moleditpy 1.9.0__tar.gz → 1.9.2__tar.gz

{moleditpy-1.9.0 → moleditpy-1.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.0
+Version: 1.9.2
 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-1.9.0 → moleditpy-1.9.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "moleditpy"
 
-version = "1.9.0"
+version = "1.9.2"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy-1.9.0 → moleditpy-1.9.2}/src/moleditpy/main.py

@@ -11,7 +11,7 @@ DOI 10.5281/zenodo.17268532
 """
 
 #Version
-VERSION = '1.9.0'
+VERSION = '1.9.2'
 
 print("-----------------------------------------------------")
 print("MoleditPy — A Python-based molecular editing software")
@@ -37,7 +37,7 @@ from PyQt6.QtWidgets import (
     QPushButton, QSplitter, QGraphicsView, QGraphicsScene, QGraphicsItem,
     QToolBar, QStatusBar, QGraphicsTextItem, QGraphicsLineItem, QDialog, QGridLayout,
     QFileDialog, QSizePolicy, QLabel, QLineEdit, QToolButton, QMenu, QMessageBox, QInputDialog,
-    QColorDialog, QCheckBox, QSlider, QFormLayout, QRadioButton, QComboBox, QListWidget, QListWidgetItem, QButtonGroup, QTabWidget, QScrollArea
+    QColorDialog, QCheckBox, QSlider, QFormLayout, QRadioButton, QComboBox, QListWidget, QListWidgetItem, QButtonGroup, QTabWidget, QScrollArea, QFrame
 )
 
 from PyQt6.QtGui import (
@@ -58,7 +58,14 @@ from rdkit.Chem import rdMolDescriptors
 
 
 # Open Babel Python binding (optional; required for fallback)
-from openbabel import pybel
+try:
+    from openbabel import pybel
+    OBABEL_AVAILABLE = True
+except Exception:
+    # pybel (Open Babel Python bindings) is optional. If not present, disable OBabel features.
+    pybel = None
+    OBABEL_AVAILABLE = False
+    print("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
 
 # PyVista
 import pyvista as pv
@@ -1025,9 +1032,6 @@ class TranslationDialog(Dialog3DPickingMixin, QDialog):
             # 移動ベクトルを計算
             translation_vector = target_pos - current_centroid
 
-            # Undo状態を保存
-            self.main_window.push_undo_state()
-
             # 全原子を平行移動
             conf = self.mol.GetConformer()
             for i in range(self.mol.GetNumAtoms()):
@@ -1036,6 +1040,7 @@ class TranslationDialog(Dialog3DPickingMixin, QDialog):
                 conf.SetAtomPosition(i, new_pos.tolist())
                 self.main_window.atom_positions_3d[i] = new_pos
 
+
             # 3D表示を更新
             self.main_window.draw_molecule_3d(self.mol)
 
@@ -1045,6 +1050,9 @@ class TranslationDialog(Dialog3DPickingMixin, QDialog):
             # Apply後に選択解除
             self.clear_selection()
 
+            # Undo状態を保存
+            self.main_window.push_undo_state()
+
         except Exception as e:
             QMessageBox.critical(self, "Error", f"Failed to apply translation: {str(e)}")
     
@@ -1522,8 +1530,6 @@ class SymmetrizeDialog(QDialog):
         key, point_group = self.get_selected_point_group()
         
         try:
-            # Undo状態を保存（操作前の状態のみ）
-            self.main_window.push_undo_state()
             
             # 現在の分子の座標を取得
             conf = self.mol.GetConformer()
@@ -1544,6 +1550,9 @@ class SymmetrizeDialog(QDialog):
             
             # 3D表示のみを更新
             self.main_window.draw_molecule_3d(self.mol)
+
+            # Undo状態を保存（操作前の状態のみ）
+            self.main_window.push_undo_state()
             
             # 成功メッセージ（ダイアログを閉じる前に表示）
             QMessageBox.information(
@@ -2659,7 +2668,8 @@ class MirrorDialog(QDialog):
             
             plane_names = ["XY", "XZ", "YZ"]
             self.main_window.statusBar().showMessage(f"Molecule mirrored across {plane_names[plane_id]} plane.")
-            
+        
+
         except Exception as e:
             QMessageBox.critical(self, "Error", f"Failed to apply mirror transformation: {str(e)}")
 
@@ -2816,26 +2826,26 @@ class PlanarizationDialog(Dialog3DPickingMixin, QDialog):
         if len(self.selected_atoms) < 3:
             QMessageBox.warning(self, "Warning", "Please select at least 3 atoms for planarization.")
             return
-        
         try:
+
             # 選択された原子の位置を取得
             selected_indices = list(self.selected_atoms)
             selected_positions = self.main_window.atom_positions_3d[selected_indices].copy()
-            
+
             # 重心を計算
             centroid = np.mean(selected_positions, axis=0)
-            
+
             # 重心を原点に移動
             centered_positions = selected_positions - centroid
-            
+
             # 主成分分析で最適な平面を見つける
             # 選択された原子の座標の共分散行列を計算
             cov_matrix = np.cov(centered_positions.T)
             eigenvalues, eigenvectors = np.linalg.eigh(cov_matrix)
-            
+
             # 固有値が最も小さい固有ベクトルが平面の法線方向
             normal_vector = eigenvectors[:, 0]  # 最小固有値に対応する固有ベクトル
-            
+
             # 目標の平面の法線ベクトルを定義
             if self.plane == 'xy':
                 target_normal = np.array([0, 0, 1])  # Z軸方向
@@ -2843,27 +2853,27 @@ class PlanarizationDialog(Dialog3DPickingMixin, QDialog):
                 target_normal = np.array([0, 1, 0])  # Y軸方向
             elif self.plane == 'yz':
                 target_normal = np.array([1, 0, 0])  # X軸方向
-            
+
             # 法線ベクトルの向きを調整（内積が正になるように）
             if np.dot(normal_vector, target_normal) < 0:
                 normal_vector = -normal_vector
-            
+
             # 回転軸と回転角度を計算
             rotation_axis = np.cross(normal_vector, target_normal)
             rotation_axis_norm = np.linalg.norm(rotation_axis)
-            
+
             if rotation_axis_norm > 1e-10:  # 回転が必要な場合
                 rotation_axis = rotation_axis / rotation_axis_norm
                 cos_angle = np.dot(normal_vector, target_normal)
                 cos_angle = np.clip(cos_angle, -1.0, 1.0)
                 rotation_angle = np.arccos(cos_angle)
-                
+
                 # Rodrigues回転公式を使用して全分子を回転
                 def rodrigues_rotation(v, axis, angle):
                     cos_a = np.cos(angle)
                     sin_a = np.sin(angle)
                     return v * cos_a + np.cross(axis, v) * sin_a + axis * np.dot(axis, v) * (1 - cos_a)
-                
+
                 # 分子全体を回転させる
                 conf = self.mol.GetConformer()
                 for i in range(self.mol.GetNumAtoms()):
@@ -2874,13 +2884,16 @@ class PlanarizationDialog(Dialog3DPickingMixin, QDialog):
                     new_pos = rotated_pos + centroid
                     conf.SetAtomPosition(i, new_pos.tolist())
                     self.main_window.atom_positions_3d[i] = new_pos
-            
+
             # 3D表示を更新
             self.main_window.draw_molecule_3d(self.mol)
-            
+
             # キラルラベルを更新
             self.main_window.update_chiral_labels()
-            
+
+            # Undo状態を保存
+            self.main_window.push_undo_state()
+
         except Exception as e:
             QMessageBox.critical(self, "Error", f"Failed to apply planarization: {str(e)}")
     
@@ -3056,27 +3069,27 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         if len(self.selected_atoms) != 2:
             QMessageBox.warning(self, "Warning", "Please select exactly 2 atoms for alignment.")
             return
-        
         try:
+
             selected_list = sorted(list(self.selected_atoms))
             atom1_idx, atom2_idx = selected_list[0], selected_list[1]
-            
+
             conf = self.mol.GetConformer()
-            
+
             # 原子の現在位置を取得
             pos1 = np.array(conf.GetAtomPosition(atom1_idx))
             pos2 = np.array(conf.GetAtomPosition(atom2_idx))
-            
+
             # 最初に全分子を移動して、atom1を原点に配置
             translation = -pos1
             for i in range(self.mol.GetNumAtoms()):
                 current_pos = np.array(conf.GetAtomPosition(i))
                 new_pos = current_pos + translation
                 conf.SetAtomPosition(i, new_pos.tolist())
-            
+
             # atom2の新しい位置を取得（移動後）
             pos2_translated = pos2 + translation
-            
+
             # atom2を選択した軸上に配置するための回転を計算
             axis_vectors = {
                 'x': np.array([1.0, 0.0, 0.0]),
@@ -3126,6 +3139,9 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
             
             # キラルラベルを更新
             self.main_window.update_chiral_labels()
+
+            # Undo状態を保存
+            self.main_window.push_undo_state()
             
             QMessageBox.information(self, "Success", f"Alignment to {self.axis.upper()}-axis completed.")
             
@@ -4903,7 +4919,7 @@ class MoleculeScene(QGraphicsScene):
         return points
 
     def delete_items(self, items_to_delete):
-        """指定されたアイテムセット（原子・結合）を安全に削除する共通メソッド"""
+        """指定されたアイテムセット（原子・結合）を安全な順序で削除する修正版"""
         try:
             if not items_to_delete:
                 return False
@@ -4916,7 +4932,7 @@ class MoleculeScene(QGraphicsScene):
                 if hasattr(atom, 'bonds'):
                     bonds_to_delete.update(atom.bonds)
 
-            # 影響を受ける（が削除はされない）原子を特定する
+            # 削除はされないが、影響を受ける原子（結合リストの更新が必要）を特定する
             atoms_to_update = set()
             for bond in bonds_to_delete:
                 if bond.atom1 and bond.atom1 not in atoms_to_delete:
@@ -4924,62 +4940,49 @@ class MoleculeScene(QGraphicsScene):
                 if bond.atom2 and bond.atom2 not in atoms_to_delete:
                     atoms_to_update.add(bond.atom2)
 
-            # --- データモデルからの削除 ---
-            # 最初に原子をデータモデルから削除（関連する結合も内部で削除される）
-            for atom in atoms_to_delete:
-                if hasattr(atom, 'atom_id'):
-                    self.data.remove_atom(atom.atom_id)
-                    
-            # 次に、明示的に選択された結合（まだ残っているもの）を削除
-            for bond in bonds_to_delete:
-                if bond.atom1 and bond.atom2 and hasattr(bond.atom1, 'atom_id') and hasattr(bond.atom2, 'atom_id'):
-                    self.data.remove_bond(bond.atom1.atom_id, bond.atom2.atom_id)
-            
-            # --- シーンからのグラフィックアイテム削除（必ず結合を先に）---
-            # まずremoveItem
+            # --- 安全な順序で削除処理を実行 ---
+
+            # 1. まず、生き残る原子の内部状態を更新する
+            for atom in atoms_to_update:
+                if hasattr(atom, 'bonds'):
+                    # これから削除される結合を自身の結合リストから除去する
+                    atom.bonds = [b for b in atom.bonds if b not in bonds_to_delete]
+
+            # 2. 次に、グラフィックシーンからアイテムを削除する（必ず結合を先に）
             for bond in bonds_to_delete:
                 if bond.scene(): 
                     self.removeItem(bond)
-                    
             for atom in atoms_to_delete:
                 if atom.scene(): 
                     self.removeItem(atom)
             
-            # その後BondItem/AtomItemの参照をクリア
+            # 3. データモデル（MolecularData）からデータを削除する
+            # ここでは安全なIDを使って操作する
             for bond in bonds_to_delete:
-                # atom1/atom2のbondsリストからこのbondを除去
-                try:
-                    if bond.atom1 and hasattr(bond.atom1, 'bonds') and bond in bond.atom1.bonds:
-                        bond.atom1.bonds = [b for b in bond.atom1.bonds if b is not bond]
-                    if bond.atom2 and hasattr(bond.atom2, 'bonds') and bond in bond.atom2.bonds:
-                        bond.atom2.bonds = [b for b in bond.atom2.bonds if b is not bond]
-                    # Clear bond references to prevent dangling pointers
-                    bond.atom1 = None
-                    bond.atom2 = None
-                except Exception as bond_cleanup_error:
-                    print(f"Error cleaning up bond references: {bond_cleanup_error}")
-            
+                # 参照が既にクリアされている可能性を考慮
+                if bond.atom1 and bond.atom2:
+                    self.data.remove_bond(bond.atom1.atom_id, bond.atom2.atom_id)
             for atom in atoms_to_delete:
-                # Clear all bond references from deleted atoms
-                try:
-                    if hasattr(atom, 'bonds'):
-                        atom.bonds.clear()
-                except Exception as atom_cleanup_error:
-                    print(f"Error cleaning up atom references: {atom_cleanup_error}")
+                if hasattr(atom, 'atom_id'):
+                    self.data.remove_atom(atom.atom_id)
 
-            # --- 生き残った原子の内部参照とスタイルを更新 ---
+            # 4. 削除されたオブジェクト間の参照をクリアし、メモリ解放を助ける
+            for bond in bonds_to_delete:
+                bond.atom1 = None
+                bond.atom2 = None
+            for atom in atoms_to_delete:
+                if hasattr(atom, 'bonds'):
+                    atom.bonds.clear()
+
+            # 5. 最後に、生き残った原子の表示スタイルを更新する
             for atom in atoms_to_update:
-                try:
-                    if hasattr(atom, 'bonds'):
-                        atom.bonds = [b for b in atom.bonds if b not in bonds_to_delete]
-                    if hasattr(atom, 'update_style'):
-                        atom.update_style()
-                except Exception as update_error:
-                    print(f"Error updating atom style: {update_error}")
+                if hasattr(atom, 'update_style'):
+                    atom.update_style()
                     
-            return True
+            return True # 変更が行われたことを示す
             
         except Exception as e:
+            # 予期せぬエラーが発生した場合でもクラッシュを防ぐ
             print(f"Error during delete_items operation: {e}")
             import traceback
             traceback.print_exc()
@@ -5720,6 +5723,7 @@ class CalculationWorker(QObject):
                 raise ValueError("No atoms to convert.")
             
             self.status_update.emit("Creating 3D structure...")
+
             mol = Chem.MolFromMolBlock(mol_block, removeHs=False)
             if mol is None:
                 raise ValueError("Failed to create molecule from MOL block.")
@@ -5926,6 +5930,9 @@ class CalculationWorker(QObject):
             self.status_update.emit("RDKit embedding failed. Attempting Open Babel fallback...")
 
             try:
+                # Check availability first
+                if not OBABEL_AVAILABLE:
+                    raise RuntimeError("Open Babel (pybel) is not available in this Python environment.")
                 # pybel expects an input format; provide mol block
                 # pybel.readstring accepts format strings like "mol" or "smi"
                 ob_mol = pybel.readstring("mol", mol_block)
@@ -6246,6 +6253,11 @@ class SettingsDialog(QDialog):
             'triple_bond_offset_factor': 2.0,
             'double_bond_radius_factor': 0.8,
             'triple_bond_radius_factor': 0.7,
+            # If True, attempts to be permissive when RDKit raises chemical/sanitization errors
+            # during file import (useful for viewing malformed XYZ/MOL files). When enabled,
+            # element symbol recognition will be coerced where possible and Chem.SanitizeMol
+            # failures will be ignored so the 3D viewer can still display the structure.
+            'skip_chemistry_checks': True,
         }
         
         # --- 選択された色を管理する専用のインスタンス変数 ---
@@ -6258,9 +6270,6 @@ class SettingsDialog(QDialog):
         self.tab_widget = QTabWidget()
         layout.addWidget(self.tab_widget)
         
-        # 基本設定タブ
-        self.create_general_tab()
-        
         # Common設定タブ
         self.create_common_tab()
         
@@ -6276,6 +6285,9 @@ class SettingsDialog(QDialog):
         # Stick設定タブ
         self.create_stick_tab()
 
+        # 基本設定タブ
+        self.create_general_tab()
+
         # 渡された設定でUIと内部変数を初期化
         self.update_ui_from_settings(current_settings)
 
@@ -6366,7 +6378,23 @@ class SettingsDialog(QDialog):
         """Common設定タブを作成"""
         common_widget = QWidget()
         form_layout = QFormLayout(common_widget)
+
+        # 化学チェックスキップオプション（Commonタブに移動）
+        self.skip_chem_checks_checkbox = QCheckBox()
+        self.skip_chem_checks_checkbox.setToolTip("When enabled, file import will try to ignore chemical/sanitization errors and allow viewing malformed files.")
+        # Immediately persist change to settings when user toggles the checkbox
+        try:
+            self.skip_chem_checks_checkbox.stateChanged.connect(lambda s: self._on_skip_chem_checks_changed(s))
+        except Exception:
+            pass
+        form_layout.addRow("Skip chemistry checks on import:", self.skip_chem_checks_checkbox)
         
+        # --- 区切り線（水平ライン） ---
+        line = QFrame()
+        line.setFrameShape(QFrame.Shape.HLine)
+        line.setFrameShadow(QFrame.Shadow.Sunken)
+        form_layout.addRow(line)
+
         # 二重結合オフセット倍率
         self.double_offset_slider = QSlider(Qt.Orientation.Horizontal)
         self.double_offset_slider.setRange(100, 400)  # 1.0 ~ 4.0
@@ -6406,6 +6434,8 @@ class SettingsDialog(QDialog):
         triple_radius_layout.addWidget(self.triple_radius_slider)
         triple_radius_layout.addWidget(self.triple_radius_label)
         form_layout.addRow("Triple Bond Thickness:", triple_radius_layout)
+
+
         
         self.tab_widget.addTab(common_widget, "Common")
     
@@ -6735,6 +6765,9 @@ class SettingsDialog(QDialog):
         triple_radius = int(settings_dict.get('triple_bond_radius_factor', self.default_settings['triple_bond_radius_factor']) * 100)
         self.triple_radius_slider.setValue(triple_radius)
         self.triple_radius_label.setText(f"{triple_radius/100:.2f}")
+        
+        # skip chemistry checks
+        self.skip_chem_checks_checkbox.setChecked(settings_dict.get('skip_chemistry_checks', self.default_settings.get('skip_chemistry_checks', False)))
       
     def select_color(self):
         """カラーピッカーを開き、選択された色を内部変数とUIに反映させる"""
@@ -6777,6 +6810,7 @@ class SettingsDialog(QDialog):
             'triple_bond_offset_factor': self.triple_offset_slider.value() / 100.0,
             'double_bond_radius_factor': self.double_radius_slider.value() / 100.0,
             'triple_bond_radius_factor': self.triple_radius_slider.value() / 100.0,
+            'skip_chemistry_checks': self.skip_chem_checks_checkbox.isChecked(),
         }
 
     def apply_settings(self):
@@ -6792,7 +6826,21 @@ class SettingsDialog(QDialog):
             if hasattr(self.parent_window, 'current_mol') and self.parent_window.current_mol:
                 self.parent_window.draw_molecule_3d(self.parent_window.current_mol)
             # ステータスバーに適用完了を表示
-            self.parent_window.statusBar().showMessage("Settings applied successfully", 2000)
+            self.parent_window.statusBar().showMessage("Settings applied successfully")
+
+    def _on_skip_chem_checks_changed(self, state):
+        """Handle user toggling of skip chemistry checks: persist and update UI.
+
+        state: Qt.Checked (2) or Qt.Unchecked (0)
+        """
+        try:
+            enabled = bool(state)
+            self.settings['skip_chemistry_checks'] = enabled
+            self.save_settings()
+            # If skip is enabled, allow Optimize button; otherwise, respect chem_check flags
+
+        except Exception:
+            pass
 
     def accept(self):
         """ダイアログの設定を適用してから閉じる"""
@@ -7048,7 +7096,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
 
 class MainWindow(QMainWindow):
 
-    start_calculation = pyqtSignal(str)
+    # start_calculation carries the MOL block and a boolean skip_chemistry_checks flag
+    start_calculation = pyqtSignal(str, bool)
     def __init__(self, initial_file=None):
         super().__init__()
         self.setAcceptDrops(True)
@@ -7068,6 +7117,11 @@ class MainWindow(QMainWindow):
         self.atom_actor = None 
         self.is_2d_editable = True
         self.is_xyz_derived = False  # XYZ由来の分子かどうかのフラグ
+        # Chemical check flags: whether a chemical/sanitization check was attempted and whether it failed
+        self.chem_check_tried = False
+        self.chem_check_failed = False
+        # 3D最適化のデフォルト手法
+        self.optimization_method = self.settings.get('optimization_method', 'MMFF_RDKIT')
         self.axes_actor = None
         self.axes_widget = None
         self._template_dialog = None  # テンプレートダイアログの参照
@@ -7699,6 +7753,63 @@ class MainWindow(QMainWindow):
         optimize_3d_action.triggered.connect(self.optimize_3d_structure)
         edit_menu.addAction(optimize_3d_action)
 
+        # --- 3D Optimization Settings submenu (below Optimize 3D) ---
+        opt3d_settings_menu = edit_menu.addMenu("3D Optimization Settings")
+        opt3d_group = QActionGroup(self)
+        opt3d_group.setExclusive(True)
+
+        # Only RDKit-backed optimization methods are offered here.
+        # Open Babel-based optimization options have been removed; Open Babel is
+        # retained only as a conversion fallback when RDKit embedding fails.
+        opt_methods = [
+            ("MMFF", "MMFF_RDKIT"),
+            ("UFF", "UFF_RDKIT"),
+        ]
+
+        # Map key -> human-readable label for status messages and later lookups
+        try:
+            self.opt3d_method_labels = {key.upper(): label for (label, key) in opt_methods}
+        except Exception:
+            self.opt3d_method_labels = {}
+
+        opt_actions = {}
+        for label, key in opt_methods:
+            action = QAction(label, self)
+            action.setCheckable(True)
+            # Ensure explicit association with the action group so exclusive checking works reliably
+            try:
+                action.setActionGroup(opt3d_group)
+            except Exception:
+                # Older PyQt variants may not have setActionGroup; adding to group below still helps
+                pass
+            action.triggered.connect(lambda checked, m=key: self.set_optimization_method(m))
+            opt3d_settings_menu.addAction(action)
+            opt3d_group.addAction(action)
+            opt_actions[key] = action
+
+        # Persist the actions mapping so other methods can update the checked state
+        self.opt3d_actions = opt_actions
+
+        # Determine the initial checked menu item from saved settings (fall back to MMFF_RDKIT)
+        try:
+            saved = (self.settings.get('optimization_method') or self.optimization_method or 'MMFF_RDKIT').upper()
+        except Exception:
+            saved = 'MMFF_RDKIT'
+
+        if saved in self.opt3d_actions and self.opt3d_actions[saved].isEnabled():
+            self.opt3d_actions[saved].setChecked(True)
+            # Ensure internal state matches
+            self.optimization_method = saved
+        else:
+            # fallback
+            if 'MMFF_RDKIT' in self.opt3d_actions:
+                self.opt3d_actions['MMFF_RDKIT'].setChecked(True)
+                self.optimization_method = 'MMFF_RDKIT'
+
+        # Note: Open Babel-based optimization menu entries were intentionally
+        # removed above. Open Babel (pybel) is still available for conversion
+        # fallback elsewhere in the code, so we don't disable menu items here.
+
         edit_menu.addSeparator()
         
         # Templates
@@ -8058,6 +8169,53 @@ class MainWindow(QMainWindow):
         if self.current_mol:
             self.draw_molecule_3d(self.current_mol)
 
+    def set_optimization_method(self, method_name):
+        """Set preferred 3D optimization method and persist to settings.
+
+        Supported values: 'GAFF', 'MMFF'
+        """
+        # Normalize input and validate
+        if not method_name:
+            return
+        method = str(method_name).strip().upper()
+        valid_methods = (
+            'MMFF_RDKIT', 'UFF_RDKIT',
+            'UFF_OBABEL', 'GAFF_OBABEL', 'MMFF94_OBABEL', 'GHEMICAL_OBABEL'
+        )
+        if method not in valid_methods:
+            # Unknown method: ignore but notify
+            self.statusBar().showMessage(f"Unknown 3D optimization method: {method_name}")
+            return
+
+        # Update internal state (store canonical uppercase key)
+        self.optimization_method = method
+
+        # Persist to settings
+        try:
+            self.settings['optimization_method'] = self.optimization_method
+            self.save_settings()
+        except Exception:
+            pass
+
+        # Update menu checked state if actions mapping exists
+        try:
+            if hasattr(self, 'opt3d_actions') and self.opt3d_actions:
+                for k, act in self.opt3d_actions.items():
+                    try:
+                        # keys in opt3d_actions may be mixed-case; compare uppercased
+                        act.setChecked(k.upper() == method)
+                    except Exception:
+                        pass
+        except Exception:
+            pass
+
+        # Also show user-friendly label if available
+        try:
+            label = self.opt3d_method_labels.get(self.optimization_method, self.optimization_method)
+        except Exception:
+            label = self.optimization_method
+        self.statusBar().showMessage(f"3D optimization method set to: {label}")
+
     def copy_selection(self):
         """選択された原子と結合をクリップボードにコピーする"""
         try:
@@ -8109,13 +8267,13 @@ class MainWindow(QMainWindow):
             mime_data = QMimeData()
             mime_data.setData(CLIPBOARD_MIME_TYPE, byte_array)
             QApplication.clipboard().setMimeData(mime_data)
-            self.statusBar().showMessage(f"Copied {len(fragment_atoms)} atoms and {len(fragment_bonds)} bonds.", 2000)
+            self.statusBar().showMessage(f"Copied {len(fragment_atoms)} atoms and {len(fragment_bonds)} bonds.")
             
         except Exception as e:
             print(f"Error during copy operation: {e}")
             import traceback
             traceback.print_exc()
-            self.statusBar().showMessage(f"Error during copy operation: {e}", 5000)
+            self.statusBar().showMessage(f"Error during copy operation: {e}")
 
     def cut_selection(self):
         """選択されたアイテムを切り取り（コピーしてから削除）"""
@@ -8135,7 +8293,7 @@ class MainWindow(QMainWindow):
             print(f"Error during cut operation: {e}")
             import traceback
             traceback.print_exc()
-            self.statusBar().showMessage(f"Error during cut operation: {e}", 5000)
+            self.statusBar().showMessage(f"Error during cut operation: {e}")
 
     def paste_from_clipboard(self):
         """クリップボードから分子フラグメントを貼り付け"""
@@ -8150,7 +8308,7 @@ class MainWindow(QMainWindow):
             try:
                 fragment_data = pickle.load(buffer)
             except pickle.UnpicklingError:
-                self.statusBar().showMessage("Error: Invalid clipboard data format", 3000)
+                self.statusBar().showMessage("Error: Invalid clipboard data format")
                 return
             
             paste_center_pos = self.view_2d.mapToScene(self.view_2d.mapFromGlobal(QCursor.pos()))
@@ -8184,7 +8342,7 @@ class MainWindow(QMainWindow):
             print(f"Error during paste operation: {e}")
             import traceback
             traceback.print_exc()
-            self.statusBar().showMessage(f"Error during paste operation: {e}", 5000)
+            self.statusBar().showMessage(f"Error during paste operation: {e}")
         self.statusBar().showMessage(f"Pasted {len(new_atoms)} atoms.", 2000)
         self.activate_select_mode()
 
@@ -8207,13 +8365,13 @@ class MainWindow(QMainWindow):
                 self.push_undo_state()
                 self.statusBar().showMessage(f"Removed {len(hydrogen_atoms)} hydrogen atoms.", 2000)
             else:
-                self.statusBar().showMessage("Failed to remove hydrogen atoms.", 3000)
+                self.statusBar().showMessage("Failed to remove hydrogen atoms.")
                 
         except Exception as e:
             print(f"Error during hydrogen removal: {e}")
             import traceback
             traceback.print_exc()
-            self.statusBar().showMessage(f"Error removing hydrogen atoms: {e}", 5000)
+            self.statusBar().showMessage(f"Error removing hydrogen atoms: {e}")
 
     def update_edit_menu_actions(self):
         """選択状態やクリップボードの状態に応じて編集メニューを更新"""
@@ -8245,7 +8403,7 @@ class MainWindow(QMainWindow):
             return
 
         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
         if not mol or mol.GetNumAtoms() == 0:
             # RDKitでの変換に失敗した場合は、独自の化学的問題チェックを実行
@@ -8269,7 +8427,7 @@ class MainWindow(QMainWindow):
             self.statusBar().showMessage(f"Error: {len(problems)} chemistry problem(s) found.")
             # 既存の選択状態をクリア
             self.scene.clearSelection() 
-            
+
             # 問題のある原子に赤枠フラグを立てる
             for prob in problems:
                 atom_idx = prob.GetAtomIdx()
@@ -8281,7 +8439,7 @@ class MainWindow(QMainWindow):
                         item = self.data.atoms[original_id]['item']
                         item.has_problem = True 
                         item.update()
-                
+
             self.view_2d.setFocus()
             return
 
@@ -8360,7 +8518,12 @@ class MainWindow(QMainWindow):
         )
         text_actor.GetTextProperty().SetOpacity(1)
         self.plotter.render()
-        self.start_calculation.emit(mol_block)
+        # Emit skip flag so the worker can ignore sanitization errors if user requested
+        self.start_calculation.emit(mol_block, False)
+
+        # 状態をUndo履歴に保存
+        self.push_undo_state()
+        self.update_chiral_labels()
         
         self.view_2d.setFocus()
 
@@ -8427,33 +8590,91 @@ class MainWindow(QMainWindow):
             self.statusBar().showMessage("No 3D molecule to optimize.")
             return
 
+        # If a prior chemical/sanitization check was attempted and failed, do not run optimization
+        if getattr(self, 'chem_check_tried', False) and getattr(self, 'chem_check_failed', False):
+            self.statusBar().showMessage("3D optimization disabled: molecule failed chemical sanitization.")
+            # Ensure the Optimize 3D button is disabled to reflect this
+            if hasattr(self, 'optimize_3d_button'):
+                try:
+                    self.optimize_3d_button.setEnabled(False)
+                except Exception:
+                    pass
+            return
+
         self.statusBar().showMessage("Optimizing 3D structure...")
         QApplication.processEvents() # UIの更新を確実に行う
 
         try:
-            # MMFF力場での最適化を試みる
-            AllChem.MMFFOptimizeMolecule(self.current_mol)
-        except Exception:
-            # MMFFが失敗した場合、UFF力場でフォールバック
-            try:
-                AllChem.UFFOptimizeMolecule(self.current_mol)
-            except Exception as e:
-                self.statusBar().showMessage(f"3D optimization failed: {e}")
+            method = getattr(self, 'optimization_method', 'MMFF_RDKIT')
+            method = method.upper() if method else 'MMFF_RDKIT'
+            # 事前チェック：コンフォーマがあるか
+            if self.current_mol.GetNumConformers() == 0:
+                self.statusBar().showMessage("No conformer found: cannot optimize. Embed molecule first.")
                 return
+            if method == 'MMFF_RDKIT':
+                try:
+                    res = AllChem.MMFFOptimizeMolecule(self.current_mol, maxIters=2000)
+                    if res != 0:
+                        # 非収束や何らかの問題が起きた可能性 -> ForceField API で詳細に試す
+                        try:
+                            mmff_props = AllChem.MMFFGetMoleculeProperties(self.current_mol)
+                            ff = AllChem.MMFFGetMoleculeForceField(self.current_mol, mmff_props, confId=0)
+                            ff_ret = ff.Minimize(maxIts=2000)
+                            if ff_ret != 0:
+                                self.statusBar().showMessage(f"MMFF minimize returned non-zero status: {ff_ret}")
+                                return
+                        except Exception as e:
+                            self.statusBar().showMessage(f"MMFF parameterization/minimize failed: {e}")
+                            return
+                except Exception as e:
+                    self.statusBar().showMessage(f"MMFF (RDKit) optimization error: {e}")
+                    return
+            elif method == 'UFF_RDKIT':
+                try:
+                    res = AllChem.UFFOptimizeMolecule(self.current_mol, maxIters=2000)
+                    if res != 0:
+                        try:
+                            ff = AllChem.UFFGetMoleculeForceField(self.current_mol, confId=0)
+                            ff_ret = ff.Minimize(maxIts=2000)
+                            if ff_ret != 0:
+                                self.statusBar().showMessage(f"UFF minimize returned non-zero status: {ff_ret}")
+                                return
+                        except Exception as e:
+                            self.statusBar().showMessage(f"UFF parameterization/minimize failed: {e}")
+                            return
+                except Exception as e:
+                    self.statusBar().showMessage(f"UFF (RDKit) optimization error: {e}")
+                    return
+            else:
+                self.statusBar().showMessage("Selected optimization method is not available. Use MMFF (RDKit) or UFF (RDKit).")
+                return
+        except Exception as e:
+            self.statusBar().showMessage(f"3D optimization error: {e}")
         
         # 最適化後の構造で3Dビューを再描画
         try:
             # 3D最適化後は3D座標から立体化学を再計算（2回目以降は3D優先）
             if self.current_mol.GetNumConformers() > 0:
                 Chem.AssignAtomChiralTagsFromStructure(self.current_mol, confId=0)
-            
             self.update_chiral_labels() # キラル中心のラベルも更新
         except Exception:
             pass
             
         self.draw_molecule_3d(self.current_mol)
         
-        self.statusBar().showMessage("3D structure optimization successful.")
+        # Show which method was used in the status bar (prefer human-readable label)
+        try:
+            used_method = getattr(self, 'optimization_method', None)
+            used_label = None
+            if used_method:
+                used_label = (getattr(self, 'opt3d_method_labels', {}) or {}).get(used_method.upper(), used_method)
+        except Exception:
+            used_label = None
+
+        if used_label:
+            self.statusBar().showMessage(f"3D structure optimization successful. Method: {used_label}")
+        else:
+            self.statusBar().showMessage("3D structure optimization successful.")
         self.push_undo_state() # Undo履歴に保存
         self.view_2d.setFocus()
 
@@ -9253,13 +9474,13 @@ class MainWindow(QMainWindow):
             self.update_window_title()
 
         except FileNotFoundError:
-            self.statusBar().showMessage(f"File not found: {file_path}", 5000)
+            self.statusBar().showMessage(f"File not found: {file_path}")
             self.restore_ui_for_editing()
         except ValueError as e:
-            self.statusBar().showMessage(f"Invalid 3D MOL file: {e}", 5000)
+            self.statusBar().showMessage(f"Invalid 3D MOL file: {e}")
             self.restore_ui_for_editing()
         except Exception as e:
-            self.statusBar().showMessage(f"Error loading 3D file: {e}", 5000)
+            self.statusBar().showMessage(f"Error loading 3D file: {e}")
             self.restore_ui_for_editing()
             import traceback
             traceback.print_exc()
@@ -9310,13 +9531,13 @@ class MainWindow(QMainWindow):
             self.update_window_title()
 
         except FileNotFoundError:
-            self.statusBar().showMessage(f"File not found: {file_path}", 5000)
+            self.statusBar().showMessage(f"File not found: {file_path}")
             self.restore_ui_for_editing()
         except ValueError as e:
-            self.statusBar().showMessage(f"Invalid XYZ file: {e}", 5000)
+            self.statusBar().showMessage(f"Invalid XYZ file: {e}")
             self.restore_ui_for_editing()
         except Exception as e:
-            self.statusBar().showMessage(f"Error loading XYZ file: {e}", 5000)
+            self.statusBar().showMessage(f"Error loading XYZ file: {e}")
             self.restore_ui_for_editing()
             import traceback
             traceback.print_exc()
@@ -9374,13 +9595,17 @@ class MainWindow(QMainWindow):
                 try:
                     # RDKitで認識される元素かどうかをチェック
                     test_atom = Chem.Atom(symbol)
-                except:
+                except Exception:
                     # 認識されない場合、最初の文字を大文字にして再試行
                     symbol = symbol.capitalize()
                     try:
                         test_atom = Chem.Atom(symbol)
-                    except:
-                        raise ValueError(f"Unrecognized element symbol: {parts[0]} at line {i+3}")
+                    except Exception:
+                        # If user requested to skip chemistry checks, coerce unknown symbols to C
+                        if self.settings.get('skip_chemistry_checks', False):
+                            symbol = 'C'
+                        else:
+                            raise ValueError(f"Unrecognized element symbol: {parts[0]} at line {i+3}")
                 
                 try:
                     x, y, z = float(parts[1]), float(parts[2]), float(parts[3])
@@ -9411,13 +9636,14 @@ class MainWindow(QMainWindow):
             # 結合を推定（距離ベース）
             self.estimate_bonds_from_distances(mol)
             
-            # 分子を最終化
+                # 分子を最終化
             try:
                 mol = mol.GetMol()
                 # 基本的な妥当性チェック
                 if mol is None:
                     raise ValueError("Failed to create valid molecule object")
-                Chem.SanitizeMol(mol)
+                # Centralized chemical/sanitization handling
+                self._apply_chem_check_and_set_flags(mol, source_desc='XYZ')
             except Exception as e:
                 # 化学的に不正な構造でも表示は可能にする
                 mol = mol.GetMol()
@@ -9506,9 +9732,10 @@ class MainWindow(QMainWindow):
         if not self.data.atoms and not self.current_mol: 
             self.statusBar().showMessage("Error: Nothing to save.")
             return
-            
-        if self.current_file_path:
-            # 既存のファイルに上書き保存
+        # 非ネイティブ形式（.mol, .sdf, .xyz など）は上書き保存せず、必ず「名前を付けて保存」にする
+        native_exts = ['.pmeprj', '.pmeraw']
+        if self.current_file_path and any(self.current_file_path.lower().endswith(ext) for ext in native_exts):
+            # 既存のPMEPRJ/PMERAWファイルの場合は上書き保存
             try:
                 if self.current_file_path.lower().endswith('.pmeraw'):
                     # 既存のPMERAWファイルの場合はPMERAW形式で保存
@@ -9536,7 +9763,7 @@ class MainWindow(QMainWindow):
                 import traceback
                 traceback.print_exc()
         else:
-            # ファイルパスがない場合は名前を付けて保存
+            # MOL/SDF/XYZなどは上書き保存せず、必ず「名前を付けて保存」にする
             self.save_project_as()
 
     def save_project_as(self):
@@ -10564,7 +10791,7 @@ class MainWindow(QMainWindow):
 
     def export_2d_png(self):
         if not self.data.atoms:
-            self.statusBar().showMessage("Nothing to export.", 2000)
+            self.statusBar().showMessage("Nothing to export.")
             return
 
         options = QFileDialog.Option.DontUseNativeDialog
@@ -10605,7 +10832,7 @@ class MainWindow(QMainWindow):
                     molecule_bounds = molecule_bounds.united(item.sceneBoundingRect())
 
             if molecule_bounds.isEmpty() or not molecule_bounds.isValid():
-                self.statusBar().showMessage("Error: Could not determine molecule bounds for export.", 5000)
+                self.statusBar().showMessage("Error: Could not determine molecule bounds for export.")
                 return
 
             if is_transparent:
@@ -10619,7 +10846,7 @@ class MainWindow(QMainWindow):
             h = max(1, int(math.ceil(rect_to_render.height())))
 
             if w <= 0 or h <= 0:
-                self.statusBar().showMessage("Error: Invalid image size calculated.", 5000)
+                self.statusBar().showMessage("Error: Invalid image size calculated.")
                 return
 
             image = QImage(w, h, QImage.Format.Format_ARGB32_Premultiplied)
@@ -10631,7 +10858,7 @@ class MainWindow(QMainWindow):
             painter = QPainter()
             ok = painter.begin(image)
             if not ok or not painter.isActive():
-                self.statusBar().showMessage("Failed to start QPainter for image rendering.", 5000)
+                self.statusBar().showMessage("Failed to start QPainter for image rendering.")
                 return
 
             try:
@@ -10644,12 +10871,12 @@ class MainWindow(QMainWindow):
 
             saved = image.save(filePath, "PNG")
             if saved:
-                self.statusBar().showMessage(f"2D view exported to {filePath}", 3000)
+                self.statusBar().showMessage(f"2D view exported to {filePath}")
             else:
-                self.statusBar().showMessage(f"Failed to save image. Check file path or permissions.", 5000)
+                self.statusBar().showMessage(f"Failed to save image. Check file path or permissions.")
 
         except Exception as e:
-            self.statusBar().showMessage(f"An unexpected error occurred during 2D export: {e}", 5000)
+            self.statusBar().showMessage(f"An unexpected error occurred during 2D export: {e}")
 
         finally:
             for item, was_visible in items_to_restore.items():
@@ -10686,7 +10913,7 @@ class MainWindow(QMainWindow):
             self.plotter.screenshot(filePath, transparent_background=is_transparent)
             self.statusBar().showMessage(f"3D view exported to {filePath}", 3000)
         except Exception as e:
-            self.statusBar().showMessage(f"Error exporting 3D PNG: {e}", 3000)
+            self.statusBar().showMessage(f"Error exporting 3D PNG: {e}")
 
 
     def open_periodic_table_dialog(self):
@@ -11071,6 +11298,8 @@ class MainWindow(QMainWindow):
                 begin_color_rgb = [int(c * 255) for c in begin_color]
                 end_color_rgb = [int(c * 255) for c in end_color]
 
+                # UI応答性維持のためイベント処理
+                QApplication.processEvents()
                 if bt == Chem.rdchem.BondType.SINGLE or bt == Chem.rdchem.BondType.AROMATIC:
                     if self.current_3d_style == 'ball_and_stick':
                         # Ball and stickは全結合をまとめて処理（高速化）
@@ -11726,6 +11955,46 @@ class MainWindow(QMainWindow):
         # 調査の結果、'style' プロパティへの代入が正しい設定方法と判明
         self.plotter.interactor.SetInteractorStyle(style)
         self.plotter.interactor.Initialize()
+
+    def _apply_chem_check_and_set_flags(self, mol, source_desc=None):
+        """Central helper to apply chemical sanitization (or skip it) and set
+        chem_check_tried / chem_check_failed flags consistently.
+
+        When sanitization fails, a warning is shown and the Optimize 3D button
+        is disabled. If the user setting 'skip_chemistry_checks' is True, no
+        sanitization is attempted and both flags remain False.
+        """
+        try:
+            self.chem_check_tried = False
+            self.chem_check_failed = False
+        except Exception:
+            # Ensure attributes exist even if called very early
+            self.chem_check_tried = False
+            self.chem_check_failed = False
+
+        if self.settings.get('skip_chemistry_checks', False):
+            # User asked to skip chemistry checks entirely
+            return
+
+        try:
+            Chem.SanitizeMol(mol)
+            self.chem_check_tried = True
+            self.chem_check_failed = False
+        except Exception:
+            # Mark that we tried sanitization and it failed
+            self.chem_check_tried = True
+            self.chem_check_failed = True
+            try:
+                desc = f" ({source_desc})" if source_desc else ''
+                self.statusBar().showMessage(f"Molecule sanitization failed{desc}; file may be malformed.")
+            except Exception:
+                pass
+            # Disable 3D optimization UI to prevent running on invalid molecules
+            if hasattr(self, 'optimize_3d_button'):
+                try:
+                    self.optimize_3d_button.setEnabled(False)
+                except Exception:
+                    pass
         
     def load_mol_file_for_3d_viewing(self, file_path=None):
         """MOL/SDFファイルを3Dビューアーで開く"""
@@ -11755,13 +12024,28 @@ class MainWindow(QMainWindow):
             if mol.GetNumConformers() == 0:
                 self.statusBar().showMessage("No 3D coordinates found. Converting to 3D...")
                 try:
-                    AllChem.EmbedMolecule(mol)
-                    # 最適化は実行しない
+                    try:
+                        AllChem.EmbedMolecule(mol)
+                        # 最適化は実行しない
+                        # 3D変換直後にUndoスタックに積む
+                        self.current_mol = mol
+                        self.push_undo_state()
+                    except Exception as e_embed:
+                        # If skipping chemistry checks, allow molecule to be displayed without 3D embedding
+                        if self.settings.get('skip_chemistry_checks', False):
+                            self.statusBar().showMessage("Warning: failed to generate 3D coordinates but skip_chemistry_checks is enabled; continuing.")
+                            # Keep mol as-is (may lack conformer); downstream code checks for conformers
+                        else:
+                            raise
                 except:
                     self.statusBar().showMessage("Failed to generate 3D coordinates")
                     return
             
             # 3Dビューアーに表示
+            # Centralized chemical/sanitization handling
+            # Ensure the skip_chemistry_checks setting is respected and flags are set
+            self._apply_chem_check_and_set_flags(mol, source_desc='MOL/SDF')
+
             self.current_mol = mol
             self.draw_molecule_3d(mol)
             
@@ -11888,7 +12172,14 @@ class MainWindow(QMainWindow):
         
         for action_name in basic_3d_actions:
             if hasattr(self, action_name):
-                getattr(self, action_name).setEnabled(enabled)
+                # If enabling globally but chemical sanitization failed earlier, keep Optimize 3D disabled
+                if enabled and action_name == 'optimize_3d_button' and getattr(self, 'chem_check_tried', False) and getattr(self, 'chem_check_failed', False):
+                    try:
+                        getattr(self, action_name).setEnabled(False)
+                    except Exception:
+                        pass
+                else:
+                    getattr(self, action_name).setEnabled(enabled)
         
         # 3D Selectボタンは常に有効にする
         if hasattr(self, 'measurement_action'):
@@ -13884,14 +14175,14 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):
             QMessageBox.warning(self, "Invalid Input", "Please enter a valid number.")
             return
         
-        # Undo状態を保存
-        self.main_window.push_undo_state()
-        
         # Apply the dihedral angle change
         self.adjust_dihedral(new_dihedral)
         
         # キラルラベルを更新
         self.main_window.update_chiral_labels()
+
+        # Undo状態を保存
+        self.main_window.push_undo_state()
     
     def adjust_dihedral(self, new_dihedral_deg):
         """二面角を調整（改善されたアルゴリズム）"""

{moleditpy-1.9.0 → moleditpy-1.9.2}/src/moleditpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moleditpy
-Version: 1.9.0
+Version: 1.9.2
 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