MoleditPy 2.4.7__tar.gz → 2.4.9__tar.gz

{moleditpy-2.4.7 → moleditpy-2.4.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.4.7
+Version: 2.4.9
 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-2.4.7 → moleditpy-2.4.9}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.4.7"
+version = "2.4.9"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.4.7 → moleditpy-2.4.9}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.4.7
+Version: 2.4.9
 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-2.4.7 → moleditpy-2.4.9}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.4.7'
+VERSION = '2.4.9'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.4.7 → moleditpy-2.4.9}/src/moleditpy/modules/main_window_app_state.py

@@ -109,7 +109,21 @@ class MainWindowAppState(object):
 
         state['version'] = VERSION 
         
-        if self.current_mol: state['mol_3d'] = self.current_mol.ToBinary()
+        if self.current_mol:
+            state['mol_3d'] = self.current_mol.ToBinary()
+            # RDKit binary serialization does not preserve custom properties like _original_atom_id.
+            # We store them separately to ensure we can restore the 2D-3D link after undo/redo.
+            mol_3d_atom_ids = []
+            for i in range(self.current_mol.GetNumAtoms()):
+                atom = self.current_mol.GetAtomWithIdx(i)
+                try:
+                    if atom.HasProp("_original_atom_id"):
+                        mol_3d_atom_ids.append(atom.GetIntProp("_original_atom_id"))
+                    else:
+                        mol_3d_atom_ids.append(None)
+                except Exception:
+                    mol_3d_atom_ids.append(None)
+            state['mol_3d_atom_ids'] = mol_3d_atom_ids
 
         state['is_3d_viewer_mode'] = not self.is_2d_editable
 
@@ -204,6 +218,27 @@ class MainWindowAppState(object):
                 self.current_mol = Chem.Mol(loaded_data['mol_3d'])
                 # デバッグ：3D構造が有効かチェック
                 if self.current_mol and self.current_mol.GetNumAtoms() > 0:
+                    # Restore _original_atom_id if present in saved state
+                    if 'mol_3d_atom_ids' in loaded_data:
+                        atom_ids = loaded_data['mol_3d_atom_ids']
+                        if len(atom_ids) == self.current_mol.GetNumAtoms():
+                            for i, aid in enumerate(atom_ids):
+                                if aid is not None:
+                                    try:
+                                        self.current_mol.GetAtomWithIdx(i).SetIntProp("_original_atom_id", int(aid))
+                                    except Exception:
+                                        pass
+                    
+                    # Re-create atom ID mapping to synchronize 2D atoms with 3D actors
+                    # This MUST be done before draw_molecule_3d for labels to be correct.
+                    try:
+                        self.create_atom_id_mapping()
+                        self.update_atom_id_menu_text()
+                        self.update_atom_id_menu_state()
+                    except Exception:
+                        pass
+
+                    # draw_molecule_3d will use the restored IDs for labels/picking if show_all_atom_info is called.
                     self.draw_molecule_3d(self.current_mol)
                     self.plotter.reset_camera()
                     # 3D関連機能を統一的に有効化
@@ -254,7 +289,11 @@ class MainWindowAppState(object):
             'atoms': {k: (v['symbol'], v['item'].pos().x(), v['item'].pos().y(), v.get('charge', 0), v.get('radical', 0)) for k, v in self.data.atoms.items()},
             'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in self.data.bonds.items()},
             '_next_atom_id': self.data._next_atom_id,
-            'mol_3d': self.current_mol.ToBinary() if self.current_mol else None
+            'mol_3d': self.current_mol.ToBinary() if self.current_mol else None,
+            'mol_3d_atom_ids': [
+                (a.GetIntProp("_original_atom_id") if a.HasProp("_original_atom_id") else None)
+                for a in self.current_mol.GetAtoms()
+            ] if self.current_mol else None
         }
         
         last_state_for_comparison = None
@@ -266,7 +305,8 @@ class MainWindowAppState(object):
                 'atoms': {k: (v['symbol'], v['pos'][0], v['pos'][1], v.get('charge', 0), v.get('radical', 0)) for k, v in last_atoms.items()},
                 'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in last_bonds.items()},
                 '_next_atom_id': last_state.get('_next_atom_id'),
-                'mol_3d': last_state.get('mol_3d', None)
+                'mol_3d': last_state.get('mol_3d', None),
+                'mol_3d_atom_ids': last_state.get('mol_3d_atom_ids', None)
             }
 
         if not last_state_for_comparison or current_state_for_comparison != last_state_for_comparison:

{moleditpy-2.4.7 → moleditpy-2.4.9}/src/moleditpy/modules/main_window_main_init.py

@@ -1838,6 +1838,39 @@ class MainWindowMainInit(object):
         # Add dynamic plugin actions (Legacy + New Registration)
         plugins = self.plugin_manager.discover_plugins(self)
         
+        # --- Update 3D Style Menu with discovered styles ---
+        # This menu is built in init_ui (before plugins are discovered), so we must update it here.
+        if hasattr(self, 'style_button') and self.style_button.menu():
+            style_menu = self.style_button.menu()
+            
+            # Find the exclusive ActionGroup from an existing action (e.g. Ball & Stick)
+            style_group = None
+            for action in style_menu.actions():
+                if action.actionGroup():
+                    style_group = action.actionGroup()
+                    break
+            
+            if style_group and self.plugin_manager.custom_3d_styles:
+                # Add separator if not present at end
+                actions = style_menu.actions()
+                if actions and not actions[-1].isSeparator():
+                    style_menu.addSeparator()
+
+                for style_name in self.plugin_manager.custom_3d_styles:
+                     # Check if already added to avoid duplicates
+                     exists = False
+                     for act in style_menu.actions():
+                         if act.text() == style_name:
+                             exists = True
+                             break
+                     
+                     if not exists:
+                         action = QAction(style_name, self, checkable=True)
+                         # Use default arg to capture loop variable
+                         action.triggered.connect(lambda checked=False, s=style_name: self.set_3d_style(s))
+                         style_menu.addAction(action)
+                         style_group.addAction(action)
+
         # 1. Add Registered Menu Actions (New System)
         if self.plugin_manager.menu_actions:
              for action_def in self.plugin_manager.menu_actions: