MoleditPy-linux 2.4.7__py3-none-any.whl → 2.4.8__py3-none-any.whl

moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.4.7'
+VERSION = '2.4.8'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux/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_linux-2.4.7.dist-info → moleditpy_linux-2.4.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.4.7
+Version: 2.4.8
 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_linux-2.4.7.dist-info → moleditpy_linux-2.4.8.dist-info}/RECORD

@@ -12,14 +12,14 @@ moleditpy_linux/modules/bond_item.py,sha256=21oX1sR5kpY-MlfUsmekkV6XATVwIAhmsH1U
 moleditpy_linux/modules/bond_length_dialog.py,sha256=6bFPGssnqlgINuqpxLv-OhjMH3_hspnaH8QtorAyu2M,14782
 moleditpy_linux/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy_linux/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy_linux/modules/constants.py,sha256=cJBVJ8ESdrhJ3CVXNEWjf8jAUcw9bjzBIm80BxT3CFw,4702
+moleditpy_linux/modules/constants.py,sha256=M1dGZR8B9RNXfzFq1GhX7lUxMmZn1b_Whtu9ShCQ6wk,4702
 moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=REsk4ePsqNmAGPMTS_jckeM7jexrU3krwun8sKqKUCs,30062
 moleditpy_linux/modules/custom_interactor_style.py,sha256=LDNODMJoNHGe1AUSrvqv6PdeJm-hpPmSpWINppnJLt0,38942
 moleditpy_linux/modules/custom_qt_interactor.py,sha256=vCZsDfRO-FtphD5cTP7Ps-5rpHZMIGloaoe6EaKzrsw,4139
 moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=z4udbkiX9PYmIGazPXsbftkk_oRRwZhcvlCqbyJzr24,6493
 moleditpy_linux/modules/dihedral_dialog.py,sha256=bOTDO6-b74vEDn_z6OyuBr5cRz3RnRj83PiaEBUyWJA,18002
 moleditpy_linux/modules/main_window.py,sha256=w52L0F7V3b0BiNhQImbulZ9N8cRKolYy06szfoMOIcg,36830
-moleditpy_linux/modules/main_window_app_state.py,sha256=8YDcGNCSpLTO1NGL9tEvNkXpUcS7JW-uK7TdUGvEqnk,35189
+moleditpy_linux/modules/main_window_app_state.py,sha256=Civ28scAuIPXdD1qix5IkUAgEgl4Wy3wCqblomF3EY4,37493
 moleditpy_linux/modules/main_window_compute.py,sha256=ipIkhH_DONXDnPzh7xeym9X-Yfx8EhsvXYOdyxsAj4c,53347
 moleditpy_linux/modules/main_window_dialog_manager.py,sha256=QR96LqHAPSOShXbc9cK-Ffq8a16JrXAoMKB0pHjESrQ,20072
 moleditpy_linux/modules/main_window_edit_3d.py,sha256=CUArB5wcsgq1C7LygAEC6URlbnn4RhRYDa5n-Y-etWI,19731
@@ -51,9 +51,9 @@ moleditpy_linux/modules/assets/file_icon.ico,sha256=yyVj084A7HuMNbV073cE_Ag3Ne40
 moleditpy_linux/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy_linux/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy_linux/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
-moleditpy_linux-2.4.7.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-moleditpy_linux-2.4.7.dist-info/METADATA,sha256=iFu5Ov9NUgyr0c5AUzscJqZKGQ0pkIpk8g-yOEgHMXo,60708
-moleditpy_linux-2.4.7.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-moleditpy_linux-2.4.7.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
-moleditpy_linux-2.4.7.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
-moleditpy_linux-2.4.7.dist-info/RECORD,,
+moleditpy_linux-2.4.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+moleditpy_linux-2.4.8.dist-info/METADATA,sha256=bPGIJkXQU-1D9JHLW-CNn270Ei-Z2eIx81XXwJQLwnU,60708
+moleditpy_linux-2.4.8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+moleditpy_linux-2.4.8.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
+moleditpy_linux-2.4.8.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
+moleditpy_linux-2.4.8.dist-info/RECORD,,