moleditpy 1.9.2__tar.gz → 1.9.3__tar.gz

{moleditpy-1.9.2 → moleditpy-1.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.2
+Version: 1.9.3
 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-1.9.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "moleditpy"
 
-version = "1.9.2"
+version = "1.9.3"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy-1.9.2 → moleditpy-1.9.3}/src/moleditpy/main.py

@@ -11,7 +11,7 @@ DOI 10.5281/zenodo.17268532
 """
 
 #Version
-VERSION = '1.9.2'
+VERSION = '1.9.3'
 
 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()

{moleditpy-1.9.2 → moleditpy-1.9.3}/src/moleditpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.2
+Version: 1.9.3
 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