moleditpy 1.2.2__tar.gz → 1.2.4__tar.gz

{moleditpy-1.2.2 → moleditpy-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.2.2
+Version: 1.2.4
 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-1.2.2 → moleditpy-1.2.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "moleditpy"
 
-version = "1.2.2"
+version = "1.2.4"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy-1.2.2 → moleditpy-1.2.4}/src/moleditpy/main.py

@@ -11,7 +11,7 @@ DOI 10.5281/zenodo.17268532
 """
 
 #Version
-VERSION = '1.2.2'
+VERSION = '1.2.4'
 
 print("-----------------------------------------------------")
 print("MoleditPy — A Python-based molecular editing software")
@@ -879,7 +879,7 @@ class MoleculeScene(QGraphicsScene):
             stereo_to_use = self.bond_stereo if self.mode.startswith('bond') else None
     
             
-            if line.length() < 10:
+            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:
                     self.start_atom.symbol=self.current_atom_symbol; self.data.atoms[self.start_atom.atom_id]['symbol']=self.current_atom_symbol; self.start_atom.update_style()
@@ -2139,6 +2139,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             # その後、カーソルの表示を更新します
             is_edit_active = mw.is_3d_edit_mode or interactor.GetAltKey()
             if is_edit_active:
+                # 編集がアクティブな場合のみ、原子のホバーチェックを行う
                 atom_under_cursor = False
                 click_pos = interactor.GetEventPosition()
                 picker = mw.plotter.picker
@@ -2982,6 +2983,7 @@ class MainWindow(QMainWindow):
         self.optimize_3d_button.setEnabled(True)
         self.export_button.setEnabled(True)
         self.edit_3d_action.setEnabled(True)
+        self.plotter.reset_camera()
         
     def on_calculation_error(self, error_message):
         self.dragged_atom_info = None
@@ -3150,8 +3152,11 @@ class MainWindow(QMainWindow):
         try:
             mol = self.data.to_rdkit_mol()
             if mol:
+                # 水素原子を明示的に追加した分子オブジェクトを生成
+                mol_with_hs = Chem.AddHs(mol)
                 mol_formula = rdMolDescriptors.CalcMolFormula(mol)
-                num_atoms = mol.GetNumAtoms()
+                # 水素を含む分子オブジェクトから原子数を取得
+                num_atoms = mol_with_hs.GetNumAtoms()
                 # 右側のラベルのテキストを更新
                 self.formula_label.setText(f"Formula: {mol_formula}   |   Atoms: {num_atoms}")
         except Exception:
@@ -3483,6 +3488,7 @@ class MainWindow(QMainWindow):
 
         try:
             # 安定版：原子IDとRDKit座標の確実なマッピング
+            view_center = self.view_2d.mapToScene(self.view_2d.viewport().rect().center())
             new_positions_map = {}
             AllChem.Compute2DCoords(mol)
             conf = mol.GetConformer()
@@ -3498,8 +3504,8 @@ class MainWindow(QMainWindow):
                 self.statusBar().showMessage("Error: Atom items not found for optimized atoms."); return
 
             # 元の図形の中心を維持
-            original_center_x = sum(item.pos().x() for item in target_atom_items) / len(target_atom_items)
-            original_center_y = sum(item.pos().y() for item in target_atom_items) / len(target_atom_items)
+            #original_center_x = sum(item.pos().x() for item in target_atom_items) / len(target_atom_items)
+            #original_center_y = sum(item.pos().y() for item in target_atom_items) / len(target_atom_items)
 
             positions = list(new_positions_map.values())
             rdkit_cx = sum(p.x for p in positions) / len(positions)
@@ -3511,8 +3517,8 @@ class MainWindow(QMainWindow):
             for atom_id, rdkit_pos in new_positions_map.items():
                 if atom_id in self.data.atoms:
                     item = self.data.atoms[atom_id]['item']
-                    sx = ((rdkit_pos.x - rdkit_cx) * SCALE) + original_center_x
-                    sy = (-(rdkit_pos.y - rdkit_cy) * SCALE) + original_center_y
+                    sx = ((rdkit_pos.x - rdkit_cx) * SCALE) + view_center.x()
+                    sy = (-(rdkit_pos.y - rdkit_cy) * SCALE) + view_center.y()
                     new_scene_pos = QPointF(sx, sy)
                     item.setPos(new_scene_pos)
                     self.data.atoms[atom_id]['pos'] = new_scene_pos
@@ -3686,6 +3692,7 @@ class MainWindow(QMainWindow):
 
 
     def draw_molecule_3d(self, mol):
+        camera_state = self.plotter.camera.copy()
         self.plotter.clear()
         conf = mol.GetConformer()
         
@@ -3759,6 +3766,8 @@ class MainWindow(QMainWindow):
                     except Exception: pass
                     self.plotter.add_point_labels(np.array(pts), labels, font_size=20, point_size=0, text_color='k', name='chiral_labels', always_visible=True, tolerance=0.01, show_points=False)
             except Exception as e: self.statusBar().showMessage(f"3D chiral label drawing error: {e}")
+        
+        self.plotter.camera = camera_state
 
 
     def toggle_chiral_labels_display(self, checked):

{moleditpy-1.2.2 → moleditpy-1.2.4}/src/moleditpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.2.2
+Version: 1.2.4
 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