MoleditPy 2.2.0a2__py3-none-any.whl → 2.2.0a3__py3-none-any.whl

moleditpy/plugins/Utility/pubchem_ressolver.py

@@ -1,244 +0,0 @@
-import sys
-import requests # API通信に必要 (pip install requests)
-from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QHBoxLayout, QTableWidget, 
-    QTableWidgetItem, QPushButton, QMessageBox, QLabel, QHeaderView, 
-    QAbstractItemView, QApplication, QLineEdit, QComboBox
-)
-from PyQt6.QtCore import Qt, QPointF
-from rdkit import Chem
-from rdkit.Chem import AllChem
-
-__version__="2025.12.25"
-__author__="HiroYokoyama"
-PLUGIN_NAME = "PubChem Name Resolver"
-
-class MoleculeResolverDialog(QDialog):
-    def __init__(self, main_window, parent=None):
-        super().__init__(parent)
-        self.main_window = main_window
-        self.setWindowTitle("PubChem Name Resolver")
-        self.resize(500, 600)
-        
-        # 取得した候補データのリスト
-        # 各要素は辞書: {'name': str, 'smiles': str, 'formula': str}
-        self.candidates_data = []
-        
-        # 生成されたRDKit分子オブジェクト（一時保存）
-        self.generated_mol = None
-
-        self.init_ui()
-
-    def init_ui(self):
-        layout = QVBoxLayout(self)
-
-        # --- 入力エリア ---
-        input_layout = QHBoxLayout()
-        
-        self.combo_type = QComboBox()
-        self.combo_type.addItems(["Auto (Name/CAS)", "SMILES"])
-        input_layout.addWidget(self.combo_type)
-
-        self.line_input = QLineEdit()
-        self.line_input.setPlaceholderText("Enter Name or SMILES...")
-        self.line_input.returnPressed.connect(self.run_search) # Enterキーで検索
-        input_layout.addWidget(self.line_input)
-        
-        self.btn_search = QPushButton("Search Online")
-        self.btn_search.clicked.connect(self.run_search)
-        input_layout.addWidget(self.btn_search)
-        
-        layout.addLayout(input_layout)
-
-        # --- 説明ラベル ---
-        self.lbl_info = QLabel("Enter a chemical identifier and click Search.")
-        layout.addWidget(self.lbl_info)
-
-        # --- 結果表示用テーブル ---
-        self.table = QTableWidget()
-        self.table.setColumnCount(3)
-        self.table.setHorizontalHeaderLabels(["Name/Synonym", "Formula", "SMILES"])
-        # ヘッダー調整
-        header = self.table.horizontalHeader()
-        header.setSectionResizeMode(0, QHeaderView.ResizeMode.Stretch)
-        header.setSectionResizeMode(1, QHeaderView.ResizeMode.ResizeToContents)
-        header.setSectionResizeMode(2, QHeaderView.ResizeMode.Stretch)
-        
-        self.table.setSelectionBehavior(QAbstractItemView.SelectionBehavior.SelectRows)
-        self.table.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
-        # 選択変更時にロードボタンを有効化するなどの処理を入れるならここ
-        layout.addWidget(self.table)
-
-        # --- ボタンエリア ---
-        btn_layout = QHBoxLayout()
-        
-        self.btn_load = QPushButton("Load to 2D Editor")
-        self.btn_load.clicked.connect(self.load_molecule)
-        
-        self.btn_close = QPushButton("Close")
-        self.btn_close.clicked.connect(self.close)
-
-        btn_layout.addWidget(self.btn_load)
-        btn_layout.addWidget(self.btn_close)
-        layout.addLayout(btn_layout)
-
-    def run_search(self):
-        query = self.line_input.text().strip()
-        if not query:
-            return
-
-        self.lbl_info.setText("Searching PubChem... please wait.")
-        self.btn_search.setEnabled(False)
-        self.table.setRowCount(0)
-        QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
-        QApplication.processEvents()
-
-        results = []
-        error_msg = None
-        network_error = False
-
-        try:
-            search_type = self.combo_type.currentText()
-
-            if search_type == "SMILES":
-                # SMILESの場合は直接リストに追加（検証含む）
-                mol = Chem.MolFromSmiles(query)
-                if mol:
-                    results.append({
-                        'name': 'User Input SMILES',
-                        'smiles': query,
-                        'formula': Chem.rdMolDescriptors.CalcMolFormula(mol)
-                    })
-                else:
-                    raise ValueError("Invalid SMILES string.")
-            
-            else: # Auto (PubChem API)
-                # PUG REST APIを使用して検索
-                # プロパティとしてSMILESと分子式を取得
-                # CanonicalSMILESも取得してフォールバックに使用
-                url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{query}/property/IsomericSMILES,CanonicalSMILES,MolecularFormula,Title/JSON"
-                
-                response = requests.get(url, timeout=10)
-                
-                if response.status_code == 200:
-                    data = response.json()
-                    props = data.get('PropertyTable', {}).get('Properties', [])
-                    for p in props:
-                        # SMILESの取得（Isomericを優先、なければCanonical、それでもなければキー検索）
-                        smiles = p.get('IsomericSMILES')
-                        if not smiles:
-                            smiles = p.get('CanonicalSMILES')
-                        
-                        # まだ取得できていない場合、キー名に'SMILES'が含まれるものを探す
-                        if not smiles:
-                            for k in p.keys():
-                                if 'SMILES' in k:
-                                    smiles = p[k]
-                                    if smiles:
-                                        break
-                        
-                        if not smiles:
-                            smiles = "" # 見つからない場合
-
-                        results.append({
-                            'name': p.get('Title', query),
-                            'smiles': smiles,
-                            'formula': p.get('MolecularFormula', '')
-                        })
-                else:
-                    # found nothing or error status
-                    pass
-
-        except requests.exceptions.RequestException:
-            network_error = True
-        except Exception as e:
-            error_msg = str(e)
-        finally:
-            QApplication.restoreOverrideCursor()
-            self.btn_search.setEnabled(True)
-
-        # UI updates after cursor restore
-        if network_error:
-            QMessageBox.critical(self, PLUGIN_NAME, "Network error. Please check your internet connection.")
-            self.lbl_info.setText("Network error.")
-        elif error_msg:
-            QMessageBox.critical(self, PLUGIN_NAME, f"Error: {error_msg}")
-            self.lbl_info.setText("Error occurred.")
-        elif not results and 'response' in locals() and response.status_code != 200:
-            self.lbl_info.setText("Not found in PubChem search.")
-        else:
-            # データを保持
-            self.candidates_data = results
-            self.update_table()
-            
-            if results:
-                self.lbl_info.setText(f"Found {len(results)} candidates. Select one and click Load to 2D Editor.")
-            else:
-                self.lbl_info.setText("No results found.")
-
-    def update_table(self):
-        self.table.setRowCount(0)
-        
-        for i, data in enumerate(self.candidates_data):
-            row_idx = self.table.rowCount()
-            self.table.insertRow(row_idx)
-            
-            self.table.setItem(row_idx, 0, QTableWidgetItem(str(data['name'])))
-            self.table.setItem(row_idx, 1, QTableWidgetItem(str(data['formula'])))
-            self.table.setItem(row_idx, 2, QTableWidgetItem(str(data['smiles'])))
-
-    def load_molecule(self):
-        """選択された行のSMILESから2D構造を生成し、メインウィンドウのエディタに入れる"""
-        selected_items = self.table.selectedItems()
-        if not selected_items:
-            QMessageBox.warning(self, PLUGIN_NAME, "Please select a molecule from the list.")
-            return
-            
-        row = selected_items[0].row()
-        smiles = self.candidates_data[row]['smiles']
-        name = self.candidates_data[row]['name']
-        
-        if not smiles:
-             QMessageBox.warning(self, PLUGIN_NAME, "No SMILES data available for this entry.")
-             return
-
-        self.lbl_info.setText("Loading into 2D Editor...")
-        QApplication.setOverrideCursor(Qt.CursorShape.WaitCursor)
-        QApplication.processEvents()
-
-        success = False
-        error_msg = None
-
-        try:
-            # メインウィンドウのSMILES読み込み機能を使用
-            if hasattr(self.main_window, "load_from_smiles"):
-                self.main_window.load_from_smiles(smiles)
-                success = True
-            else:
-                error_msg = "Main window does not support 'load_from_smiles'."
-
-        except Exception as e:
-            error_msg = str(e)
-            
-        finally:
-            QApplication.restoreOverrideCursor()
-
-        if success:
-             self.lbl_info.setText(f"Loaded: {name}")
-             QMessageBox.information(self, PLUGIN_NAME, f"Successfully loaded: {name}")
-             self.accept() # ダイアログを閉じる
-        elif error_msg:
-             QMessageBox.critical(self, PLUGIN_NAME, f"Error: {error_msg}")
-             self.lbl_info.setText("Load failed.")
-
-def run(mw):
-    if hasattr(mw, "_molecule_resolver_dialog") and mw._molecule_resolver_dialog.isVisible():
-        mw._molecule_resolver_dialog.raise_()
-        mw._molecule_resolver_dialog.activateWindow()
-        return
-
-    dialog = MoleculeResolverDialog(mw, parent=mw)
-    mw._molecule_resolver_dialog = dialog
-    dialog.show()
-
-# initialize removed as it only registered the menu action

moleditpy/plugins/Utility/vdw_radii_overlay.py

@@ -1,432 +0,0 @@
-
-import os
-import json
-import traceback
-import pyvista as pv
-import numpy as np
-import functools
-import types
-from PyQt6.QtWidgets import (QDialog, QVBoxLayout, QLabel, 
-                             QSlider, QHBoxLayout, QPushButton, QDoubleSpinBox)
-from PyQt6.QtGui import QAction, QColor
-from PyQt6.QtCore import Qt, QTimer
-
-# Try to import VDW radii from constants, fallback if needed
-try:
-    from moleditpy.modules.constants import pt, CPK_COLORS_PV
-except ImportError:
-    try:
-        from modules.constants import pt, CPK_COLORS_PV
-    except ImportError:
-        try:
-            from rdkit import Chem
-            pt = Chem.GetPeriodicTable()
-        except Exception:
-            pt = None
-        CPK_COLORS_PV = {} # Last resort fallback
-
-
-# Plugin Metadata
-__version__="2025.12.17"
-__author__="HiroYokoyama"
-PLUGIN_NAME = "VDW Radii Overlay"
-SETTINGS_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), "vdw_radii_overlay.json")
-
-# Global State
-_config_window = None
-_vdw_settings = {
-    "occupancy": 0.3,  # Opacity (0.0 - 1.0)
-    "resolution": 0.125 # Voxel spacing in Angstroms
-}
-
-def load_settings():
-    global _vdw_settings
-    try:
-        if os.path.exists(SETTINGS_FILE):
-            with open(SETTINGS_FILE, 'r') as f:
-                saved = json.load(f)
-                if "occupancy" in saved:
-                    _vdw_settings["occupancy"] = float(saved["occupancy"])
-                if "resolution" in saved:
-                    _vdw_settings["resolution"] = float(saved["resolution"])
-    except Exception as e:
-        print(f"Error loading VDW settings: {e}")
-
-def save_settings():
-    try:
-        with open(SETTINGS_FILE, 'w') as f:
-            json.dump(_vdw_settings, f, indent=4)
-    except Exception as e:
-        print(f"Error saving VDW settings: {e}")
-
-class VDWConfigWindow(QDialog):
-    def __init__(self, main_window):
-        super().__init__(parent=main_window)
-        self.mw = main_window
-        self.setWindowTitle("VDW Overlay Settings")
-        self.setModal(False)
-        self.resize(350, 150)
-        self.init_ui()
-
-    def init_ui(self):
-        layout = QVBoxLayout()
-        
-        # Occupancy Slider
-        occ_layout = QHBoxLayout()
-        occ_layout.addWidget(QLabel("Occupancy:"))
-        self.slider_occ = QSlider(Qt.Orientation.Horizontal)
-        self.slider_occ.setRange(0, 100)
-        current_occ = _vdw_settings.get("occupancy", 0.3)
-        self.slider_occ.setValue(int(current_occ * 100))
-        self.slider_occ.valueChanged.connect(self.on_occupancy_slider_changed)
-        occ_layout.addWidget(self.slider_occ)
-        
-        self.spin_occ = QDoubleSpinBox()
-        self.spin_occ.setRange(0.0, 1.0)
-        self.spin_occ.setSingleStep(0.05)
-        self.spin_occ.setValue(current_occ)
-        self.spin_occ.valueChanged.connect(self.on_occupancy_spin_changed)
-        occ_layout.addWidget(self.spin_occ)
-        
-        layout.addLayout(occ_layout)
-
-        # Resolution Slider
-        res_layout = QHBoxLayout()
-        res_layout.addWidget(QLabel("Resolution (Å):"))
-        self.slider_res = QSlider(Qt.Orientation.Horizontal)
-        self.slider_res.setRange(5, 50) # 0.05 to 0.50
-        current_res = _vdw_settings.get("resolution", 0.125)
-        self.slider_res.setValue(int(current_res * 100))
-        self.slider_res.valueChanged.connect(self.on_resolution_slider_changed)
-        res_layout.addWidget(self.slider_res)
-        
-        self.spin_res = QDoubleSpinBox()
-        self.spin_res.setRange(0.05, 0.50)
-        self.spin_res.setSingleStep(0.005)
-        self.spin_res.setDecimals(3)
-        self.spin_res.setValue(current_res)
-        self.spin_res.valueChanged.connect(self.on_resolution_spin_changed)
-        res_layout.addWidget(self.spin_res)
-        
-        layout.addLayout(res_layout)
-        
-        # Reset Button
-        btn_reset = QPushButton("Reset to Defaults")
-        btn_reset.clicked.connect(self.reset_defaults)
-        layout.addWidget(btn_reset)
-
-        # Close Button
-        btn_close = QPushButton("Close")
-        btn_close.clicked.connect(self.close)
-        layout.addWidget(btn_close)
-        
-        self.setLayout(layout)
-
-    def on_occupancy_slider_changed(self, value):
-        val_float = value / 100.0
-        self.spin_occ.blockSignals(True)
-        self.spin_occ.setValue(val_float)
-        self.spin_occ.blockSignals(False)
-        self._update_occupancy(val_float)
-
-    def on_occupancy_spin_changed(self, value):
-        val_int = int(value * 100)
-        self.slider_occ.blockSignals(True)
-        self.slider_occ.setValue(val_int)
-        self.slider_occ.blockSignals(False)
-        self._update_occupancy(value)
-
-    def _update_occupancy(self, value):
-        _vdw_settings["occupancy"] = value
-        save_settings()
-        self.update_view()
-
-    def on_resolution_slider_changed(self, value):
-        val_float = value / 100.0
-        self.spin_res.blockSignals(True)
-        self.spin_res.setValue(val_float)
-        self.spin_res.blockSignals(False)
-        self._update_resolution(val_float)
-
-    def on_resolution_spin_changed(self, value):
-        val_int = int(value * 100)
-        self.slider_res.blockSignals(True)
-        self.slider_res.setValue(val_int)
-        self.slider_res.blockSignals(False)
-        self._update_resolution(value)
-        
-    def _update_resolution(self, value):
-        _vdw_settings["resolution"] = value
-        save_settings()
-        self.update_view()
-
-    def reset_defaults(self):
-        # Default values
-        def_occ = 0.3
-        def_res = 0.125
-        
-        # Block signals to prevent redundant updates/saves during setting
-        self.slider_occ.blockSignals(True)
-        self.spin_occ.blockSignals(True)
-        self.slider_res.blockSignals(True)
-        self.spin_res.blockSignals(True)
-        
-        # Set values
-        self.slider_occ.setValue(int(def_occ * 100))
-        self.spin_occ.setValue(def_occ)
-        self.slider_res.setValue(int(def_res * 100))
-        self.spin_res.setValue(def_res)
-        
-        # Unblock
-        self.slider_occ.blockSignals(False)
-        self.spin_occ.blockSignals(False)
-        self.slider_res.blockSignals(False)
-        self.spin_res.blockSignals(False)
-        
-        # Update settings and view once
-        _vdw_settings["occupancy"] = def_occ
-        _vdw_settings["resolution"] = def_res
-        save_settings()
-        self.update_view()
-
-    def refresh_ui_values(self):
-        """Update UI elements from global settings."""
-        occ = _vdw_settings.get("occupancy", 0.3)
-        res = _vdw_settings.get("resolution", 0.125)
-        
-        self.slider_occ.blockSignals(True)
-        self.spin_occ.blockSignals(True)
-        self.slider_res.blockSignals(True)
-        self.spin_res.blockSignals(True)
-
-        self.slider_occ.setValue(int(occ * 100))
-        self.spin_occ.setValue(occ)
-        self.slider_res.setValue(int(res * 100))
-        self.spin_res.setValue(res)
-
-        self.slider_occ.blockSignals(False)
-        self.spin_occ.blockSignals(False)
-        self.slider_res.blockSignals(False)
-        self.spin_res.blockSignals(False)
-
-    def update_view(self):
-        # Trigger redraw if we are in the correct mode
-        if hasattr(self.mw, 'current_3d_style') and self.mw.current_3d_style == "vdw_overlay":
-            if getattr(self.mw, 'current_mol', None):
-                # Trigger redraw
-                if hasattr(self.mw, 'draw_molecule_3d'):
-                    self.mw.draw_molecule_3d(self.mw.current_mol)
-
-def draw_vdw_overlay(mw, mol):
-    """
-    Callback for drawing the VDW overlay style.
-    Registered via context.register_3d_style.
-    """
-    # 1. Draw standard Ball & Stick
-    # Attempt to locate the standard draw method
-    draw_std = None
-    if hasattr(mw, 'main_window_view_3d') and hasattr(mw.main_window_view_3d, 'draw_standard_3d_style'):
-        draw_std = mw.main_window_view_3d.draw_standard_3d_style
-    elif hasattr(mw, 'view3d') and hasattr(mw.view3d, 'draw_standard_3d_style'):
-        draw_std = mw.view3d.draw_standard_3d_style
-    
-    if draw_std:
-        draw_std(mol, style_override='ball_and_stick')
-    else:
-        print("VDW Plugin Error: could not find draw_standard_3d_style")
-        return
-
-    # 2. Draw VDW Surface Overlay
-    if mol and mol.GetNumAtoms() > 0:
-        try:
-            positions = []
-            radii = []
-            atom_colors = []
-            
-            # Use custom colors if available (API-based or legacy)
-            custom_map = getattr(mw, '_plugin_color_overrides', {})
-            if not custom_map:
-                custom_map = getattr(mw, 'custom_atom_colors', {})
-            
-            if mol.GetNumConformers() > 0:
-                conf = mol.GetConformer()
-                for i in range(mol.GetNumAtoms()):
-                    atom = mol.GetAtomWithIdx(i)
-                    pos = conf.GetAtomPosition(i)
-                    positions.append([pos.x, pos.y, pos.z])
-                    
-                    sym = atom.GetSymbol()
-                    # GetRvdw returns standard VDW radius. 
-                    r = 1.5 # Default
-                    if pt:
-                        r = pt.GetRvdw(atom.GetAtomicNum())
-                    radii.append(r)
-                    
-                    # Color handling
-                    if i in custom_map:
-                        val = custom_map[i]
-                        # Handling new API (Hex string) vs Legacy (List/Tuple)
-                        if isinstance(val, str) and val.startswith('#'):
-                            # Convert Hex to RGB [0-1]
-                            qc = QColor(val)
-                            c = [qc.redF(), qc.greenF(), qc.blueF()]
-                        else:
-                            # Assume legacy list/tuple
-                            c = val
-                            # Normalize 0-255 to 0-1 if needed
-                            if any(x > 1.0 for x in c):
-                                c = [x/255.0 for x in c]
-                    else:
-                        c = CPK_COLORS_PV.get(sym, [0.8, 0.8, 0.8]) # Default grey if missing
-                    atom_colors.append(c)
-            
-            if positions:
-                positions = np.array(positions)
-                radii = np.array(radii)
-                atom_colors = np.array(atom_colors)
-
-                # --- Generate Merged Surface (SDF) ---
-                
-                # 1. Define Grid Bounds
-                padding = radii.max() + 1.0
-                min_bounds = positions.min(axis=0) - padding
-                max_bounds = positions.max(axis=0) + padding
-                
-                # Resolution (voxel size in Angstroms)
-                res_val = _vdw_settings.get("resolution", 0.125)
-                # Clamp to safe limits just in case
-                if res_val < 0.01: res_val = 0.01
-                spacing = (res_val, res_val, res_val) 
-                
-                dims = np.ceil((max_bounds - min_bounds) / spacing).astype(int)
-                
-                grid = pv.ImageData()
-                grid.dimensions = dims
-                grid.origin = min_bounds
-                grid.spacing = spacing
-                
-                grid_points = grid.points
-                n_points = grid_points.shape[0]
-                values = np.empty(n_points)
-                
-                # Process in chunks of 100k points
-                chunk_size = 100000 
-                for start_idx in range(0, n_points, chunk_size):
-                    end_idx = min(start_idx + chunk_size, n_points)
-                    chunk_pts = grid_points[start_idx:end_idx]
-                    
-                    d = np.linalg.norm(chunk_pts[:, np.newaxis, :] - positions[np.newaxis, :, :], axis=2)
-                    d_surface = d - radii[np.newaxis, :]
-                    values[start_idx:end_idx] = d_surface.min(axis=1)
-
-                grid.point_data["values"] = values
-                
-                # 3. Contour at iso-value 0 to get the surface
-                mesh = grid.contour([0], scalars="values")
-                
-                # 4. Map Colors to Surface Vertices
-                mesh_points = mesh.points
-                if mesh_points.shape[0] > 0:
-                    n_mesh_pts = mesh_points.shape[0]
-                    mesh_colors = np.zeros((n_mesh_pts, 3))
-                    
-                    chunk_size = 50000
-                    for start_idx in range(0, n_mesh_pts, chunk_size):
-                        end_idx = min(start_idx + chunk_size, n_mesh_pts)
-                        chunk_pts = mesh_points[start_idx:end_idx]
-                        
-                        d_center = np.linalg.norm(chunk_pts[:, np.newaxis, :] - positions[np.newaxis, :, :], axis=2)
-                        d_surface = d_center - radii[np.newaxis, :]
-                        nearest_atom_indices = np.argmin(d_surface, axis=1)
-                        mesh_colors[start_idx:end_idx] = atom_colors[nearest_atom_indices]
-                    
-                    mesh.point_data["AtomColors"] = mesh_colors
-                
-                    opacity = _vdw_settings.get("occupancy", 0.3)
-                    
-                    # Assume mw.plotter is available
-                    if hasattr(mw, 'plotter'):
-                        mw.plotter.add_mesh(
-                            mesh,
-                            scalars="AtomColors", 
-                            rgb=True,
-                            opacity=opacity,
-                            smooth_shading=True,
-                            specular=0.2, 
-                            name="vdw_overlay_mesh"
-                        )
-
-        except Exception as e:
-            print(f"VDW Overlay Error: {e}")
-            traceback.print_exc()
-
-def run(mw):
-    global _config_window
-    load_settings()
-    
-    if _config_window is None:
-        _config_window = VDWConfigWindow(mw)
-        _config_window.finished.connect(lambda: _cleanup_config())
-    
-    # Ensure UI reflects the loaded settings (important if window was already open or reused)
-    _config_window.refresh_ui_values()
-    
-    _config_window.show()
-    _config_window.raise_()
-    _config_window.activateWindow()
-
-def initialize(context):
-    """
-    New Plugin System Entry Point
-    """
-    mw = context.get_main_window()
-    load_settings()
-    
-    # Register 3D Style
-    if hasattr(context, 'register_3d_style'):
-        context.register_3d_style("vdw_overlay", draw_vdw_overlay)
-    else:
-        print("Error: PluginContext does not support register_3d_style")
-
-    # 1. Register Configuration Menu - REMOVED in favor of run()
-    # (Managed by run() function now)
-
-    # 2. Inject into Style Menu (Legacy behavior preserved via mw access)
-    def add_menu_item():
-        # Locate the "3D Style" tool button on the main toolbar
-        style_button = getattr(mw, 'style_button', None)
-        
-        if style_button and style_button.menu():
-            style_menu = style_button.menu()
-            
-            # Check if already added
-            exists = False
-            for a in style_menu.actions():
-                if a.text() == "VDW Overlay":
-                    exists = True
-                    break
-            
-            if not exists:
-                # Add to action group for mutual exclusion
-                existing_actions = style_menu.actions()
-                group = None
-                if existing_actions:
-                    group = existing_actions[0].actionGroup()
-                
-                action = QAction("VDW Overlay", mw)
-                action.setCheckable(True)
-                
-                if group:
-                    group.addAction(action)
-                
-                # Connect to set_3d_style
-                action.triggered.connect(lambda: mw.set_3d_style("vdw_overlay"))
-                
-                style_menu.addAction(action)
-    
-    # Run after 2000ms to ensure UI is ready
-    QTimer.singleShot(2000, add_menu_item)
-
-def _cleanup_config():
-    global _config_window
-    _config_window = None