MoleditPy 2.5.1__tar.gz → 2.6.0__tar.gz

{moleditpy-2.5.1 → moleditpy-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.5.1
+Version: 2.6.0
 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-2.5.1 → moleditpy-2.6.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.5.1"
+version = "2.6.0"
 
 license = {file = "LICENSE"}
 
@@ -48,4 +48,4 @@ Issues = "https://github.com/HiroYokoyama/python_molecular_editor/issues"
 moleditpy = "moleditpy.__main__:main"
 
 [tool.setuptools.package-data]
-"moleditpy" = ["modules/assets/*"]
+"moleditpy" = ["assets/*"]

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.5.1
+Version: 2.6.0
 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-2.5.1 → moleditpy-2.6.0}/src/MoleditPy.egg-info/SOURCES.txt

@@ -16,6 +16,10 @@ src/moleditpy.egg-info/dependency_links.txt
 src/moleditpy.egg-info/entry_points.txt
 src/moleditpy.egg-info/requires.txt
 src/moleditpy.egg-info/top_level.txt
+src/moleditpy/assets/file_icon.ico
+src/moleditpy/assets/icon.icns
+src/moleditpy/assets/icon.ico
+src/moleditpy/assets/icon.png
 src/moleditpy/modules/__init__.py
 src/moleditpy/modules/about_dialog.py
 src/moleditpy/modules/align_plane_dialog.py
@@ -48,6 +52,7 @@ src/moleditpy/modules/main_window_ui_manager.py
 src/moleditpy/modules/main_window_view_3d.py
 src/moleditpy/modules/main_window_view_loaders.py
 src/moleditpy/modules/mirror_dialog.py
+src/moleditpy/modules/mol_geometry.py
 src/moleditpy/modules/molecular_data.py
 src/moleditpy/modules/molecule_scene.py
 src/moleditpy/modules/move_group_dialog.py
@@ -61,8 +66,4 @@ src/moleditpy/modules/template_preview_item.py
 src/moleditpy/modules/template_preview_view.py
 src/moleditpy/modules/translation_dialog.py
 src/moleditpy/modules/user_template_dialog.py
-src/moleditpy/modules/zoomable_view.py
-src/moleditpy/modules/assets/file_icon.ico
-src/moleditpy/modules/assets/icon.icns
-src/moleditpy/modules/assets/icon.ico
-src/moleditpy/modules/assets/icon.png
+src/moleditpy/modules/zoomable_view.py

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/__main__.py

@@ -16,11 +16,8 @@ print("MoleditPy — A Python-based molecular editing software")
 print("-----------------------------------------------------\n")
 
 try:
-    # Preferred when running as a package: python -m moleditpy
     from .main import main
 except Exception:
-    # Fallback when running the file directly: python __main__.py
-    # This will import the top-level `main` module in the same folder.
     from main import main
 
 # --- Application Execution ---

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/main.py

@@ -17,11 +17,8 @@ import ctypes
 from PyQt6.QtWidgets import QApplication
 
 try:
-    # When executed as part of the package (python -m moleditpy)
     from .modules.main_window import MainWindow
 except Exception:
-    # When executed as a standalone script (python main.py) the package-relative
-    # import won't work; fall back to absolute import that works with sys.path
     from modules.main_window import MainWindow
 
 def main():

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/__init__.py

@@ -15,7 +15,7 @@ DOI: 10.5281/zenodo.17268532
 # Do not import `pybel` at module import time. Only expose the presence
 # of Open Babel via `OBABEL_AVAILABLE`. Modules should import `pybel`
 # lazily if and when they need it.
-try:
+try: # pragma: no cover
     import importlib.util
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except Exception:
@@ -26,7 +26,7 @@ except Exception:
 # 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:
+try: # pragma: no cover
     import sip as _sip  # type: ignore
     _sip_isdeleted = getattr(_sip, 'isdeleted', None)
 except Exception:
@@ -40,7 +40,7 @@ def sip_isdeleted_safe(obj) -> bool:
     occurs while checking, it returns False (i.e. not deleted) so that the
     caller can continue other lightweight guards (like checking scene()).
     """
-    try:
+    try: # pragma: no cover
         if _sip_isdeleted is None:
             return False
         return bool(_sip_isdeleted(obj))

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/about_dialog.py

@@ -21,7 +21,7 @@ try:
 except Exception:
     from modules.constants import VERSION
 
-class AboutDialog(QDialog):
+class AboutDialog(QDialog): # pragma: no cover
     def __init__(self, main_window, parent=None):
         super().__init__(parent)
         self.main_window = main_window
@@ -37,7 +37,7 @@ class AboutDialog(QDialog):
         self.image_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
         
         # Load the original icon image
-        icon_path = os.path.join(os.path.dirname(__file__), 'assets', 'icon.png')
+        icon_path = os.path.join(os.path.dirname(__file__), '..', 'assets', 'icon.png')
         if os.path.exists(icon_path):
             original_pixmap = QPixmap(icon_path)
             # Scale to 2x size (160x160)

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/align_plane_dialog.py

@@ -21,7 +21,7 @@ try:
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
 
-class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
+class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, plane, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -44,7 +44,7 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         plane_names = {'xy': 'XY', 'xz': 'XZ', 'yz': 'YZ'}
         self.setWindowTitle(f"Align to {plane_names[self.plane]} Plane")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions
@@ -163,39 +163,12 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
     
     def show_atom_labels(self):
         """選択された原子にラベルを表示"""
-        # 既存のラベルをクリア
-        self.clear_atom_labels()
-        
-        # 新しいラベルを表示
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-            
         if self.selected_atoms:
             sorted_atoms = sorted(self.selected_atoms)
-            
-            for i, atom_idx in enumerate(sorted_atoms):
-                pos = self.main_window.atom_positions_3d[atom_idx]
-                label_text = f"#{i+1}"
-                
-                # ラベルを追加
-                label_actor = self.main_window.plotter.add_point_labels(
-                    [pos], [label_text], 
-                    point_size=20, 
-                    font_size=12,
-                    text_color='blue',
-                    always_visible=True
-                )
-                self.selection_labels.append(label_actor)
-    
-    def clear_atom_labels(self):
-        """原子ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
+            pairs = [(idx, f"#{i+1}") for i, idx in enumerate(sorted_atoms)]
+            self.show_atom_labels_for(pairs, color='blue')
+        else:
+            self.clear_atom_labels()
     
     def apply_PlaneAlign(self):
         """alignを適用（回転ベース）"""

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/alignment_dialog.py

@@ -13,7 +13,7 @@ DOI: 10.5281/zenodo.17268532
 from PyQt6.QtWidgets import (
     QDialog, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
 )
-from PyQt6.QtCore import Qt
+
 from PyQt6.QtWidgets import QMessageBox
 import numpy as np
 
@@ -22,7 +22,7 @@ try:
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
 
-class AlignmentDialog(Dialog3DPickingMixin, QDialog):
+class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, axis, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -46,7 +46,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         axis_names = {'x': 'X-axis', 'y': 'Y-axis', 'z': 'Z-axis'}
         self.setWindowTitle(f"Align to {axis_names[self.axis]}")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions
@@ -133,24 +133,6 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         self.selected_atoms.clear()
         self.update_display()
     
-    def add_selection_label(self, atom_idx, label_text):
-        """選択された原子にラベルを追加"""
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-        
-        # 原子の位置を取得
-        pos = self.main_window.atom_positions_3d[atom_idx]
-        
-        # ラベルを追加
-        label_actor = self.main_window.plotter.add_point_labels(
-            [pos], [label_text], 
-            point_size=20, 
-            font_size=12,
-            text_color='yellow',
-            always_visible=True
-        )
-        self.selection_labels.append(label_actor)
-    
     def remove_atom_label(self, atom_idx):
         """特定の原子のラベルを削除"""
         # 簡単化のため、全ラベルをクリアして再描画
@@ -159,16 +141,6 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
             if idx != atom_idx:
                 self.add_selection_label(idx, f"Atom {i}")
     
-    def clear_selection_labels(self):
-        """選択ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
-    
     def apply_alignment(self):
         """アライメントを適用"""
         if len(self.selected_atoms) != 2:

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/angle_dialog.py

@@ -16,15 +16,17 @@ from PyQt6.QtWidgets import (
 
 try:
     from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+    from .mol_geometry import get_connected_group
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
+    from modules.mol_geometry import get_connected_group
 
 from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import QMessageBox
 import numpy as np
 
 
-class AngleDialog(Dialog3DPickingMixin, QDialog):
+class AngleDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -44,8 +46,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
     
     def init_ui(self):
         self.setWindowTitle("Adjust Angle")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
-  # 常に前面表示
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions
@@ -170,69 +171,10 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
     
     def show_atom_labels(self):
         """選択された原子にラベルを表示"""
-        # 既存のラベルをクリア
-        self.clear_atom_labels()
-        
-        # 新しいラベルを表示
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-        
         selected_atoms = [self.atom1_idx, self.atom2_idx, self.atom3_idx]
         labels = ["1st", "2nd (vertex)", "3rd"]
-        colors = ["yellow", "yellow", "yellow"]  # 全て黄色に統一
-        
-        for i, atom_idx in enumerate(selected_atoms):
-            if atom_idx is not None:
-                pos = self.main_window.atom_positions_3d[atom_idx]
-                label_text = f"{labels[i]}"
-                
-                # ラベルを追加
-                label_actor = self.main_window.plotter.add_point_labels(
-                    [pos], [label_text], 
-                    point_size=20, 
-                    font_size=12,
-                    text_color=colors[i],
-                    always_visible=True
-                )
-                self.selection_labels.append(label_actor)
-    
-    def clear_atom_labels(self):
-        """原子ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
-    
-    def clear_selection_labels(self):
-        """選択ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
-    
-    def add_selection_label(self, atom_idx, label_text):
-        """選択された原子にラベルを追加"""
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-        
-        # 原子の位置を取得
-        pos = self.main_window.atom_positions_3d[atom_idx]
-        
-        # ラベルを追加
-        label_actor = self.main_window.plotter.add_point_labels(
-            [pos], [label_text], 
-            point_size=20, 
-            font_size=12,
-            text_color='yellow',
-            always_visible=True
-        )
-        self.selection_labels.append(label_actor)
+        pairs = [(idx, labels[i]) for i, idx in enumerate(selected_atoms) if idx is not None]
+        self.show_atom_labels_for(pairs)
     
     def update_display(self):
         """表示を更新"""
@@ -373,8 +315,8 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
             half_rotation = total_rotation_angle / 2
             
             # Get both connected groups
-            group1_atoms = self.get_connected_group(self.atom1_idx, exclude=self.atom2_idx)
-            group3_atoms = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            group1_atoms = get_connected_group(self.mol, self.atom1_idx, exclude=self.atom2_idx)
+            group3_atoms = get_connected_group(self.mol, self.atom3_idx, exclude=self.atom2_idx)
             
             # Rotate group 1 by -half_rotation
             for atom_idx in group1_atoms:
@@ -402,7 +344,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
             self.main_window.atom_positions_3d[self.atom3_idx] = new_pos3
         else:
             # Rotate the connected group around atom2 (vertex) - default behavior
-            atoms_to_move = self.get_connected_group(self.atom3_idx, exclude=self.atom2_idx)
+            atoms_to_move = get_connected_group(self.mol, self.atom3_idx, exclude=self.atom2_idx)
             
             for atom_idx in atoms_to_move:
                 current_pos = np.array(conf.GetAtomPosition(atom_idx))
@@ -418,23 +360,4 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
         # Update the 3D view
         self.main_window.draw_molecule_3d(self.mol)
     
-    def get_connected_group(self, start_atom, exclude=None):
-        """指定された原子から連結されているグループを取得"""
-        visited = set()
-        to_visit = [start_atom]
-        
-        while to_visit:
-            current = to_visit.pop()
-            if current in visited or current == exclude:
-                continue
-            
-            visited.add(current)
-            
-            # Get neighboring atoms
-            atom = self.mol.GetAtomWithIdx(current)
-            for bond in atom.GetBonds():
-                other_idx = bond.GetOtherAtomIdx(current)
-                if other_idx not in visited and other_idx != exclude:
-                    to_visit.append(other_idx)
-        
-        return visited
+

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/atom_item.py

@@ -23,13 +23,13 @@ from PyQt6.QtCore import (
 try:
     from .constants import (
         ATOM_RADIUS, DESIRED_ATOM_PIXEL_RADIUS,
-        FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        FONT_FAMILY, FONT_WEIGHT_BOLD,
         CPK_COLORS,
     )
 except Exception:
     from modules.constants import (
         ATOM_RADIUS, DESIRED_ATOM_PIXEL_RADIUS,
-        FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        FONT_FAMILY, FONT_WEIGHT_BOLD,
         CPK_COLORS,
     )
     

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/bond_item.py

@@ -24,13 +24,13 @@ from PyQt6.QtCore import (
 try:
     from .constants import (
         EZ_LABEL_BOX_SIZE, EZ_LABEL_TEXT_OUTLINE, EZ_LABEL_MARGIN,
-        BOND_OFFSET, FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        FONT_FAMILY, FONT_WEIGHT_BOLD,
         HOVER_PEN_WIDTH, DESIRED_BOND_PIXEL_WIDTH,
     )
 except Exception:
     from modules.constants import (
         EZ_LABEL_BOX_SIZE, EZ_LABEL_TEXT_OUTLINE, EZ_LABEL_MARGIN,
-        BOND_OFFSET, FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        FONT_FAMILY, FONT_WEIGHT_BOLD,
         HOVER_PEN_WIDTH, DESIRED_BOND_PIXEL_WIDTH,
     )
 
@@ -206,9 +206,6 @@ class BondItem(QGraphicsItem):
         except Exception:
             return None
 
-
-
-
     def paint(self, painter, option, widget):
         if self.atom1 is None or self.atom2 is None:
             return
@@ -341,7 +338,6 @@ class BondItem(QGraphicsItem):
                                     if bond and bond.IsInRing():
                                         is_in_ring = True
                                         # 環の中心を計算（この結合を含む最小環）
-                                        from rdkit import Chem
                                         ring_info = mol.GetRingInfo()
                                         for ring in ring_info.AtomRings():
                                             if rdkit_idx1 in ring and rdkit_idx2 in ring:

{moleditpy-2.5.1 → moleditpy-2.6.0}/src/moleditpy/modules/bond_length_dialog.py

@@ -15,11 +15,12 @@ from PyQt6.QtWidgets import (
 )
 
 from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+from .mol_geometry import get_connected_group
 
 from PyQt6.QtCore import Qt
 import numpy as np
 
-class BondLengthDialog(Dialog3DPickingMixin, QDialog):
+class BondLengthDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -37,8 +38,8 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
     
     def init_ui(self):
         self.setWindowTitle("Adjust Bond Length")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
-  # 常に前面表示
+        self.setModal(False)
+
         layout = QVBoxLayout(self)
         
         # Instructions
@@ -158,69 +159,10 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
     
     def show_atom_labels(self):
         """選択された原子にラベルを表示"""
-        # 既存のラベルをクリア
-        self.clear_atom_labels()
-        
-        # 新しいラベルを表示
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-        
         selected_atoms = [self.atom1_idx, self.atom2_idx]
         labels = ["1st", "2nd"]
-        colors = ["yellow", "yellow"]
-        
-        for i, atom_idx in enumerate(selected_atoms):
-            if atom_idx is not None:
-                pos = self.main_window.atom_positions_3d[atom_idx]
-                label_text = f"{labels[i]}"
-                
-                # ラベルを追加
-                label_actor = self.main_window.plotter.add_point_labels(
-                    [pos], [label_text], 
-                    point_size=20, 
-                    font_size=12,
-                    text_color=colors[i],
-                    always_visible=True
-                )
-                self.selection_labels.append(label_actor)
-    
-    def clear_atom_labels(self):
-        """原子ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
-    
-    def clear_selection_labels(self):
-        """選択ラベルをクリア"""
-        if hasattr(self, 'selection_labels'):
-            for label_actor in self.selection_labels:
-                try:
-                    self.main_window.plotter.remove_actor(label_actor)
-                except Exception:
-                    pass
-            self.selection_labels = []
-    
-    def add_selection_label(self, atom_idx, label_text):
-        """選択された原子にラベルを追加"""
-        if not hasattr(self, 'selection_labels'):
-            self.selection_labels = []
-        
-        # 原子の位置を取得
-        pos = self.main_window.atom_positions_3d[atom_idx]
-        
-        # ラベルを追加
-        label_actor = self.main_window.plotter.add_point_labels(
-            [pos], [label_text], 
-            point_size=20, 
-            font_size=12,
-            text_color='yellow',
-            always_visible=True
-        )
-        self.selection_labels.append(label_actor)
+        pairs = [(idx, labels[i]) for i, idx in enumerate(selected_atoms) if idx is not None]
+        self.show_atom_labels_for(pairs)
     
     def update_display(self):
         """表示を更新"""
@@ -317,8 +259,8 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
             new_pos2 = bond_center + direction * half_distance
             
             # Get both connected groups
-            group1_atoms = self.get_connected_group(self.atom1_idx, exclude=self.atom2_idx)
-            group2_atoms = self.get_connected_group(self.atom2_idx, exclude=self.atom1_idx)
+            group1_atoms = get_connected_group(self.mol, self.atom1_idx, exclude=self.atom2_idx)
+            group2_atoms = get_connected_group(self.mol, self.atom2_idx, exclude=self.atom1_idx)
             
             # Calculate displacements
             displacement1 = new_pos1 - pos1
@@ -346,7 +288,7 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
         else:
             # Move the connected group (default behavior)
             new_pos2 = pos1 + direction * new_distance
-            atoms_to_move = self.get_connected_group(self.atom2_idx, exclude=self.atom1_idx)
+            atoms_to_move = get_connected_group(self.mol, self.atom2_idx, exclude=self.atom1_idx)
             displacement = new_pos2 - pos2
             
             for atom_idx in atoms_to_move:
@@ -358,23 +300,4 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
         # Update the 3D view
         self.main_window.draw_molecule_3d(self.mol)
     
-    def get_connected_group(self, start_atom, exclude=None):
-        """指定された原子から連結されているグループを取得"""
-        visited = set()
-        to_visit = [start_atom]
-        
-        while to_visit:
-            current = to_visit.pop()
-            if current in visited or current == exclude:
-                continue
-            
-            visited.add(current)
-            
-            # Get neighboring atoms
-            atom = self.mol.GetAtomWithIdx(current)
-            for bond in atom.GetBonds():
-                other_idx = bond.GetOtherAtomIdx(current)
-                if other_idx not in visited and other_idx != exclude:
-                    to_visit.append(other_idx)
-        
-        return visited
+