MoleditPy 2.4.6__py3-none-any.whl → 2.4.8__py3-none-any.whl

moleditpy/modules/bond_item.py

@@ -164,43 +164,50 @@ class BondItem(QGraphicsItem):
         return rect
 
     def shape(self):
+        """Define the precise collision/selection area, separate from the drawing area (boundingRect)."""
         path = QPainterPath()
         try:
             line = self.get_line_in_local_coords()
+            # Create a simple path along the bond line
+            path.moveTo(line.p1())
+            path.lineTo(line.p2())
+            
+            # Stroke it to give it some width (e.g., 10px or dynamic based on settings) generally easier to click
+            # even if the visual width is smaller.
+            stroker = QPainterPathStroker()
+            stroker.setWidth(DESIRED_BOND_PIXEL_WIDTH) # Use constant (20.0)
+            path = stroker.createStroke(path)
+            
+            # If there's an E/Z label, add its rect to the selection shape
+            label_rect = self.get_ez_label_local_rect()
+            if label_rect:
+                path.addRect(label_rect)
+                
         except Exception:
-            return path 
-        if line.length() == 0:
-            return path
-
-        scene = self.scene()
-        if not scene or not scene.views():
-            return super().shape()
-
-        view = scene.views()[0]
-        scale = view.transform().m11()
+            # Fallback to a small rect around the origin if calculation fails
+            path.addRect(QRectF(-5, -5, 10, 10))
+            
+        return path
 
-        # Dynamic bond width
-        width_2d = 2.0
+    def get_ez_label_local_rect(self):
+        """Helper to get E/Z label rect in local coordinates."""
+        if self.order != 2 or self.stereo not in [3, 4]:
+            return None
         try:
-            if view.window() and hasattr(view.window(), 'settings'):
-                width_2d = view.window().settings.get('bond_width_2d', 2.0)
+            line = self.get_line_in_local_coords()
+            center = line.center()
+            
+            # Logic similar to boundingRect but returning just the label box
+            font_size = 20
+            # ... (Simpler logic: just return a box around center)
+            # Standard size estimate
+            box_size = 30 
+            return QRectF(center.x() - box_size/2, center.y() - box_size/2, box_size, box_size)
         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
+            return None
 
 
-        stroker = QPainterPathStroker()
-        stroker.setWidth(scene_width)
-        stroker.setCapStyle(Qt.PenCapStyle.RoundCap)  
-        stroker.setJoinStyle(Qt.PenJoinStyle.RoundJoin) 
 
-        center_line_path = QPainterPath(line.p1())
-        center_line_path.lineTo(line.p2())
-        
-        return stroker.createStroke(center_line_path)
 
     def paint(self, painter, option, widget):
         if self.atom1 is None or self.atom2 is None:

moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.4.6'
+VERSION = '2.4.8'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

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-2.4.6.dist-info → moleditpy-2.4.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.4.6
+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-2.4.6.dist-info → moleditpy-2.4.8.dist-info}/RECORD

@@ -8,18 +8,18 @@ moleditpy/modules/alignment_dialog.py,sha256=CPubSJI52mNSXmWt7oKQ2un5lXnN8_K4Z-L
 moleditpy/modules/analysis_window.py,sha256=zjP5ipSTpKw8oLr1eKdoxW8Bk1SslGlPqsVucD-x_5w,9403
 moleditpy/modules/angle_dialog.py,sha256=uc2WbvSfRe892xoEirqpZ78pf2Smwzkinkso6zLWr0Y,17751
 moleditpy/modules/atom_item.py,sha256=9x0xojz6eih-N6UFgGJHNdRshgOurx3F5ysMzcHup6Y,18034
-moleditpy/modules/bond_item.py,sha256=jEg2CNMBrq74XihWRULzUTgN9g8k4IdT3AS_a2JPpFM,23644
+moleditpy/modules/bond_item.py,sha256=21oX1sR5kpY-MlfUsmekkV6XATVwIAhmsH1UMwV34rg,24225
 moleditpy/modules/bond_length_dialog.py,sha256=6bFPGssnqlgINuqpxLv-OhjMH3_hspnaH8QtorAyu2M,14782
 moleditpy/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy/modules/constants.py,sha256=8qXgVTGzHGMtCAXYqkRNrXWxS0TEpAKjY6am42-YF9Y,4702
+moleditpy/modules/constants.py,sha256=M1dGZR8B9RNXfzFq1GhX7lUxMmZn1b_Whtu9ShCQ6wk,4702
 moleditpy/modules/constrained_optimization_dialog.py,sha256=REsk4ePsqNmAGPMTS_jckeM7jexrU3krwun8sKqKUCs,30062
 moleditpy/modules/custom_interactor_style.py,sha256=LDNODMJoNHGe1AUSrvqv6PdeJm-hpPmSpWINppnJLt0,38942
 moleditpy/modules/custom_qt_interactor.py,sha256=vCZsDfRO-FtphD5cTP7Ps-5rpHZMIGloaoe6EaKzrsw,4139
 moleditpy/modules/dialog3_d_picking_mixin.py,sha256=z4udbkiX9PYmIGazPXsbftkk_oRRwZhcvlCqbyJzr24,6493
 moleditpy/modules/dihedral_dialog.py,sha256=bOTDO6-b74vEDn_z6OyuBr5cRz3RnRj83PiaEBUyWJA,18002
 moleditpy/modules/main_window.py,sha256=w52L0F7V3b0BiNhQImbulZ9N8cRKolYy06szfoMOIcg,36830
-moleditpy/modules/main_window_app_state.py,sha256=8YDcGNCSpLTO1NGL9tEvNkXpUcS7JW-uK7TdUGvEqnk,35189
+moleditpy/modules/main_window_app_state.py,sha256=Civ28scAuIPXdD1qix5IkUAgEgl4Wy3wCqblomF3EY4,37493
 moleditpy/modules/main_window_compute.py,sha256=ipIkhH_DONXDnPzh7xeym9X-Yfx8EhsvXYOdyxsAj4c,53347
 moleditpy/modules/main_window_dialog_manager.py,sha256=QR96LqHAPSOShXbc9cK-Ffq8a16JrXAoMKB0pHjESrQ,20072
 moleditpy/modules/main_window_edit_3d.py,sha256=CUArB5wcsgq1C7LygAEC6URlbnn4RhRYDa5n-Y-etWI,19731
@@ -51,9 +51,9 @@ moleditpy/modules/assets/file_icon.ico,sha256=yyVj084A7HuMNbV073cE_Ag3Ne405qgOP3
 moleditpy/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
-moleditpy-2.4.6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-moleditpy-2.4.6.dist-info/METADATA,sha256=UR9T-fjKgryzsDETGIPYZmpCG4Fs-ghP-94vjjvmiQs,60629
-moleditpy-2.4.6.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-moleditpy-2.4.6.dist-info/entry_points.txt,sha256=yH1h9JjALhok1foXT3-hYrC4ufoZt8b7oiBcsdnGNNM,54
-moleditpy-2.4.6.dist-info/top_level.txt,sha256=ARICrS4ihlPXqywlKl6o-oJa3Qz3gZRWu_VZsQ3_c44,10
-moleditpy-2.4.6.dist-info/RECORD,,
+moleditpy-2.4.8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+moleditpy-2.4.8.dist-info/METADATA,sha256=dXEV8a4OwiNRfpQ0vg6EkSN9j1hqLf4j63xJJ3FSsto,60629
+moleditpy-2.4.8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+moleditpy-2.4.8.dist-info/entry_points.txt,sha256=yH1h9JjALhok1foXT3-hYrC4ufoZt8b7oiBcsdnGNNM,54
+moleditpy-2.4.8.dist-info/top_level.txt,sha256=ARICrS4ihlPXqywlKl6o-oJa3Qz3gZRWu_VZsQ3_c44,10
+moleditpy-2.4.8.dist-info/RECORD,,

{moleditpy-2.4.6.dist-info → moleditpy-2.4.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.10.1)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any