 50))
+        layout_menu.addAction(equal_panels_action)
+        
+        layout_2d_focus_action = QAction("2D Focus (70:30)", self)
+        layout_2d_focus_action.setShortcut(QKeySequence("Ctrl+2"))
+        layout_2d_focus_action.triggered.connect(lambda: self.set_panel_layout(70, 30))
+        layout_menu.addAction(layout_2d_focus_action)
+        
+        layout_3d_focus_action = QAction("3D Focus (30:70)", self)
+        layout_3d_focus_action.setShortcut(QKeySequence("Ctrl+3"))
+        layout_3d_focus_action.triggered.connect(lambda: self.set_panel_layout(30, 70))
+        layout_menu.addAction(layout_3d_focus_action)
+        
+        layout_menu.addSeparator()
+        
+        toggle_2d_panel_action = QAction("Toggle 2D Panel", self)
+        toggle_2d_panel_action.setShortcut(QKeySequence("Ctrl+H"))
+        toggle_2d_panel_action.triggered.connect(self.toggle_2d_panel)
+        layout_menu.addAction(toggle_2d_panel_action)
+
+        view_menu.addSeparator()
+
+        self.toggle_chiral_action = QAction("Show Chiral Labels", self, checkable=True)
+        self.toggle_chiral_action.setChecked(self.show_chiral_labels)
+        self.toggle_chiral_action.triggered.connect(self.toggle_chiral_labels_display)
+        view_menu.addAction(self.toggle_chiral_action)
+
+        view_menu.addSeparator()
+
+        # 3D Atom Info submenu
+        atom_info_menu = view_menu.addMenu("3D Atom Info Display")
+        
+        self.show_atom_id_action = QAction("Show Original ID / Index", self, checkable=True)
+        self.show_atom_id_action.triggered.connect(lambda: self.toggle_atom_info_display('id'))
+        atom_info_menu.addAction(self.show_atom_id_action)
+        
+        self.show_rdkit_id_action = QAction("Show RDKit Index", self, checkable=True)
+        self.show_rdkit_id_action.triggered.connect(lambda: self.toggle_atom_info_display('rdkit_id'))
+        atom_info_menu.addAction(self.show_rdkit_id_action)
+        
+        self.show_atom_coords_action = QAction("Show Coordinates (X,Y,Z)", self, checkable=True)
+        self.show_atom_coords_action.triggered.connect(lambda: self.toggle_atom_info_display('coords'))
+        atom_info_menu.addAction(self.show_atom_coords_action)
+        
+        self.show_atom_symbol_action = QAction("Show Element Symbol", self, checkable=True)
+        self.show_atom_symbol_action.triggered.connect(lambda: self.toggle_atom_info_display('symbol'))
+        atom_info_menu.addAction(self.show_atom_symbol_action)
+
+        analysis_menu = menu_bar.addMenu("&Analysis")
+        self.analysis_action = QAction("Show Analysis...", self)
+        self.analysis_action.triggered.connect(self.open_analysis_window)
+        self.analysis_action.setEnabled(False)
+        analysis_menu.addAction(self.analysis_action)
+
+        # 3D Edit menu
+        edit_3d_menu = menu_bar.addMenu("3D &Edit")
+        
+        # Translation action
+        translation_action = QAction("Translation...", self)
+        translation_action.triggered.connect(self.open_translation_dialog)
+        translation_action.setEnabled(False)
+        edit_3d_menu.addAction(translation_action)
+        self.translation_action = translation_action
+        
+        # Move Group action
+        move_group_action = QAction("Move Group...", self)
+        move_group_action.triggered.connect(self.open_move_group_dialog)
+        move_group_action.setEnabled(False)
+        edit_3d_menu.addAction(move_group_action)
+        self.move_group_action = move_group_action
+        
+        edit_3d_menu.addSeparator()
+        
+        # Alignment submenu (統合)
+        align_menu = edit_3d_menu.addMenu("Align to")
+        align_menu.setEnabled(False)
+        self.align_menu = align_menu
+        
+        # Axis alignment submenu
+        axis_align_menu = align_menu.addMenu("Axis")
+        
+        align_x_action = QAction("X-axis", self)
+        align_x_action.triggered.connect(lambda: self.open_alignment_dialog('x'))
+        align_x_action.setEnabled(False)
+        axis_align_menu.addAction(align_x_action)
+        self.align_x_action = align_x_action
+        
+        align_y_action = QAction("Y-axis", self)
+        align_y_action.triggered.connect(lambda: self.open_alignment_dialog('y'))
+        align_y_action.setEnabled(False)
+        axis_align_menu.addAction(align_y_action)
+        self.align_y_action = align_y_action
+        
+        align_z_action = QAction("Z-axis", self)
+        align_z_action.triggered.connect(lambda: self.open_alignment_dialog('z'))
+        align_z_action.setEnabled(False)
+        axis_align_menu.addAction(align_z_action)
+        self.align_z_action = align_z_action
+        
+        # Plane alignment submenu (旧align)
+        plane_align_menu = align_menu.addMenu("Plane")
+        
+        alignplane_xy_action = QAction("XY-plane", self)
+        alignplane_xy_action.triggered.connect(lambda: self.open_align_plane_dialog('xy'))
+        alignplane_xy_action.setEnabled(False)
+        plane_align_menu.addAction(alignplane_xy_action)
+        self.alignplane_xy_action = alignplane_xy_action
+
+        alignplane_xz_action = QAction("XZ-plane", self)
+        alignplane_xz_action.triggered.connect(lambda: self.open_align_plane_dialog('xz'))
+        alignplane_xz_action.setEnabled(False)
+        plane_align_menu.addAction(alignplane_xz_action)
+        self.alignplane_xz_action = alignplane_xz_action
+
+        alignplane_yz_action = QAction("YZ-plane", self)
+        alignplane_yz_action.triggered.connect(lambda: self.open_align_plane_dialog('yz'))
+        alignplane_yz_action.setEnabled(False)
+        plane_align_menu.addAction(alignplane_yz_action)
+        self.alignplane_yz_action = alignplane_yz_action
+
+        edit_3d_menu.addSeparator()
+
+        # Mirror action
+        mirror_action = QAction("Mirror...", self)
+        mirror_action.triggered.connect(self.open_mirror_dialog)
+        mirror_action.setEnabled(False)
+        edit_3d_menu.addAction(mirror_action)
+        self.mirror_action = mirror_action
+
+        edit_3d_menu.addSeparator()
+        
+        # Planarize selection (best-fit plane)
+        planarize_action = QAction("Planarize...", self)
+        planarize_action.triggered.connect(lambda: self.open_planarize_dialog(None))
+        planarize_action.setEnabled(False)
+        edit_3d_menu.addAction(planarize_action)
+        self.planarize_action = planarize_action
+        
+        edit_3d_menu.addSeparator()
+        
+        # Bond length conversion
+        bond_length_action = QAction("Adjust Bond Length...", self)
+        bond_length_action.triggered.connect(self.open_bond_length_dialog)
+        bond_length_action.setEnabled(False)
+        edit_3d_menu.addAction(bond_length_action)
+        self.bond_length_action = bond_length_action
+        
+        # Angle conversion
+        angle_action = QAction("Adjust Angle...", self)
+        angle_action.triggered.connect(self.open_angle_dialog)
+        angle_action.setEnabled(False)
+        edit_3d_menu.addAction(angle_action)
+        self.angle_action = angle_action
+        
+        # Dihedral angle conversion
+        dihedral_action = QAction("Adjust Dihedral Angle...", self)
+        dihedral_action.triggered.connect(self.open_dihedral_dialog)
+        dihedral_action.setEnabled(False)
+        edit_3d_menu.addAction(dihedral_action)
+        self.dihedral_action = dihedral_action
+
+        edit_3d_menu.addSeparator()
+        
+        # Constrained Optimization action
+        constrained_opt_action = QAction("Constrained Optimization...", self)
+        constrained_opt_action.triggered.connect(self.open_constrained_optimization_dialog)
+        constrained_opt_action.setEnabled(False)  # 3Dモデルロード時に有効化
+        edit_3d_menu.addAction(constrained_opt_action)
+        self.constrained_opt_action = constrained_opt_action
+
+        # Plugin menu
+        plugin_menu = menu_bar.addMenu("&Plugin")
+        
+        # Only keep the Manager action, moving others to the Manager Window
+        manage_plugins_action = QAction("Plugin Manager...", self)
+        def show_plugin_manager():
+            from .plugin_manager_window import PluginManagerWindow
+            dlg = PluginManagerWindow(self.plugin_manager, self)
+            dlg.exec()
+            self.update_plugin_menu(plugin_menu) # Refresh after closing
+        manage_plugins_action.triggered.connect(show_plugin_manager)
+        plugin_menu.addAction(manage_plugins_action)
+
+
+
+        
+        plugin_menu.addSeparator()
+        
+        # Initial population of plugins
+        self.update_plugin_menu(plugin_menu)
+
+        settings_menu = menu_bar.addMenu("&Settings")
+        # 1) 3D View settings (existing)
+        view_settings_action = QAction("Settings...", self)
+        view_settings_action.triggered.connect(self.open_settings_dialog)
+        settings_menu.addAction(view_settings_action)
+        
+        # Color settings (CPK/Bond) — keep with other settings
+        color_action = QAction("CPK Colors...", self)
+        color_action.triggered.connect(lambda: ColorSettingsDialog(self.settings, parent=self).exec_())
+        settings_menu.addAction(color_action)
+    
+        # 2) 3D Conversion settings — submenu with radio/check actions
+        conversion_menu = settings_menu.addMenu("3D Conversion")
+        conv_group = QActionGroup(self)
+        conv_group.setExclusive(True)
+        # helper to set conversion mode and persist
+        def _set_conv_mode(mode):
+            try:
+                self.settings['3d_conversion_mode'] = mode
+                # defer disk write
+                try:
+                    self.settings_dirty = True
+                except Exception:
+                    pass
+                self.statusBar().showMessage(f"3D conversion mode set to: {mode}")
+            except Exception:
+                pass
+
+        conv_options = [
+            ("RDKit -> Open Babel (fallback)", 'fallback'),
+            ("RDKit only", 'rdkit'),
+            ("Open Babel only", 'obabel'),
+            ("Direct (use 2D coords + add H)", 'direct')
+        ]
+        self.conv_actions = {}
+        for label, key in conv_options:
+            a = QAction(label, self)
+            a.setCheckable(True)
+            # If Open Babel isn't available, disable the Open Babel-only option
+            # and also disable the fallback option since it depends on Open Babel.
+            if not OBABEL_AVAILABLE:
+                if key == 'obabel' or key == 'fallback':
+                    a.setEnabled(False)
+            a.triggered.connect(lambda checked, m=key: _set_conv_mode(m))
+            conversion_menu.addAction(a)
+            conv_group.addAction(a)
+            self.conv_actions[key] = a
+
+        # Initialize checked state from settings (fallback default)
+        # Determine saved conversion mode. If Open Babel is not available,
+        # prefer 'rdkit' as the default rather than 'fallback'. Also ensure
+        # the settings reflect the actual enabled choice.
+        try:
+            default_mode = 'rdkit' if not OBABEL_AVAILABLE else 'fallback'
+            saved_conv = self.settings.get('3d_conversion_mode', default_mode)
+        except Exception:
+            saved_conv = 'rdkit' if not OBABEL_AVAILABLE else 'fallback'
+
+        # If the saved mode is disabled/unavailable, fall back to an enabled option.
+        if saved_conv not in self.conv_actions or not self.conv_actions[saved_conv].isEnabled():
+            # Prefer 'rdkit' if available, else pick whichever action is enabled
+            preferred = 'rdkit' if 'rdkit' in self.conv_actions and self.conv_actions['rdkit'].isEnabled() else None
+            if not preferred:
+                for k, act in self.conv_actions.items():
+                    if act.isEnabled():
+                        preferred = k
+                        break
+            saved_conv = preferred or 'rdkit'
+
+        # Set the checked state and persist the chosen conversion mode
+        try:
+            if saved_conv in self.conv_actions:
+                try:
+                    self.conv_actions[saved_conv].setChecked(True)
+                except Exception:
+                    pass
+            self.settings['3d_conversion_mode'] = saved_conv
+            try:
+                self.settings_dirty = True
+            except Exception:
+                pass
+        except Exception:
+            pass
+
+        # 3) 3D Optimization Settings (single location under Settings menu)
+        optimization_menu = settings_menu.addMenu("3D Optimization Settings")
+
+        # Only RDKit-backed optimization methods are offered here.
+        opt_methods = [
+            ("MMFF94s", "MMFF_RDKIT"),
+            ("MMFF94", "MMFF94_RDKIT"),
+            ("UFF", "UFF_RDKIT"),
+        ]
+
+        # Map key -> human-readable label for status messages and later lookups
+        try:
+            self.opt3d_method_labels = {key.upper(): label for (label, key) in opt_methods}
+        except Exception:
+            self.opt3d_method_labels = {}
+
+        opt_group = QActionGroup(self)
+        opt_group.setExclusive(True)
+        opt_actions = {}
+        for label, key in opt_methods:
+            action = QAction(label, self)
+            action.setCheckable(True)
+            try:
+                action.setActionGroup(opt_group)
+            except Exception:
+                pass
+            action.triggered.connect(lambda checked, m=key: self.set_optimization_method(m))
+            optimization_menu.addAction(action)
+            opt_group.addAction(action)
+            opt_actions[key] = action
+
+        # Persist the actions mapping so other methods can update the checked state
+        self.opt3d_actions = opt_actions
+
+        # Determine the initial checked menu item from saved settings (fall back to MMFF_RDKIT)
+        try:
+            saved_opt = (self.settings.get('optimization_method') or self.optimization_method or 'MMFF_RDKIT').upper()
+        except Exception:
+            saved_opt = 'MMFF_RDKIT'
+
+        try:
+            if saved_opt in self.opt3d_actions and self.opt3d_actions[saved_opt].isEnabled():
+                self.opt3d_actions[saved_opt].setChecked(True)
+                self.optimization_method = saved_opt
+            else:
+                if 'MMFF_RDKIT' in self.opt3d_actions:
+                    self.opt3d_actions['MMFF_RDKIT'].setChecked(True)
+                    self.optimization_method = 'MMFF_RDKIT'
+        except Exception:
+            pass
+    
+        # 4) Reset all settings to defaults
+        settings_menu.addSeparator()
+        reset_settings_action = QAction("Reset All Settings", self)
+        reset_settings_action.triggered.connect(self.reset_all_settings_menu)
+        settings_menu.addAction(reset_settings_action)
+
+        help_menu = menu_bar.addMenu("&Help")
+        about_action = QAction("About", self)
+        about_action.triggered.connect(self.show_about_dialog)
+        help_menu.addAction(about_action)
+
+        github_action = QAction("GitHub", self)
+        github_action.triggered.connect(
+            lambda: QDesktopServices.openUrl(QUrl("https://github.com/HiroYokoyama/python_molecular_editor"))
+        )
+        help_menu.addAction(github_action)
+
+        github_wiki_action = QAction("GitHub Wiki", self)
+        github_wiki_action.triggered.connect(
+            lambda: QDesktopServices.openUrl(QUrl("https://github.com/HiroYokoyama/python_molecular_editor/wiki"))
+        )
+        help_menu.addAction(github_wiki_action)
+
+        manual_action = QAction("User Manual", self)
+        manual_action.triggered.connect(
+            lambda: QDesktopServices.openUrl(QUrl("https://hiroyokoyama.github.io/python_molecular_editor/manual/manual"))
+        )
+        help_menu.addAction(manual_action)
+
+
+
+        # 3D関連機能の初期状態を統一的に設定
+        self._enable_3d_features(False)
+        
+
+
+    def init_worker_thread(self):
+        # Initialize shared state for calculation runs.
+        # NOTE: we no longer create a persistent worker/thread here. Instead,
+        # each conversion run will create its own CalculationWorker + QThread
+        # so multiple conversions may run in parallel.
+        # Shared halt id set used to request early termination of specific worker runs
+        self.halt_ids = set()
+        # IDs used to correlate start/halt/finish
+        self.next_conversion_id = 1
+        # Track currently-active conversion worker IDs so Halt can target all
+        # running conversions. Use a set because multiple conversions may run
+        # concurrently.
+        self.active_worker_ids = set()
+        # Track active threads for diagnostics/cleanup (weak references ok)
+        try:
+            self._active_calc_threads = []
+        except Exception:
+            self._active_calc_threads = []
+
+
+
+
+    def load_command_line_file(self, file_path):
+        """コマンドライン引数で指定されたファイルを開く"""
+        if not file_path or not os.path.exists(file_path):
+            return
+        
+        # Helper for extension
+        _, ext_with_dot = os.path.splitext(file_path)
+        ext_with_dot = ext_with_dot.lower()
+        # Legacy variable name (no dot)
+        file_ext = ext_with_dot.lstrip('.')
+
+        # 1. Custom Plugin Openers
+        # 1. Custom Plugin Openers
+        if ext_with_dot in self.plugin_manager.file_openers:
+            openers = self.plugin_manager.file_openers[ext_with_dot]
+            # Iterate through openers (already sorted by priority)
+            for opener_info in openers:
+                try:
+                    callback = opener_info['callback']
+                    # Try to call the opener
+                    callback(file_path)
+                    
+                    self.current_file_path = file_path
+                    self.update_window_title()
+                    return # Success
+                except Exception as e:
+                    print(f"Plugin opener failed for '{opener_info.get('plugin', 'Unknown')}': {e}")
+                    # If this opener fails, try the next one or fall through to default
+                    continue
+        
+        
+        if file_ext in ['mol', 'sdf']:
+            self.load_mol_file_for_3d_viewing(file_path)
+        elif file_ext == 'xyz':
+            self.load_xyz_for_3d_viewing(file_path)
+        elif file_ext in ['pmeraw', 'pmeprj']:
+            self.open_project_file(file_path=file_path)
+        else:
+            self.statusBar().showMessage(f"Unsupported file type: {file_ext}")
+        
+
+
+    def apply_initial_settings(self):
+        """UIの初期化が完了した後に、保存された設定を3Dビューに適用する"""
+        
+        try:
+            self.update_cpk_colors_from_settings()
+        except Exception:
+            pass
+
+        if self.plotter and self.plotter.renderer:
+            bg_color = self.settings.get('background_color', '#919191')
+            self.plotter.set_background(bg_color)
+            self.apply_3d_settings()
+        
+        try:
+            if hasattr(self, 'scene') and self.scene:
+                # Apply 2D background color
+                bg_color_2d = self.settings.get('background_color_2d', '#FFFFFF')
+                self.scene.setBackgroundBrush(QBrush(QColor(bg_color_2d)))
+
+                for it in list(self.scene.items()):
+                    if hasattr(it, 'update_style'):
+                        it.update_style()
+                self.scene.update()
+                for v in list(self.scene.views()):
+                    v.viewport().update()
+        except Exception:
+            pass
+
+
+
+    def open_settings_dialog(self):
+        dialog = SettingsDialog(self.settings, self)
+        # accept()メソッドで設定の適用と3Dビューの更新を行うため、ここでは不要
+        dialog.exec()
+
+
+
+
+    def reset_all_settings_menu(self):
+        # Expose the same functionality as SettingsDialog.reset_all_settings
+        dlg = QMessageBox(self)
+        dlg.setIcon(QMessageBox.Icon.Warning)
+        dlg.setWindowTitle("Reset All Settings")
+        dlg.setText("Are you sure you want to reset all settings to defaults?")
+        dlg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
+        res = dlg.exec()
+        if res == QMessageBox.StandardButton.Yes:
+            try:
+                # Remove settings file and reload defaults
+                if os.path.exists(self.settings_file):
+                    os.remove(self.settings_file)
+                self.load_settings()
+                # Do not write to disk immediately; mark dirty so settings will be saved on exit
+                try:
+                    self.settings_dirty = True
+                except Exception:
+                    pass
+                # If ColorSettingsDialog is open, refresh its UI to reflect the reset
+                try:
+                    for w in QApplication.topLevelWidgets():
+                        try:
+                            if isinstance(w, ColorSettingsDialog):
+                                try:
+                                    w.refresh_ui()
+                                except Exception:
+                                    pass
+                        except Exception:
+                            pass
+                except Exception:
+                    pass
+                # Ensure global CPK mapping is rebuilt from defaults and UI is updated
+                try:
+                    self.update_cpk_colors_from_settings()
+                except Exception:
+                    pass
+                # Refresh UI/menu state for conversion and optimization
+                try:
+                    # update optimization method
+                    self.optimization_method = self.settings.get('optimization_method', 'MMFF_RDKIT')
+                    if hasattr(self, 'opt3d_actions') and self.optimization_method:
+                        key = (self.optimization_method or '').upper()
+                        if key in self.opt3d_actions:
+                            # uncheck all then check the saved one
+                            for act in self.opt3d_actions.values():
+                                act.setChecked(False)
+                            try:
+                                self.opt3d_actions[key].setChecked(True)
+                            except Exception:
+                                pass
+
+                    # update conversion mode
+                    conv_mode = self.settings.get('3d_conversion_mode', 'fallback')
+                    if hasattr(self, 'conv_actions') and conv_mode in self.conv_actions:
+                        try:
+                            for act in self.conv_actions.values():
+                                act.setChecked(False)
+                            self.conv_actions[conv_mode].setChecked(True)
+                        except Exception:
+                            pass
+
+                    # 3Dビューの設定を適用
+                    self.apply_3d_settings()
+                    # 現在の分子を再描画（設定変更を反映）
+                    if hasattr(self, 'current_mol') and self.current_mol:
+                        self.draw_molecule_3d(self.current_mol)
+                    
+                    QMessageBox.information(self, "Reset Complete", "All settings have been reset to defaults.")
+                    
+                except Exception:
+                    pass
+                # Update 2D scene styling to reflect default CPK colors
+                try:
+                    # Reset 2D background specifically
+                    if hasattr(self, 'scene') and self.scene:
+                        bg_c = self.settings.get('background_color_2d', '#FFFFFF')
+                        self.scene.setBackgroundBrush(QBrush(QColor(bg_c)))
+                    
+                    self.update_cpk_colors_from_settings()
+                except Exception:
+                    pass
+                try:
+                    if hasattr(self, 'scene') and self.scene:
+                        for it in list(self.scene.items()):
+                            try:
+                                if hasattr(it, 'update_style'):
+                                    it.update_style()
+                            except Exception:
+                                pass
+                        try:
+                            # Force a full scene update and viewport repaint for all views
+                            self.scene.update()
+                            for v in list(self.scene.views()):
+                                try:
+                                    v.viewport().update()
+                                except Exception:
+                                    pass
+                        except Exception:
+                            pass
+                except Exception:
+                    pass
+                # Also refresh any open SettingsDialog instances so their UI matches
+                try:
+                    for w in QApplication.topLevelWidgets():
+                        try:
+                            if isinstance(w, SettingsDialog):
+                                try:
+                                    w.update_ui_from_settings(self.settings)
+                                except Exception:
+                                    pass
+                        except Exception:
+                            pass
+                except Exception:
+                    pass
+            except Exception as e:
+                QMessageBox.warning(self, "Reset Failed", f"Could not reset settings: {e}")
+            
+
+
+
+    def load_settings(self):
+        default_settings = {
+            'background_color': '#919191',
+            'projection_mode': 'Perspective',
+            'lighting_enabled': True,
+            'specular': 0.2,
+            'specular_power': 20,
+            'light_intensity': 1.0,
+            'show_3d_axes': True,
+            # Ball and Stick model parameters
+            'ball_stick_atom_scale': 1.0,
+            'ball_stick_bond_radius': 0.1,
+            'ball_stick_resolution': 16,
+            # CPK (Space-filling) model parameters
+            'cpk_atom_scale': 1.0,
+            'cpk_resolution': 32,
+            # Wireframe model parameters
+            'wireframe_bond_radius': 0.01,
+            'wireframe_resolution': 6,
+            # Stick model parameters
+            'stick_bond_radius': 0.15,
+            'stick_resolution': 16,
+            # Multiple bond offset parameters (per-model)
+            'ball_stick_double_bond_offset_factor': 2.0,
+            'ball_stick_triple_bond_offset_factor': 2.0,
+            'ball_stick_double_bond_radius_factor': 0.8,
+            'ball_stick_triple_bond_radius_factor': 0.75,
+            'wireframe_double_bond_offset_factor': 3.0,
+            'wireframe_triple_bond_offset_factor': 3.0,
+            'wireframe_double_bond_radius_factor': 0.8,
+            'wireframe_triple_bond_radius_factor': 0.75,
+            'stick_double_bond_offset_factor': 1.5,
+            'stick_triple_bond_offset_factor': 1.0,
+            'stick_double_bond_radius_factor': 0.60,
+            'stick_triple_bond_radius_factor': 0.40,
+            'aromatic_torus_thickness_factor': 0.6,
+            # Ensure conversion/optimization defaults are present
+            # If True, attempts to be permissive when RDKit raises chemical/sanitization errors
+            # during file import (useful for viewing malformed XYZ/MOL files).
+            'skip_chemistry_checks': False,
+            '3d_conversion_mode': 'fallback',
+            'optimization_method': 'MMFF_RDKIT',
+            # Color overrides
+            'ball_stick_bond_color': '#7F7F7F',
+            'cpk_colors': {},  # symbol->hex overrides
+            # Whether to kekulize aromatic systems for 3D display
+            'display_kekule_3d': False,
+            'always_ask_charge': False,
+            'display_aromatic_circles_3d': False,
+            'ball_stick_use_cpk_bond_color': False,
+            
+            # --- 2D Settings Defaults ---
+            'bond_width_2d': 2.0,
+            'bond_spacing_double_2d': 3.5,
+            'bond_spacing_triple_2d': 3.5,
+            'atom_font_size_2d': 20,
+            'background_color_2d': '#FFFFFF',
+            'bond_color_2d': '#222222', # Almost black
+            'atom_use_bond_color_2d': False,
+            'bond_cap_style_2d': 'Round',
+        }
+
+        try:
+            if os.path.exists(self.settings_file):
+                with open(self.settings_file, 'r') as f:
+                    loaded_settings = json.load(f)
+                # Ensure any missing default keys are inserted and persisted.
+                changed = False
+                for key, value in default_settings.items():
+                    if key not in loaded_settings:
+                        loaded_settings[key] = value
+                        changed = True
+
+                self.settings = loaded_settings
+
+                # Migration: if older global multi-bond keys exist, copy them to per-model keys
+                legacy_keys = ['double_bond_offset_factor', 'triple_bond_offset_factor', 'double_bond_radius_factor', 'triple_bond_radius_factor']
+                migrated = False
+                # If legacy keys exist, propagate to per-model keys when per-model keys missing
+                if any(k in self.settings for k in legacy_keys):
+                    # For each per-model key, if missing, set from legacy fallback
+                    def copy_if_missing(new_key, legacy_key, default_val):
+                        nonlocal migrated
+                        if new_key not in self.settings:
+                            if legacy_key in self.settings:
+                                self.settings[new_key] = self.settings[legacy_key]
+                                migrated = True
+                            else:
+                                self.settings[new_key] = default_val
+                                migrated = True
+
+                    per_model_map = [
+                        ('ball_stick_double_bond_offset_factor', 'double_bond_offset_factor', 2.0),
+                        ('ball_stick_triple_bond_offset_factor', 'triple_bond_offset_factor', 2.0),
+                        ('ball_stick_double_bond_radius_factor', 'double_bond_radius_factor', 0.8),
+                        ('ball_stick_triple_bond_radius_factor', 'triple_bond_radius_factor', 0.75),
+                        ('wireframe_double_bond_offset_factor', 'double_bond_offset_factor', 3.0),
+                        ('wireframe_triple_bond_offset_factor', 'triple_bond_offset_factor', 3.0),
+                        ('wireframe_double_bond_radius_factor', 'double_bond_radius_factor', 0.8),
+                        ('wireframe_triple_bond_radius_factor', 'triple_bond_radius_factor', 0.75),
+                        ('stick_double_bond_offset_factor', 'double_bond_offset_factor', 1.5),
+                        ('stick_triple_bond_offset_factor', 'triple_bond_offset_factor', 1.0),
+                        ('stick_double_bond_radius_factor', 'double_bond_radius_factor', 0.60),
+                        ('stick_triple_bond_radius_factor', 'triple_bond_radius_factor', 0.40),
+                    ]
+                    for new_k, legacy_k, default_v in per_model_map:
+                        copy_if_missing(new_k, legacy_k, default_v)
+
+                    # Optionally remove legacy keys to avoid confusion (keep them for now but mark dirty)
+                    if migrated:
+                        changed = True
+
+                # If we added any defaults (e.g. skip_chemistry_checks) or migrated keys, write them back so
+                # the configuration file reflects the effective defaults without requiring
+                # the user to edit the file manually.
+                if changed:
+                    # Don't write immediately; mark dirty and let closeEvent persist
+                    try:
+                        self.settings_dirty = True
+                    except Exception:
+                        pass
+            
+            else:
+                # No settings file - use defaults. Mark dirty so defaults will be written on exit.
+                self.settings = default_settings
+                try:
+                    self.settings_dirty = True
+                except Exception:
+                    pass
+        
+        except Exception:
+            self.settings = default_settings
+
+
+
+    def save_settings(self):
+        try:
+            if not os.path.exists(self.settings_dir):
+                os.makedirs(self.settings_dir)
+            with open(self.settings_file, 'w') as f:
+                json.dump(self.settings, f, indent=4)
+        except Exception as e:
+            print(f"Error saving settings: {e}")
+
+    def update_plugin_menu(self, plugin_menu):
+        """Discovers plugins and updates the plugin menu actions."""
+        if not self.plugin_manager:
+            return
+        
+        PLUGIN_ACTION_TAG = "plugin_managed"
+
+        # Helper to clear tagged actions from a menu
+        def clear_plugin_actions(menu):
+            if not menu: return
+            for act in list(menu.actions()):
+                if act.data() == PLUGIN_ACTION_TAG:
+                    menu.removeAction(act)
+                # Recurse into submenus to clean deep actions
+                elif act.menu():
+                    clear_plugin_actions(act.menu())
+
+        # Clear existing plugin actions from main Plugin menu
+        plugin_menu.clear()
+        
+        # Clear tagged actions from ALL top-level menus in the Menu Bar
+        # This ensures we catch actions added to standard menus (File, Edit) OR custom menus
+        for top_action in self.menuBar().actions():
+            if top_action.menu():
+                 clear_plugin_actions(top_action.menu())
+            
+        # Clear Export menu (if button exists)
+        if hasattr(self, 'export_button') and self.export_button.menu():
+            clear_plugin_actions(self.export_button.menu())
+
+        # Only keep the Manager action
+        manage_plugins_action = QAction("Plugin Manager...", self)
+        def show_plugin_manager():
+            from .plugin_manager_window import PluginManagerWindow
+            dlg = PluginManagerWindow(self.plugin_manager, self)
+            dlg.exec()
+            self.update_plugin_menu(plugin_menu) # Refresh after closing
+        manage_plugins_action.triggered.connect(show_plugin_manager)
+        plugin_menu.addAction(manage_plugins_action)
+        
+        plugin_menu.addSeparator()
+        
+        # Add dynamic plugin actions (Legacy + New Registration)
+        plugins = self.plugin_manager.discover_plugins(self)
+        
+        # 1. Add Registered Menu Actions (New System)
+        if self.plugin_manager.menu_actions:
+             for action_def in self.plugin_manager.menu_actions:
+                 path = action_def['path']
+                 callback = action_def['callback']
+                 text = action_def['text']
+                 # Create/Find menu path
+                 current_menu = self.menuBar() # Or find specific top-level
+                 
+                 # Handling top-level menus vs nested
+                 parts = path.split('/')
+                 
+                 # If path starts with existing top-level (File, Edit, etc), grab it
+                 # Otherwise create new top-level
+                 top_level_title = parts[0]
+                 found_top = False
+                 for act in self.menuBar().actions():
+                     if act.menu() and act.text().replace('&', '') == top_level_title:
+                         current_menu = act.menu()
+                         found_top = True
+                         break
+                 
+                 if not found_top:
+                     current_menu = self.menuBar().addMenu(top_level_title)
+                 
+                 # Traverse rest
+                 for part in parts[1:-1]:
+                      found_sub = False
+                      for act in current_menu.actions():
+                          if act.menu() and act.text().replace('&', '') == part:
+                              current_menu = act.menu()
+                              found_sub = True
+                              break
+                      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)
+                 action.triggered.connect(callback)
+                 
+                 # Apply shortcut if provided
+                 if action_def.get('shortcut'):
+                     action.setShortcut(QKeySequence(action_def['shortcut']))
+                 
+                 action.setData(PLUGIN_ACTION_TAG) # TAG THE ACTION
+                 current_menu.addAction(action)
+
+        # 2. Add Toolbar Buttons (New System)
+        # Use dedicated plugin toolbar
+        if hasattr(self, 'plugin_toolbar'):
+             self.plugin_toolbar.clear()
+
+             if self.plugin_manager.toolbar_actions:
+                 self.plugin_toolbar.show()
+                 for action_def in self.plugin_manager.toolbar_actions:
+                     text = action_def['text']
+                     callback = action_def['callback']
+                     
+                     action = QAction(text, self)
+                     action.triggered.connect(callback)
+                     if action_def['icon']:
+                          if os.path.exists(action_def['icon']):
+                               action.setIcon(QIcon(action_def['icon']))
+                     if action_def['tooltip']:
+                          action.setToolTip(action_def['tooltip'])
+                     self.plugin_toolbar.addAction(action)
+             else:
+                 self.plugin_toolbar.hide()
+
+        # 3. Legacy Menu Building (Folder based)
+        if not plugins:
+            no_plugin_action = QAction("(No plugins found)", self)
+            no_plugin_action.setEnabled(False)
+            plugin_menu.addAction(no_plugin_action)
+        else:
+            # Sort plugins: 
+            # 1. Categories (A-Z)
+            # 2. Within Category: Items (A-Z)
+            # 3. Root items (A-Z)
+            
+            # Group plugins by category
+            categorized_plugins = {}
+            root_plugins = []
+            
+            for p in plugins:
+                if hasattr(p['module'], 'run'):
+                    category = p.get('category', p.get('rel_folder', '')).strip()
+                    if category:
+                        if category not in categorized_plugins:
+                            categorized_plugins[category] = []
+                        categorized_plugins[category].append(p)
+                    else:
+                        root_plugins.append(p)
+            
+            # Sort categories
+            sorted_categories = sorted(categorized_plugins.keys())
+            
+            # Build menu: Categories first
+            for cat in sorted_categories:
+                # Create/Get Category Menu (Nested support)
+                parts = cat.split(os.sep)
+                parent_menu = plugin_menu
+                
+                # Traverse/Create nested menus
+                for part in parts:
+                    found_sub = False
+                    for act in parent_menu.actions():
+                        if act.menu() and act.text().replace('&', '') == part:
+                            parent_menu = act.menu()
+                            found_sub = True
+                            break
+                    if not found_sub:
+                        parent_menu = parent_menu.addMenu(part)
+
+                # Add items to the leaf category menu (Sorted A-Z)
+                cat_items = sorted(categorized_plugins[cat], key=lambda x: x['name'])
+                for p in cat_items:
+                    action = QAction(p['name'], self)
+                    action.triggered.connect(lambda checked, mod=p['module']: self.plugin_manager.run_plugin(mod, self))
+                    parent_menu.addAction(action)
+
+            # Add separator if needed  <-- REMOVED per user request
+            # if sorted_categories and root_plugins:
+            #      plugin_menu.addSeparator()
+
+            # Build menu: Root items last (Sorted A-Z)
+            root_plugins.sort(key=lambda x: x['name'])
+            for p in root_plugins:
+                action = QAction(p['name'], self)
+                action.triggered.connect(lambda checked, mod=p['module']: self.plugin_manager.run_plugin(mod, self))
+                plugin_menu.addAction(action)
+
+        # 4. Integrate Export Actions into Export Button and Menu
+        # 4. Integrate Export Actions into Export Button AND Main File->Export Menu
+        if self.plugin_manager.export_actions:
+            # Find Main File -> Export menu
+            main_export_menu = None
+            for top_action in self.menuBar().actions():
+                if top_action.text().replace('&', '') == 'File' and top_action.menu():
+                    for sub_action in top_action.menu().actions():
+                         if sub_action.text().replace('&', '') == 'Export' and sub_action.menu():
+                             main_export_menu = sub_action.menu()
+                             break
+                if main_export_menu: break
+
+            # List of menus to populate
+            target_menus = []
+            if hasattr(self, 'export_button') and self.export_button.menu():
+                target_menus.append(self.export_button.menu())
+            if main_export_menu:
+                target_menus.append(main_export_menu)
+
+            for menu in target_menus:
+                 # Add separator 
+                 sep = menu.addSeparator()
+                 sep.setData(PLUGIN_ACTION_TAG)
+                 
+                 for exp in self.plugin_manager.export_actions:
+                     label = exp['label']
+                     callback = exp['callback']
+                     
+                     a = QAction(label, self)
+                     a.triggered.connect(callback)
+                     a.setData(PLUGIN_ACTION_TAG)
+                     menu.addAction(a)
+
+        # 5. Integrate File Openers into Import Menu
+        if hasattr(self, 'import_menu') and self.plugin_manager.file_openers:
+             # Add separator 
+             sep = self.import_menu.addSeparator()
+             sep.setData(PLUGIN_ACTION_TAG)
+             
+             # Group by Plugin Name
+             plugin_map = {}
+             for ext, openers_list in self.plugin_manager.file_openers.items():
+                 # Handles potential multiple openers for same extension
+                 for info in openers_list:
+                     p_name = info.get('plugin', 'Plugin')
+                     if p_name not in plugin_map:
+                         plugin_map[p_name] = {}
+                     # We can only register one callback per plugin per extension in the menu for now.
+                     # Since we process them, let's just take the one present (if a plugin registers multiple openers for same ext - weird but ok)
+                     plugin_map[p_name][ext] = info['callback']
+            
+             for p_name, ext_map in sorted(plugin_map.items()):
+                 # Create combined label: "Import .ext1/.ext2 (PluginName)..."
+                 extensions = sorted(ext_map.keys())
+                 ext_str = "/".join(extensions)
+                 
+                 # TRUNCATION LOGIC
+                 MAX_EXT_LEN = 30
+                 if len(ext_str) > MAX_EXT_LEN:
+                     # Find last slash within limit
+                     cutoff = ext_str.rfind('/', 0, MAX_EXT_LEN)
+                     if cutoff != -1:
+                        ext_str = ext_str[:cutoff] + "/..."
+                     else:
+                        # Fallback if first extension is super long (unlikely but safe)
+                        ext_str = ext_str[:MAX_EXT_LEN] + "..."
+                     
+                 label = f"Import {ext_str} ({p_name})..."
+                 
+                 # Create combined filter: "PluginName Files (*.ext1 *.ext2)"
+                 filter_exts = " ".join([f"*{e}" for e in extensions])
+                 filter_str = f"{p_name} Files ({filter_exts});;All Files (*)"
+                 
+                 # Factory for callback to fix closure capture
+                 def make_unified_cb(extensions_map, dialog_filter, plugin_nm):
+                     def _cb():
+                         fpath, _ = QFileDialog.getOpenFileName(
+                             self, f"Import {plugin_nm} Files", "", 
+                             dialog_filter
+                         )
+                         if fpath:
+                             _, extension = os.path.splitext(fpath)
+                             extension = extension.lower()
+                             # Dispatch to specific callback
+                             if extension in extensions_map:
+                                 extensions_map[extension](fpath)
+                                 self.current_file_path = fpath 
+                                 self.update_window_title()
+                             else:
+                                 self.statusBar().showMessage(f"No handler for extension {extension}")
+                     return _cb
+
+                 a = QAction(label, self)
+                 a.triggered.connect(make_unified_cb(ext_map, filter_str, p_name))
+                 a.setData(PLUGIN_ACTION_TAG)
+                 self.import_menu.addAction(a)
+    
+        # 6. Integrate Analysis Tools into Analysis Menu
+        # Find Analysis menu again as it might not be defined if cleanup block was generic
+        analysis_menu = None
+        for action in self.menuBar().actions():
+             if action.text().replace('&', '') == 'Analysis':
+                 analysis_menu = action.menu()
+                 break
+
+        if analysis_menu and self.plugin_manager.analysis_tools:
+             # Add separator
+             sep = analysis_menu.addSeparator()
+             sep.setData(PLUGIN_ACTION_TAG)
+             
+             for tool in self.plugin_manager.analysis_tools:
+                 label = f"{tool['label']} ({tool.get('plugin', 'Plugin')})"
+                 
+                 a = QAction(label, self)
+                 a.triggered.connect(tool['callback'])
+                 a.setData(PLUGIN_ACTION_TAG)
+                 analysis_menu.addAction(a)
+