moleditpy 2.6.0__tar.gz → 2.6.1__tar.gz

{moleditpy-2.6.0 → moleditpy-2.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.6.0
+Version: 2.6.1
 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-2.6.0 → moleditpy-2.6.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.6.0"
+version = "2.6.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.6.0
+Version: 2.6.1
 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-2.6.0 → moleditpy-2.6.1}/src/MoleditPy.egg-info/SOURCES.txt

@@ -62,6 +62,7 @@ src/moleditpy/modules/plugin_interface.py
 src/moleditpy/modules/plugin_manager.py
 src/moleditpy/modules/plugin_manager_window.py
 src/moleditpy/modules/settings_dialog.py
+src/moleditpy/modules/sip_isdeleted_safe.py
 src/moleditpy/modules/template_preview_item.py
 src/moleditpy/modules/template_preview_view.py
 src/moleditpy/modules/translation_dialog.py

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/moleditpy/main.py

@@ -11,8 +11,8 @@ DOI: 10.5281/zenodo.17268532
 """
 
 
-import sys
 import ctypes
+import sys
 
 from PyQt6.QtWidgets import QApplication
 

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/moleditpy/modules/__init__.py

@@ -10,24 +10,14 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-
-# Open Babel Python binding (optional; required for fallback)
-# Do not import `pybel` at module import time. Only expose the presence
-# of Open Babel via `OBABEL_AVAILABLE`. Modules should import `pybel`
-# lazily if and when they need it.
 try: # pragma: no cover
     import importlib.util
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except Exception:
     OBABEL_AVAILABLE = False
 
-# Optional SIP helper: on some PyQt6 builds sip.isdeleted is available and
-# allows safely detecting C++ wrapper objects that have been deleted. Import
-# it once at module import time and expose a small, robust wrapper so callers
-# can avoid re-importing sip repeatedly and so we centralize exception
-# handling (this reduces crash risk during teardown and deletion operations).
 try: # pragma: no cover
-    import sip as _sip  # type: ignore
+    from PyQt6 import sip as _sip  # type: ignore
     _sip_isdeleted = getattr(_sip, 'isdeleted', None)
 except Exception:
     _sip = None

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/moleditpy/modules/about_dialog.py

@@ -10,12 +10,12 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QLabel, QPushButton, QHBoxLayout
-)
-from PyQt6.QtGui import QPixmap, QPainter, QPen, QCursor
-from PyQt6.QtCore import Qt
 import os
+
+from PyQt6.QtCore import Qt
+from PyQt6.QtGui import QCursor, QPainter, QPen, QPixmap
+from PyQt6.QtWidgets import QDialog, QHBoxLayout, QLabel, QPushButton, QVBoxLayout
+
 try:
     from .constants import VERSION
 except Exception:
@@ -28,14 +28,14 @@ class AboutDialog(QDialog): # pragma: no cover
         self.setWindowTitle("About MoleditPy")
         self.setFixedSize(250, 300)
         self.init_ui()
-    
+
     def init_ui(self):
         layout = QVBoxLayout(self)
-        
+
         # Create a clickable image label
         self.image_label = QLabel()
         self.image_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
-        
+
         # Load the original icon image
         icon_path = os.path.join(os.path.dirname(__file__), '..', 'assets', 'icon.png')
         if os.path.exists(icon_path):
@@ -50,7 +50,7 @@ class AboutDialog(QDialog): # pragma: no cover
             painter.setPen(QPen(Qt.GlobalColor.black, 2))
             painter.drawText(pixmap.rect(), Qt.AlignmentFlag.AlignCenter, "MoleditPy")
             painter.end()
-        
+
         self.image_label.setPixmap(pixmap)
         try:
             self.image_label.setCursor(QCursor(Qt.CursorShape.ArrowCursor))
@@ -58,27 +58,27 @@ class AboutDialog(QDialog): # pragma: no cover
             pass
 
         self.image_label.mousePressEvent = self.image_mouse_press_event
-        
+
         layout.addWidget(self.image_label)
-        
+
         # Add text information
         info_text = f"MoleditPy Ver. {VERSION}\nAuthor: Hiromichi Yokoyama\nLicense: GPL-3.0 license"
         info_label = QLabel(info_text)
         info_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
         layout.addWidget(info_label)
-        
+
         # Add OK button
         ok_button = QPushButton("OK")
         ok_button.setFixedSize(80, 30)  # 小さいサイズに固定
         ok_button.clicked.connect(self.accept)
-        
+
         # Center the button
         button_layout = QHBoxLayout()
         button_layout.addStretch()
         button_layout.addWidget(ok_button)
         button_layout.addStretch()
         layout.addLayout(button_layout)
-    
+
     def image_clicked(self, event):
         """Easter egg: Clear all and load bipyrimidine from SMILES"""
         # Clear the current scene

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/moleditpy/modules/align_plane_dialog.py

@@ -10,11 +10,16 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+import numpy as np
+from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QLabel, QHBoxLayout, QPushButton, QMessageBox
+    QDialog,
+    QHBoxLayout,
+    QLabel,
+    QMessageBox,
+    QPushButton,
+    QVBoxLayout,
 )
-from PyQt6.QtCore import Qt
-import numpy as np
 
 try:
     from .dialog3_d_picking_mixin import Dialog3DPickingMixin
@@ -29,47 +34,47 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
         self.main_window = main_window
         self.plane = plane
         self.selected_atoms = set()
-        
+
         # 事前選択された原子を追加
         if preselected_atoms:
             self.selected_atoms.update(preselected_atoms)
-        
+
         self.init_ui()
-        
+
         # 事前選択された原子にラベルを追加
         if self.selected_atoms:
             self.show_atom_labels()
             self.update_display()
-    
+
     def init_ui(self):
         plane_names = {'xy': 'XY', 'xz': 'XZ', 'yz': 'YZ'}
         self.setWindowTitle(f"Align to {plane_names[self.plane]} Plane")
         self.setModal(False)
         layout = QVBoxLayout(self)
-        
+
         # Instructions
         instruction_label = QLabel(f"Click atoms in the 3D view to select them for align to the {plane_names[self.plane]} plane. At least 3 atoms are required.")
         instruction_label.setWordWrap(True)
         layout.addWidget(instruction_label)
-        
+
         # Selected atoms display
         self.selection_label = QLabel("No atoms selected")
         layout.addWidget(self.selection_label)
-        
+
         # Buttons
         button_layout = QHBoxLayout()
         self.clear_button = QPushButton("Clear Selection")
         self.clear_button.clicked.connect(self.clear_selection)
         button_layout.addWidget(self.clear_button)
-        
+
         # Select all atoms button
         self.select_all_button = QPushButton("Select All Atoms")
         self.select_all_button.setToolTip("Select all atoms in the molecule for alignment")
         self.select_all_button.clicked.connect(self.select_all_atoms)
         button_layout.addWidget(self.select_all_button)
-        
+
         button_layout.addStretch()
-        
+
         self.apply_button = QPushButton("Apply align")
         self.apply_button.clicked.connect(self.apply_PlaneAlign)
         self.apply_button.setEnabled(False)
@@ -78,35 +83,35 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
         close_button = QPushButton("Close")
         close_button.clicked.connect(self.reject)
         button_layout.addWidget(close_button)
-        
+
         layout.addLayout(button_layout)
-        
+
         # Connect to main window's picker
         self.picker_connection = None
         self.enable_picking()
-    
+
     def enable_picking(self):
         """3Dビューでの原子選択を有効にする"""
         self.main_window.plotter.interactor.installEventFilter(self)
         self.picking_enabled = True
-    
+
     def disable_picking(self):
         """3Dビューでの原子選択を無効にする"""
         if hasattr(self, 'picking_enabled') and self.picking_enabled:
             self.main_window.plotter.interactor.removeEventFilter(self)
             self.picking_enabled = False
-    
+
     def on_atom_picked(self, atom_idx):
         """原子がピックされたときの処理"""
         if atom_idx in self.selected_atoms:
             self.selected_atoms.remove(atom_idx)
         else:
             self.selected_atoms.add(atom_idx)
-        
+
         # 原子ラベルを表示
         self.show_atom_labels()
         self.update_display()
-    
+
     def keyPressEvent(self, event):
         """キーボードイベントを処理"""
         if event.key() == Qt.Key.Key_Return or event.key() == Qt.Key.Key_Enter:
@@ -115,13 +120,13 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
             event.accept()
         else:
             super().keyPressEvent(event)
-    
+
     def clear_selection(self):
         """選択をクリア"""
         self.selected_atoms.clear()
         self.clear_atom_labels()
         self.update_display()
-    
+
     def select_all_atoms(self):
         """Select all atoms in the current molecule and update labels/UI."""
         try:
@@ -144,7 +149,7 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
 
         except Exception as e:
             QMessageBox.warning(self, "Warning", f"Failed to select all atoms: {e}")
-    
+
     def update_display(self):
         """表示を更新"""
         count = len(self.selected_atoms)
@@ -157,10 +162,10 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
             for i, atom_idx in enumerate(atom_list):
                 symbol = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
                 atom_display.append(f"#{i+1}: {symbol}({atom_idx})")
-            
+
             self.selection_label.setText(f"Selected {count} atoms: {', '.join(atom_display)}")
             self.apply_button.setEnabled(count >= 3)
-    
+
     def show_atom_labels(self):
         """選択された原子にラベルを表示"""
         if self.selected_atoms:
@@ -169,7 +174,7 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
             self.show_atom_labels_for(pairs, color='blue')
         else:
             self.clear_atom_labels()
-    
+
     def apply_PlaneAlign(self):
         """alignを適用（回転ベース）"""
         if len(self.selected_atoms) < 3:
@@ -202,6 +207,8 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
                 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
+            else:
+                target_normal = np.array([0, 0, 1])  # Default to Z-axis (XY plane)
 
             # 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:
@@ -245,19 +252,19 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
 
         except Exception as e:
             QMessageBox.critical(self, "Error", f"Failed to apply align: {str(e)}")
-    
+
     def closeEvent(self, event):
         """ダイアログが閉じられる時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
         super().closeEvent(event)
-    
+
     def reject(self):
         """キャンセル時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
         super().reject()
-    
+
     def accept(self):
         """OK時の処理"""
         self.clear_atom_labels()

{moleditpy-2.6.0 → moleditpy-2.6.1}/src/moleditpy/modules/alignment_dialog.py

@@ -10,13 +10,16 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+import numpy as np
 from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QLabel, QHBoxLayout, QPushButton
+    QDialog,
+    QHBoxLayout,
+    QLabel,
+    QMessageBox,
+    QPushButton,
+    QVBoxLayout,
 )
 
-from PyQt6.QtWidgets import QMessageBox
-import numpy as np
-
 try:
     from .dialog3_d_picking_mixin import Dialog3DPickingMixin
 except Exception:
@@ -30,72 +33,72 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
         self.main_window = main_window
         self.axis = axis
         self.selected_atoms = set()
-        
+
         # 事前選択された原子を追加（最大2個まで）
         if preselected_atoms:
             self.selected_atoms.update(preselected_atoms[:2])
-        
+
         self.init_ui()
-        
+
         # 事前選択された原子にラベルを追加
         if self.selected_atoms:
             for i, atom_idx in enumerate(sorted(self.selected_atoms), 1):
                 self.add_selection_label(atom_idx, f"Atom {i}")
             self.update_display()
-    
+
     def init_ui(self):
         axis_names = {'x': 'X-axis', 'y': 'Y-axis', 'z': 'Z-axis'}
         self.setWindowTitle(f"Align to {axis_names[self.axis]}")
         self.setModal(False)
         layout = QVBoxLayout(self)
-        
+
         # Instructions
         instruction_label = QLabel(f"Click atoms in the 3D view to select them for alignment to the {axis_names[self.axis]}. Exactly 2 atoms are required. The first atom will be moved to the origin, and the second atom will be positioned on the {axis_names[self.axis]}.")
         instruction_label.setWordWrap(True)
         layout.addWidget(instruction_label)
-        
+
         # Selected atoms display
         self.selection_label = QLabel("No atoms selected")
         layout.addWidget(self.selection_label)
-        
+
         # Buttons
         button_layout = QHBoxLayout()
         self.clear_button = QPushButton("Clear Selection")
         self.clear_button.clicked.connect(self.clear_selection)
         button_layout.addWidget(self.clear_button)
-        
+
         button_layout.addStretch()
-        
+
         self.apply_button = QPushButton("Apply Alignment")
         self.apply_button.clicked.connect(self.apply_alignment)
         self.apply_button.setEnabled(False)
         button_layout.addWidget(self.apply_button)
-        
+
         close_button = QPushButton("Close")
         close_button.clicked.connect(self.reject)
         button_layout.addWidget(close_button)
-        
+
         layout.addLayout(button_layout)
-        
+
         # Connect to main window's picker
         self.picker_connection = None
         self.enable_picking()
-    
+
     def enable_picking(self):
         """3Dビューでの原子選択を有効にする"""
         # Dialog3DPickingMixinの機能を使用
         super().enable_picking()
-    
+
     def disable_picking(self):
         """3Dビューでの原子選択を無効にする"""
         # Dialog3DPickingMixinの機能を使用
         super().disable_picking()
-    
+
     def on_atom_picked(self, atom_idx):
         """原子がクリックされた時の処理"""
         if self.main_window.current_mol is None:
             return
-            
+
         if atom_idx in self.selected_atoms:
             # 既に選択されている場合は選択解除
             self.selected_atoms.remove(atom_idx)
@@ -107,9 +110,9 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
                 # ラベルの順番を示す
                 label_text = f"Atom {len(self.selected_atoms)}"
                 self.add_selection_label(atom_idx, label_text)
-        
+
         self.update_display()
-    
+
     def update_display(self):
         """選択状態の表示を更新"""
         if len(self.selected_atoms) == 0:
@@ -126,13 +129,13 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
             atom2 = self.mol.GetAtomWithIdx(selected_list[1])
             self.selection_label.setText(f"Selected 2 atoms: {atom1.GetSymbol()}{selected_list[0]+1}, {atom2.GetSymbol()}{selected_list[1]+1}")
             self.apply_button.setEnabled(True)
-    
+
     def clear_selection(self):
         """選択をクリア"""
         self.clear_selection_labels()
         self.selected_atoms.clear()
         self.update_display()
-    
+
     def remove_atom_label(self, atom_idx):
         """特定の原子のラベルを削除"""
         # 簡単化のため、全ラベルをクリアして再描画
@@ -140,7 +143,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
         for i, idx in enumerate(sorted(self.selected_atoms), 1):
             if idx != atom_idx:
                 self.add_selection_label(idx, f"Atom {i}")
-    
+
     def apply_alignment(self):
         """アライメントを適用"""
         if len(self.selected_atoms) != 2:
@@ -174,69 +177,69 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
                 'z': np.array([0.0, 0.0, 1.0])
             }
             target_axis = axis_vectors[self.axis]
-            
+
             # atom2から原点への方向ベクトル
             current_vector = pos2_translated
             current_length = np.linalg.norm(current_vector)
-            
+
             if current_length > 1e-10:  # ゼロベクトルでない場合
                 current_vector_normalized = current_vector / current_length
-                
+
                 # 回転軸と角度を計算
                 rotation_axis = np.cross(current_vector_normalized, target_axis)
                 rotation_axis_length = np.linalg.norm(rotation_axis)
-                
+
                 if rotation_axis_length > 1e-10:  # 回転が必要
                     rotation_axis = rotation_axis / rotation_axis_length
                     cos_angle = np.dot(current_vector_normalized, target_axis)
                     cos_angle = np.clip(cos_angle, -1.0, 1.0)
                     rotation_angle = np.arccos(cos_angle)
-                    
+
                     # ロドリゲスの回転公式を使用
                     def rodrigues_rotation(v, k, theta):
                         cos_theta = np.cos(theta)
                         sin_theta = np.sin(theta)
-                        return (v * cos_theta + 
-                               np.cross(k, v) * sin_theta + 
+                        return (v * cos_theta +
+                               np.cross(k, v) * sin_theta +
                                k * np.dot(k, v) * (1 - cos_theta))
-                    
+
                     # 全ての原子に回転を適用
                     for i in range(self.mol.GetNumAtoms()):
                         current_pos = np.array(conf.GetAtomPosition(i))
                         rotated_pos = rodrigues_rotation(current_pos, rotation_axis, rotation_angle)
                         conf.SetAtomPosition(i, rotated_pos.tolist())
-            
+
             # 3D座標を更新
             self.main_window.atom_positions_3d = np.array([
                 list(conf.GetAtomPosition(i)) for i in range(self.mol.GetNumAtoms())
             ])
-            
+
             # 3Dビューを更新
             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()
-            
+
             QMessageBox.information(self, "Success", f"Alignment to {self.axis.upper()}-axis completed.")
-            
+
         except Exception as e:
             QMessageBox.critical(self, "Error", f"Failed to apply alignment: {str(e)}")
-    
+
     def closeEvent(self, event):
         """ダイアログが閉じられる時の処理"""
         self.clear_selection_labels()
         self.disable_picking()
         super().closeEvent(event)
-    
+
     def reject(self):
         """キャンセル時の処理"""
         self.clear_selection_labels()
         self.disable_picking()
         super().reject()
-    
+
     def accept(self):
         """OK時の処理"""
         self.clear_selection_labels()