moleditpy 1.9.2__tar.gz → 1.9.4__tar.gz

{moleditpy-1.9.2 → moleditpy-1.9.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.2
+Version: 1.9.4
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor

{moleditpy-1.9.2 → moleditpy-1.9.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "moleditpy"
 
-version = "1.9.2"
+version = "1.9.4"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy-1.9.2 → moleditpy-1.9.4}/src/moleditpy/main.py

@@ -11,7 +11,7 @@ DOI 10.5281/zenodo.17268532
 """
 
 #Version
-VERSION = '1.9.2'
+VERSION = '1.9.4'
 
 print("-----------------------------------------------------")
 print("MoleditPy — A Python-based molecular editing software")
@@ -4315,7 +4315,6 @@ class MoleculeScene(QGraphicsScene):
             super().mouseMoveEvent(event)
 
     def mouseReleaseEvent(self, event):
-        
         if not self.window.is_2d_editable:
             return 
 
@@ -4329,22 +4328,19 @@ class MoleculeScene(QGraphicsScene):
         if self.mode.startswith('template') and is_click:
             if self.template_context and self.template_context.get('points'):
                 context = self.template_context
-                
                 # Check if this is a user template
                 if self.mode.startswith('template_user'):
                     self.add_user_template_fragment(context)
                 else:
                     self.add_molecule_fragment(context['points'], context['bonds_info'], existing_items=context.get('items', []))
-                
                 self.data_changed_in_event = True
-                
                 # イベント処理をここで完了させ、下のアイテムが選択されるのを防ぐ
                 self.start_atom=None; self.start_pos = None; self.press_pos = None
                 if self.data_changed_in_event: self.window.push_undo_state()
                 return
 
         released_item = self.itemAt(end_pos, self.views()[0].transform())
-        
+
         # 1. 特殊モード（ラジカル/電荷）の処理
         if (self.mode == 'radical') and is_click and isinstance(released_item, AtomItem):
             atom = released_item
@@ -4371,7 +4367,6 @@ class MoleculeScene(QGraphicsScene):
 
         elif self.mode.startswith('bond') and is_click and isinstance(released_item, BondItem):
             b = released_item 
-            
             if self.mode == 'bond_2_5':
                 try:
                     if b.order == 2:
@@ -4391,53 +4386,40 @@ class MoleculeScene(QGraphicsScene):
                     if hasattr(self.window, 'statusBar'):
                         self.window.statusBar().showMessage(f"Error changing E/Z stereochemistry: {e}", 5000)
                 return # この後の処理は行わない
-            
             elif self.bond_stereo != 0 and b.order == self.bond_order and b.stereo == self.bond_stereo:
                 # 方向性を反転させる
                 old_id1, old_id2 = b.atom1.atom_id, b.atom2.atom_id
-                
                 # 1. 古い方向の結合をデータから削除
                 self.data.remove_bond(old_id1, old_id2)
-                
                 # 2. 逆方向で結合をデータに再追加
                 new_key, _ = self.data.add_bond(old_id2, old_id1, self.bond_order, self.bond_stereo)
-                
                 # 3. BondItemの原子参照を入れ替え、新しいデータと関連付ける
                 b.atom1, b.atom2 = b.atom2, b.atom1
                 self.data.bonds[new_key]['item'] = b
-                
                 # 4. 見た目を更新
                 b.update_position()
-
             else:
                 # 既存の結合を一度削除
                 self.data.remove_bond(b.atom1.atom_id, b.atom2.atom_id)
-
                 # BondItemが記憶している方向(b.atom1 -> b.atom2)で、新しい結合様式を再作成
                 # これにより、修正済みのadd_bondが呼ばれ、正しい方向で保存される
                 new_key, _ = self.data.add_bond(b.atom1.atom_id, b.atom2.atom_id, self.bond_order, self.bond_stereo)
-
                 # BondItemの見た目とデータ参照を更新
                 b.prepareGeometryChange()
                 b.order = self.bond_order
                 b.stereo = self.bond_stereo
                 self.data.bonds[new_key]['item'] = b
                 b.update()
-
             self.clearSelection()
             self.data_changed_in_event = True
-
         # 3. 新規原子・結合の作成処理 (atom_* モード および すべての bond_* モードで許可)
         elif self.start_atom and (self.mode.startswith('atom') or self.mode.startswith('bond')):
             line = QLineF(self.start_atom.pos(), end_pos); end_item = self.itemAt(end_pos, self.views()[0].transform())
-
             # 使用する結合様式を決定
             # atomモードの場合は bond_order/stereo を None にして create_bond にデフォルト値(1, 0)を適用
             # bond_* モードの場合は現在の設定 (self.bond_order/stereo) を使用
             order_to_use = self.bond_order if self.mode.startswith('bond') else None
             stereo_to_use = self.bond_stereo if self.mode.startswith('bond') else None
-    
-            
             if is_click:
                 # 短いクリック: 既存原子のシンボル更新 (atomモードのみ)
                 if self.mode.startswith('atom') and self.start_atom.symbol != self.current_atom_symbol:
@@ -4451,25 +4433,20 @@ class MoleculeScene(QGraphicsScene):
                     new_id = self.create_atom(self.current_atom_symbol, end_pos); new_item = self.data.atoms[new_id]['item']
                     self.create_bond(self.start_atom, new_item, bond_order=order_to_use, bond_stereo=stereo_to_use)
                 self.data_changed_in_event = True
-                
         # 4. 空白領域からの新規作成処理 (atom_* モード および すべての bond_* モードで許可)
         elif self.start_pos and (self.mode.startswith('atom') or self.mode.startswith('bond')):
             line = QLineF(self.start_pos, end_pos)
-
             # 使用する結合様式を決定
             order_to_use = self.bond_order if self.mode.startswith('bond') else None
             stereo_to_use = self.bond_stereo if self.mode.startswith('bond') else None
-    
             if line.length() < 10:
                 self.create_atom(self.current_atom_symbol, end_pos); self.data_changed_in_event = True
             else:
                 end_item = self.itemAt(end_pos, self.views()[0].transform())
-
                 if isinstance(end_item, AtomItem):
                     start_id = self.create_atom(self.current_atom_symbol, self.start_pos)
                     start_item = self.data.atoms[start_id]['item']
                     self.create_bond(start_item, end_item, bond_order=order_to_use, bond_stereo=stereo_to_use)
-                
                 else:
                     start_id = self.create_atom(self.current_atom_symbol, self.start_pos)
                     end_id = self.create_atom(self.current_atom_symbol, end_pos)
@@ -4480,11 +4457,9 @@ class MoleculeScene(QGraphicsScene):
                         bond_stereo=stereo_to_use
                     )
                 self.data_changed_in_event = True 
-        
         # 5. それ以外の処理 (Selectモードなど)
         else: super().mouseReleaseEvent(event)
 
-
         # 削除されたオブジェクトを安全にチェック
         moved_atoms = []
         for item, old_pos in self.initial_positions_in_event.items():
@@ -4495,7 +4470,6 @@ class MoleculeScene(QGraphicsScene):
             except RuntimeError:
                 # オブジェクトが削除されている場合はスキップ
                 continue
-                
         if moved_atoms:
             self.data_changed_in_event = True
             bonds_to_update = set()
@@ -4507,12 +4481,9 @@ class MoleculeScene(QGraphicsScene):
                     # オブジェクトが削除されている場合はスキップ
                     continue
             for bond in bonds_to_update: bond.update_position()
-            
             # 原子移動後に測定ラベルの位置を更新
             self.window.update_2d_measurement_labels()
-            
             if self.views(): self.views()[0].viewport().update()
-        
         self.start_atom=None; self.start_pos = None; self.press_pos = None; self.temp_line = None
         self.template_context = {}
         # Clear user template data when switching modes
@@ -7009,7 +6980,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             if abs(current_pos[0] - self._mouse_press_pos[0]) > 3 or abs(current_pos[1] - self._mouse_press_pos[1]) > 3:
                 self._mouse_moved_during_drag = True
 
-        if self._is_dragging_atom:
+        if self._is_dragging_atom and mw.dragged_atom_info is not None:
             # カスタムの原子ドラッグ処理
             self.is_dragging = True
             atom_id = mw.dragged_atom_info['id']
@@ -7075,6 +7046,72 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     mw.draw_molecule_3d(mw.current_mol)
                 mw.push_undo_state()
             mw.dragged_atom_info = None
+            # Always ensure the visual representation matches the actual
+            # RDKit conformer coordinates when the mouse is released.
+            try:
+                if mw.current_mol and mw.current_mol.GetNumConformers() > 0:
+                    conf = mw.current_mol.GetConformer()
+                    # Rebuild the authoritative atom_positions_3d from the conformer
+                    mw.atom_positions_3d = np.array([list(conf.GetAtomPosition(i)) for i in range(mw.current_mol.GetNumAtoms())])
+
+                    # If a glyph_source exists (typical), update its points and mark modified
+                    if hasattr(mw, 'glyph_source') and mw.glyph_source is not None:
+                        try:
+                            mw.glyph_source.points = mw.atom_positions_3d
+                            mw.glyph_source.Modified()
+                        except Exception:
+                            # Fallback to a full redraw if updating glyph_source fails
+                            try:
+                                mw.draw_molecule_3d(mw.current_mol)
+                            except Exception:
+                                pass
+
+                    # Refresh overlays and labels that depend on atom_positions_3d
+                    try:
+                        mw.update_3d_selection_display()
+                    except Exception:
+                        pass
+                    try:
+                        mw.update_measurement_labels_display()
+                    except Exception:
+                        pass
+                    try:
+                        mw.update_2d_measurement_labels()
+                    except Exception:
+                        pass
+                    try:
+                        mw.show_all_atom_info()
+                    except Exception:
+                        pass
+
+                    # Final render to make sure everything is consistent
+                    try:
+                        if hasattr(mw, 'plotter') and mw.plotter:
+                            mw.plotter.render()
+                    except Exception:
+                        pass
+                    # As a final safety-net, ensure the visual scene exactly matches
+                    # the authoritative RDKit conformer coordinates. This forces a
+                    # full redraw if any lower-level updates failed to sync.
+                    try:
+                        if mw.current_mol and mw.current_mol.GetNumConformers() > 0:
+                            # Redraw the molecule and render to guarantee consistency
+                            try:
+                                mw.draw_molecule_3d(mw.current_mol)
+                            except Exception:
+                                # If a full redraw fails, at least attempt a render
+                                pass
+                            try:
+                                if hasattr(mw, 'plotter') and mw.plotter:
+                                    mw.plotter.render()
+                            except Exception:
+                                pass
+                    except Exception:
+                        # Silently ignore any errors during this final sync step
+                        pass
+            except Exception:
+                # Do not allow a failure here to interrupt release flow
+                pass
         else:
             # カメラ回転の後始末を親クラスに任せます
             super().OnLeftButtonUp()
@@ -7812,14 +7849,6 @@ class MainWindow(QMainWindow):
 
         edit_menu.addSeparator()
         
-        # Templates
-        template_action = QAction("Templates...", self)
-        template_action.setShortcut(QKeySequence("Ctrl+T"))
-        template_action.triggered.connect(self.open_template_dialog)
-        edit_menu.addAction(template_action)
-        
-        edit_menu.addSeparator()
-        
         select_all_action = QAction("Select All", self); select_all_action.setShortcut(QKeySequence.StandardKey.SelectAll)
         select_all_action.triggered.connect(self.select_all); edit_menu.addAction(select_all_action)
         
@@ -8402,6 +8431,15 @@ class MainWindow(QMainWindow):
             self.view_2d.setFocus() 
             return
 
+        # 描画モード変更時に測定モードと3D編集モードをリセット
+        if self.measurement_mode:
+            self.measurement_action.setChecked(False)
+            self.toggle_measurement_mode(False)  # 測定モードを無効化
+        
+        if self.is_3d_edit_mode:
+            self.edit_3d_action.setChecked(False)
+            self.toggle_3d_edit_mode(False)  # 3D編集モードを無効化
+
         mol = self.data.to_rdkit_mol(use_2d_stereo=False)
 
         # 分子オブジェクトが作成できない場合でも化学的問題をチェック
@@ -9975,6 +10013,18 @@ class MainWindow(QMainWindow):
                     for i in range(self.current_mol.GetNumAtoms()):
                         atom = self.current_mol.GetAtomWithIdx(i)
                         pos = conf.GetAtomPosition(i)
+
+                        # Try to preserve original editor atom ID (if present) so it can be
+                        # restored when loading PMEPRJ files. RDKit atom properties may
+                        # contain _original_atom_id when the molecule was created from
+                        # the editor's 2D structure.
+                        original_id = None
+                        try:
+                            if atom.HasProp("_original_atom_id"):
+                                original_id = atom.GetIntProp("_original_atom_id")
+                        except Exception:
+                            original_id = None
+
                         atom_3d = {
                             "index": i,
                             "symbol": atom.GetSymbol(),
@@ -9984,7 +10034,9 @@ class MainWindow(QMainWindow):
                             "z": pos.z,
                             "formal_charge": atom.GetFormalCharge(),
                             "num_explicit_hs": atom.GetNumExplicitHs(),
-                            "num_implicit_hs": atom.GetNumImplicitHs()
+                            "num_implicit_hs": atom.GetNumImplicitHs(),
+                            # include original editor atom id when available for round-trip
+                            "original_id": original_id
                         }
                         atoms_3d.append(atom_3d)
                 
@@ -10130,6 +10182,8 @@ class MainWindow(QMainWindow):
         """JSONデータから状態を復元"""
         self.dragged_atom_info = None
         self.clear_2d_editor(push_to_undo=False)
+        self._enable_3d_edit_actions(False)
+        self._enable_3d_features(False)
 
         # 3Dビューアーモードの設定
         is_3d_mode = json_data.get("is_3d_viewer_mode", False)
@@ -10216,6 +10270,18 @@ class MainWindow(QMainWindow):
                                         atom_data["y"], 
                                         atom_data["z"]
                                     ]
+                                # Restore original editor atom id into RDKit atom property
+                                try:
+                                    original_id = atom_data.get("original_id", None)
+                                    if original_id is not None and idx < self.current_mol.GetNumAtoms():
+                                        rd_atom = self.current_mol.GetAtomWithIdx(idx)
+                                        # set as int prop so other code expecting _original_atom_id works
+                                        rd_atom.SetIntProp("_original_atom_id", int(original_id))
+                                except Exception:
+                                    pass
+                                self._enable_3d_edit_actions(True)
+                                self._enable_3d_features(True)
+
                         # 3D分子があれば必ず3D表示
                         self.draw_molecule_3d(self.current_mol)
                         # ViewerモードならUIも切り替え
@@ -10223,6 +10289,8 @@ class MainWindow(QMainWindow):
                             self._enter_3d_viewer_ui_mode()
                         else:
                             self.is_2d_editable = True
+                        self.plotter.reset_camera()
+                            
             except Exception as e:
                 print(f"Warning: Could not restore 3D molecular data: {e}")
                 self.current_mol = None

{moleditpy-1.9.2 → moleditpy-1.9.4}/src/moleditpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.2
+Version: 1.9.4
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor