MoleditPy 2.3.3__tar.gz → 2.4.1__tar.gz

{moleditpy-2.3.3 → moleditpy-2.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.3.3
+Version: 2.4.1
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-2.3.3 → moleditpy-2.4.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.3.3"
+version = "2.4.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.3.3
+Version: 2.4.1
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/atom_item.py

@@ -13,7 +13,7 @@ DOI: 10.5281/zenodo.17268532
 from PyQt6.QtWidgets import QGraphicsItem
 
 from PyQt6.QtGui import (
-    QPen, QBrush, QColor, QFont, QPainterPath, QFontMetricsF
+    QPen, QBrush, QColor, QFont, QPainterPath, QFontMetricsF, QPainter
 )
 
 from PyQt6.QtCore import (
@@ -45,14 +45,41 @@ class AtomItem(QGraphicsItem):
         self.setPos(pos)
         self.implicit_h_count = 0 
         self.setFlags(QGraphicsItem.GraphicsItemFlag.ItemIsMovable | QGraphicsItem.GraphicsItemFlag.ItemIsSelectable)
-        self.setZValue(1); self.font = QFont(FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD); self.update_style()
+        self.setZValue(1)
+        self.update_style()
         self.setAcceptHoverEvents(True)
         self.hovered = False
         self.has_problem = False 
 
+
+    def update_style(self):
+        # Allow updating font preference dynamically
+        font_size = 20
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    font_size = win.settings.get('atom_font_size_2d', 20)
+        except Exception:
+            pass
+        self.font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
+        self.prepareGeometryChange()
+        
+        self.is_visible = not (self.symbol == 'C' and len(self.bonds) > 0 and self.charge == 0 and self.radical == 0)
+        self.update()
+
     def boundingRect(self):
         # --- paint()メソッドと完全に同じロジックでテキストの位置とサイズを計算 ---
-        font = QFont(FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD)
+        # Get dynamic font size
+        font_size = 20
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    font_size = win.settings.get('atom_font_size_2d', 20)
+        except Exception:
+            pass
+        font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
         fm = QFontMetricsF(font)
 
         hydrogen_part = ""
@@ -164,9 +191,21 @@ class AtomItem(QGraphicsItem):
         return path
 
     def paint(self, painter, option, widget):
+        # Color logic: check if we should use bond color (uniform) or CPK (element-specific)
         color = CPK_COLORS.get(self.symbol, CPK_COLORS['DEFAULT'])
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    if win.settings.get('atom_use_bond_color_2d', False):
+                        bond_col = win.settings.get('bond_color_2d', '#222222')
+                        color = QColor(bond_col)
+        except Exception:
+            pass
+
         if self.is_visible:
             # 1. 描画の準備
+            # Ensure correct font is used (self.font should be updated by update_style)
             painter.setFont(self.font)
             fm = painter.fontMetrics()
 
@@ -253,19 +292,29 @@ class AtomItem(QGraphicsItem):
                 offset_x = -symbol_rect.width() // 2
                 text_rect.moveTo(offset_x, -text_rect.height() // 2)
 
-            # 2. 原子記号の背景を白で塗りつぶす
+            # 2. 原子記号の背景を処理（白で塗りつぶす か 透明なら切り抜く）
             if self.scene():
                 bg_brush = self.scene().backgroundBrush()
                 bg_rect = text_rect.adjusted(-5, -8, 5, 8)
-                painter.setBrush(bg_brush)
-                painter.setPen(Qt.PenStyle.NoPen)
-                painter.drawEllipse(bg_rect)
+                
+                if bg_brush.style() == Qt.BrushStyle.NoBrush:
+                    # 背景が透明の場合は、CompositionMode_Clearを使って
+                    # 重なっている結合の線を「消しゴム」のように消す
+                    painter.save()
+                    painter.setCompositionMode(QPainter.CompositionMode.CompositionMode_Clear)
+                    painter.setBrush(QColor(0, 0, 0, 255)) # 色は何でも良い（アルファが重要）
+                    painter.setPen(Qt.PenStyle.NoPen)
+                    painter.drawEllipse(bg_rect)
+                    painter.restore()
+                else:
+                    # 背景がある場合は、その背景色で塗りつぶす（従来通り）
+                    painter.setBrush(bg_brush)
+                    painter.setPen(Qt.PenStyle.NoPen)
+                    painter.drawEllipse(bg_rect)
             
             # 3. 原子記号自体を描画
-            if self.symbol == 'H':
-                painter.setPen(QPen(Qt.GlobalColor.black))
-            else:
-                painter.setPen(QPen(color))
+            # Color is already determined above
+            painter.setPen(QPen(color))
             painter.drawText(text_rect, int(alignment_flag), display_text)
             
             # --- 電荷とラジカルの描画  ---
@@ -316,9 +365,7 @@ class AtomItem(QGraphicsItem):
             painter.setPen(pen)
             painter.drawRect(self.boundingRect())
 
-    def update_style(self):
-        self.is_visible = not (self.symbol == 'C' and len(self.bonds) > 0 and self.charge == 0 and self.radical == 0)
-        self.update()
+
 
 
     # 約203行目 AtomItem クラス内

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/bond_item.py

@@ -105,7 +105,21 @@ class BondItem(QGraphicsItem):
             line = self.get_line_in_local_coords()
         except Exception:
             line = QLineF(0, 0, 0, 0)
-        bond_offset = globals().get('BOND_OFFSET', 2)
+        
+        # Get dynamic bond offset (spacing)
+        bond_offset = 3.5
+        try:
+            if self.scene() and hasattr(self.scene(), 'views') and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    # Use specific spacing based on bond order
+                    if getattr(self, 'order', 1) == 3:
+                        bond_offset = win.settings.get('bond_spacing_triple_2d', 3.5)
+                    else:
+                        bond_offset = win.settings.get('bond_spacing_double_2d', 3.5)
+        except Exception:
+             bond_offset = globals().get('BOND_OFFSET', 3.5)
+
         extra = (getattr(self, 'order', 1) - 1) * bond_offset + 20
         rect = QRectF(line.p1(), line.p2()).normalized().adjusted(-extra, -extra, extra, extra)
 
@@ -142,7 +156,18 @@ class BondItem(QGraphicsItem):
         view = scene.views()[0]
         scale = view.transform().m11()
 
-        scene_width = DESIRED_BOND_PIXEL_WIDTH / scale
+        # Dynamic bond width
+        width_2d = 2.0
+        try:
+            if view.window() and hasattr(view.window(), 'settings'):
+                width_2d = view.window().settings.get('bond_width_2d', 2.0)
+        except Exception:
+            pass
+
+        # Hit area should be roughly closely matched or slightly larger than visual
+        # Ensure minimum hit width for usability
+        scene_width = max(DESIRED_BOND_PIXEL_WIDTH, width_2d * 10) / scale
+
 
         stroker = QPainterPathStroker()
         stroker.setWidth(scene_width)
@@ -160,24 +185,44 @@ class BondItem(QGraphicsItem):
         line = self.get_line_in_local_coords()
         if line.length() == 0: return
 
-        # --- 1. 選択状態に応じてペンとブラシを準備 ---
-        if self.isSelected():
-            selection_color = QColor("blue")
-            painter.setPen(QPen(selection_color, 3))
-            painter.setBrush(QBrush(selection_color))
-        else:
-            # Allow bond color override from app settings (2D color)
-            try:
-                sc = self.scene()
-                if sc is not None and hasattr(sc, 'window') and sc.window is not None:
-                    bond_hex = sc.window.settings.get('bond_color', '#222222')
-                    bond_color = QColor(bond_hex)
-                    painter.setPen(QPen(bond_color, 2))
+        # Allow bond color override from app settings (2D color)
+        width_2d = 2.0
+        
+        try:
+            sc = self.scene()
+            if sc is not None and hasattr(sc, 'window') and sc.window is not None:
+                # Get settings
+                settings = sc.window.settings
+                
+                # Width
+                width_2d = settings.get('bond_width_2d', 2.0)
+                
+                # Cap Style logic
+                cap_style_str = settings.get('bond_cap_style_2d', 'Round')
+                cap_style = Qt.PenCapStyle.RoundCap # Default
+                
+                if cap_style_str == 'Flat':
+                    cap_style = Qt.PenCapStyle.FlatCap
+                elif cap_style_str == 'Square':
+                    cap_style = Qt.PenCapStyle.SquareCap
+                
+                # Color
+                if self.isSelected():
+                    bond_color = QColor("blue") # Selection color
                 else:
-                    painter.setPen(self.pen)
-            except Exception:
+                    bond_hex = settings.get('bond_color_2d', '#222222')
+                    bond_color = QColor(bond_hex)
+                
+                pen = QPen(bond_color, width_2d)
+                pen.setCapStyle(cap_style)
+                painter.setPen(pen)
+                
+            else:
                 painter.setPen(self.pen)
-            painter.setBrush(QBrush(Qt.GlobalColor.black))
+        except Exception:
+            painter.setPen(self.pen)
+            
+        painter.setBrush(QBrush(Qt.GlobalColor.black))
 
         # --- 立体化学 (Wedge/Dash) の描画 ---
         if self.order == 1 and self.stereo in [1, 2]:
@@ -213,7 +258,19 @@ class BondItem(QGraphicsItem):
                 painter.drawLine(line)
             else:
                 v = line.unitVector().normalVector()
-                offset = QPointF(v.dx(), v.dy()) * BOND_OFFSET
+                # Use dynamic offset
+                bond_offset = 3.5
+                try:
+                    sc = self.scene()
+                    if sc and sc.views() and hasattr(sc.views()[0].window(), 'settings'):
+                        if self.order == 3:
+                            bond_offset = sc.views()[0].window().settings.get('bond_spacing_triple_2d', 3.5)
+                        else:
+                            bond_offset = sc.views()[0].window().settings.get('bond_spacing_double_2d', 3.5)
+                except Exception:
+                    bond_offset = globals().get('BOND_OFFSET', 3.5)
+                
+                offset = QPointF(v.dx(), v.dy()) * bond_offset
 
                 if self.order == 2:
                     # 環構造かどうかを判定し、描画方法を変更
@@ -274,7 +331,8 @@ class BondItem(QGraphicsItem):
                         is_in_ring = False
                     
                     v = line.unitVector().normalVector()
-                    offset = QPointF(v.dx(), v.dy()) * BOND_OFFSET
+                    # Re-calculate offset in case loop variable scope issue, though strictly not needed if offset defined above works
+                    offset = QPointF(v.dx(), v.dy()) * bond_offset
                     
                     if is_in_ring and ring_center:
                         # 環構造: 1本の中心線（単結合位置） + 1本の短い内側線

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.3.3'
+VERSION = '2.4.1'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/main_window.py

@@ -500,6 +500,10 @@ class MainWindow(QMainWindow):
         # --- MOVED TO main_window_export.py ---
         return self.main_window_export.export_2d_png()
 
+    def export_2d_svg(self):
+        # --- MOVED TO main_window_export.py ---
+        return self.main_window_export.export_2d_svg()
+
     def export_3d_png(self):
         # --- MOVED TO main_window_export.py ---
         return self.main_window_export.export_3d_png()
@@ -524,6 +528,10 @@ class MainWindow(QMainWindow):
         # --- MOVED TO main_window_edit_actions.py ---
         return self.main_window_edit_actions.adjust_molecule_positions_to_avoid_collisions(mol, frags)
 
+    def open_rotate_2d_dialog(self):
+        # --- MOVED TO main_window_edit_actions.py ---
+        return self.main_window_edit_actions.open_rotate_2d_dialog()
+
     def draw_molecule_3d(self, mol):
         # --- MOVED TO main_window_view_3d.py ---
         return self.main_window_view_3d.draw_molecule_3d(mol)

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/main_window_edit_actions.py

@@ -34,7 +34,7 @@ from rdkit.Chem import AllChem
 
 # PyQt6 Modules
 from PyQt6.QtWidgets import (
-    QApplication
+    QApplication, QDialog, QVBoxLayout, QHBoxLayout, QLabel, QSpinBox, QSlider, QPushButton
 )
 
 from PyQt6.QtGui import (
@@ -43,9 +43,51 @@ from PyQt6.QtGui import (
 
 
 from PyQt6.QtCore import (
-    QPointF, QLineF, QMimeData, QByteArray, QTimer
+    QPointF, QLineF, QMimeData, QByteArray, QTimer, Qt
 )
 
+class Rotate2DDialog(QDialog):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Rotate 2D")
+        self.setFixedWidth(300)
+        
+        layout = QVBoxLayout(self)
+        
+        # Angle input
+        input_layout = QHBoxLayout()
+        input_layout.addWidget(QLabel("Angle (degrees):"))
+        self.angle_spin = QSpinBox()
+        self.angle_spin.setRange(-360, 360)
+        self.angle_spin.setValue(45)
+        input_layout.addWidget(self.angle_spin)
+        layout.addLayout(input_layout)
+        
+        # Slider
+        self.slider = QSlider(Qt.Orientation.Horizontal)
+        self.slider.setRange(-180, 180)
+        self.slider.setValue(45)
+        self.slider.setTickPosition(QSlider.TickPosition.TicksBelow)
+        self.slider.setTickInterval(15)
+        layout.addWidget(self.slider)
+
+        # Sync slider and spinbox
+        self.angle_spin.valueChanged.connect(self.slider.setValue)
+        self.slider.valueChanged.connect(self.angle_spin.setValue)
+        
+        # Buttons
+        btn_layout = QHBoxLayout()
+        ok_btn = QPushButton("Rotate")
+        ok_btn.clicked.connect(self.accept)
+        cancel_btn = QPushButton("Cancel")
+        cancel_btn.clicked.connect(self.reject)
+        btn_layout.addWidget(ok_btn)
+        btn_layout.addWidget(cancel_btn)
+        layout.addLayout(btn_layout)
+    
+    def get_angle(self):
+        return self.angle_spin.value()
+
 
 # Use centralized Open Babel availability from package-level __init__
 # Use per-package modules availability (local __init__).
@@ -568,6 +610,67 @@ class MainWindowEditActions(object):
 
 
 
+    def open_rotate_2d_dialog(self):
+        """2D回転ダイアログを開く"""
+        dialog = Rotate2DDialog(self)
+        if dialog.exec() == QDialog.DialogCode.Accepted:
+            angle = dialog.get_angle()
+            self.rotate_molecule_2d(angle)
+
+    def rotate_molecule_2d(self, angle_degrees):
+        """2D分子を指定角度回転させる（選択範囲があればそれのみ、なければ全体）"""
+        try:
+            # Determine target atoms
+            selected_items = self.scene.selectedItems()
+            target_atoms = [item for item in selected_items if isinstance(item, AtomItem)]
+            
+            # If no selection, rotate everything
+            if not target_atoms:
+                target_atoms = [data['item'] for data in self.data.atoms.values() if data.get('item') and not sip_isdeleted_safe(data['item'])]
+            
+            if not target_atoms:
+                self.statusBar().showMessage("No atoms to rotate.")
+                return
+
+            # Calculate Center
+            xs = [atom.pos().x() for atom in target_atoms]
+            ys = [atom.pos().y() for atom in target_atoms]
+            if not xs: return
+            
+            center_x = sum(xs) / len(xs)
+            center_y = sum(ys) / len(ys)
+            center = QPointF(center_x, center_y)
+            
+            rad = math.radians(angle_degrees)
+            cos_a = math.cos(rad)
+            sin_a = math.sin(rad)
+            
+            for atom in target_atoms:
+                # Relative pos
+                dx = atom.pos().x() - center_x
+                dy = atom.pos().y() - center_y
+                
+                # Rotate
+                new_dx = dx * cos_a - dy * sin_a
+                new_dy = dx * sin_a + dy * cos_a
+                
+                new_pos = QPointF(center_x + new_dx, center_y + new_dy)
+                atom.setPos(new_pos)
+            
+            # Update bonds
+            self.scene.update_connected_bonds(target_atoms)
+            
+            self.push_undo_state()
+            self.statusBar().showMessage(f"Rotated {len(target_atoms)} atoms by {angle_degrees} degrees.")
+            self.scene.update()
+            
+        except Exception as e:
+            print(f"Error rotating molecule: {e}")
+            traceback.print_exc()
+            self.statusBar().showMessage(f"Error rotating: {e}")
+
+
+
 
     def select_all(self):
         for item in self.scene.items():

{moleditpy-2.3.3 → moleditpy-2.4.1}/src/moleditpy/modules/main_window_export.py

@@ -37,9 +37,11 @@ from PyQt6.QtGui import (
     QBrush, QColor, QPainter, QImage
 )
 
+from PyQt6.QtSvg import QSvgGenerator
+
 
 from PyQt6.QtCore import (
-    Qt, QRectF
+    Qt, QRectF, QSize
 )
 
 import pyvista as pv
@@ -672,7 +674,7 @@ class MainWindowExport(object):
             filePath += ".png"
 
         reply = QMessageBox.question(self, 'Choose Background',
-                                     'Do you want a transparent background?\n(Choose "No" for a white background)',
+                                     'Do you want a transparent background?\n(Choose "No" to use the current background color)',
                                      QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No | QMessageBox.StandardButton.Cancel,
                                      QMessageBox.StandardButton.Yes)
 
@@ -706,8 +708,7 @@ class MainWindowExport(object):
 
             if is_transparent:
                 self.scene.setBackgroundBrush(QBrush(Qt.BrushStyle.NoBrush))
-            else:
-                self.scene.setBackgroundBrush(QBrush(QColor("#FFFFFF")))
+            # Else: keep original_background (current 2D background)
 
             rect_to_render = molecule_bounds.adjusted(-20, -20, 20, 20)
 
@@ -719,10 +720,8 @@ class MainWindowExport(object):
                 return
 
             image = QImage(w, h, QImage.Format.Format_ARGB32_Premultiplied)
-            if is_transparent:
-                image.fill(Qt.GlobalColor.transparent)
-            else:
-                image.fill(Qt.GlobalColor.white)
+            # Always fill with transparent; render will paint opaque background if present
+            image.fill(Qt.GlobalColor.transparent)
 
             painter = QPainter()
             ok = painter.begin(image)
@@ -756,6 +755,118 @@ class MainWindowExport(object):
 
 
 
+    def export_2d_svg(self):
+        """2D drawingをSVGとしてエクスポート"""
+        if not self.data.atoms:
+            self.statusBar().showMessage("Nothing to export.")
+            return
+
+        # default filename
+        default_name = "untitled-2d"
+        try:
+            if self.current_file_path:
+                base = os.path.basename(self.current_file_path)
+                name = os.path.splitext(base)[0]
+                default_name = f"{name}-2d"
+        except Exception:
+            default_name = "untitled-2d"
+
+        # prefer same directory
+        default_path = default_name
+        try:
+            if self.current_file_path:
+                default_path = os.path.join(os.path.dirname(self.current_file_path), default_name)
+        except Exception:
+            default_path = default_name
+
+        filePath, _ = QFileDialog.getSaveFileName(self, "Export 2D as SVG", default_path, "SVG Files (*.svg)")
+        if not filePath:
+            return
+
+        if not (filePath.lower().endswith(".svg")):
+            filePath += ".svg"
+
+        # Ask about transparency
+        reply = QMessageBox.question(self, 'Choose Background',
+                                     'Do you want a transparent background?\n(Choose "No" to use the current background color)',
+                                     QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No | QMessageBox.StandardButton.Cancel,
+                                     QMessageBox.StandardButton.Yes)
+
+        if reply == QMessageBox.StandardButton.Cancel:
+            self.statusBar().showMessage("Export cancelled.", 2000)
+            return
+
+        is_transparent = (reply == QMessageBox.StandardButton.Yes)
+
+        try:
+            # 1. Hide non-molecular items if needed (optional, keeping consistent with PNG export)
+            items_to_restore = {}
+            original_background = self.scene.backgroundBrush()
+            
+            all_items = list(self.scene.items())
+            for item in all_items:
+                is_mol_part = isinstance(item, (AtomItem, BondItem))
+                if not (is_mol_part and item.isVisible()):
+                    # Keep measurement items visible if they are part of the scene? 
+                    # For now, let's stick to hiding everything that isn't atom/bond,
+                    # similar to png export logic, or we can decide to export everything visible.
+                    # The PNG export hides non-atom/bond items. Let's follow that for consistency.
+                    items_to_restore[item] = item.isVisible()
+                    item.hide()
+
+            # 2. Calculate bounds
+            molecule_bounds = QRectF()
+            for item in self.scene.items():
+                if isinstance(item, (AtomItem, BondItem)) and item.isVisible():
+                    molecule_bounds = molecule_bounds.united(item.sceneBoundingRect())
+
+            if molecule_bounds.isEmpty() or not molecule_bounds.isValid():
+                self.statusBar().showMessage("Error: Could not determine molecule bounds for export.")
+                # Restore
+                for item, was_visible in items_to_restore.items():
+                    item.setVisible(was_visible)
+                return
+
+            if is_transparent:
+                self.scene.setBackgroundBrush(QBrush(Qt.BrushStyle.NoBrush))
+            
+            # Margin
+            rect_to_render = molecule_bounds.adjusted(-20, -20, 20, 20)
+            
+            width = int(rect_to_render.width())
+            height = int(rect_to_render.height())
+
+            # 3. Setup QSvgGenerator
+            generator = QSvgGenerator()
+            generator.setFileName(filePath)
+            generator.setSize(QSize(width, height))
+            generator.setViewBox(rect_to_render)
+            generator.setTitle("MoleditPy Molecule")
+            
+            # 4. Render
+            painter = QPainter()
+            painter.begin(generator)
+            try:
+                self.scene.render(painter, rect_to_render, rect_to_render)
+            finally:
+                painter.end()
+
+            self.statusBar().showMessage(f"2D view exported to {filePath}")
+
+        except Exception as e:
+            self.statusBar().showMessage(f"An unexpected error occurred during SVG export: {e}")
+
+        finally:
+            # Restore
+            for item, was_visible in items_to_restore.items():
+                item.setVisible(was_visible)
+            if 'original_background' in locals():
+                self.scene.setBackgroundBrush(original_background)
+            if self.view_2d:
+                self.view_2d.viewport().update()
+
+
+
     def export_3d_png(self):
         if not self.current_mol:
             self.statusBar().showMessage("No 3D molecule to export.", 2000)