moleditpy 2.6.0__tar.gz → 2.6.2__tar.gz

{moleditpy-2.6.0 → moleditpy-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.6.0
+Version: 2.6.2
 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>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-2.6.0 → moleditpy-2.6.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.6.0"
+version = "2.6.2"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.6.0
+Version: 2.6.2
 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>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy-2.6.0 → moleditpy-2.6.2}/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-2.6.2}/src/moleditpy/__init__.py

@@ -10,8 +10,6 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-
 """Top-level package for moleditpy.
 
 """
-

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/moleditpy/__main__.py

@@ -10,7 +10,6 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-
 print("-----------------------------------------------------")
 print("MoleditPy — A Python-based molecular editing software")
 print("-----------------------------------------------------\n")
@@ -21,6 +20,5 @@ except Exception:
     from main import main
 
 # --- Application Execution ---
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
-

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/moleditpy/main.py

@@ -10,9 +10,8 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-
-import sys
 import ctypes
+import sys
 
 from PyQt6.QtWidgets import QApplication
 
@@ -21,10 +20,11 @@ try:
 except Exception:
     from modules.main_window import MainWindow
 
+
 def main():
     # --- Windows タスクバーアイコンのための追加処理 ---
-    if sys.platform == 'win32':
-        myappid = 'hyoko.moleditpy.1.0' # アプリケーション固有のID（任意）
+    if sys.platform == "win32":
+        myappid = "hyoko.moleditpy.1.0"  # アプリケーション固有のID（任意）
         ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
     app = QApplication(sys.argv)

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/moleditpy/modules/__init__.py

@@ -10,29 +10,22 @@ 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
+try:
     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
-    _sip_isdeleted = getattr(_sip, 'isdeleted', None)
+try:
+    from PyQt6 import sip as _sip  # type: ignore
+
+    _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
     _sip_isdeleted = None
 
+
 def sip_isdeleted_safe(obj) -> bool:
     """Return True if sip reports the given wrapper object as deleted.
 
@@ -40,10 +33,9 @@ def sip_isdeleted_safe(obj) -> bool:
     occurs while checking, it returns False (i.e. not deleted) so that the
     caller can continue other lightweight guards (like checking scene()).
     """
-    try: # pragma: no cover
+    try:
         if _sip_isdeleted is None:
             return False
         return bool(_sip_isdeleted(obj))
     except Exception:
         return False
-

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/moleditpy/modules/about_dialog.py

@@ -10,38 +10,44 @@ 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:
     from modules.constants import VERSION
 
-class AboutDialog(QDialog): # pragma: no cover
+
+class AboutDialog(QDialog):  # pragma: no cover
     def __init__(self, main_window, parent=None):
         super().__init__(parent)
         self.main_window = main_window
         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')
+        icon_path = os.path.join(os.path.dirname(__file__), "..", "assets", "icon.png")
         if os.path.exists(icon_path):
             original_pixmap = QPixmap(icon_path)
             # Scale to 2x size (160x160)
-            pixmap = original_pixmap.scaled(160, 160, Qt.AspectRatioMode.KeepAspectRatio, Qt.TransformationMode.SmoothTransformation)
+            pixmap = original_pixmap.scaled(
+                160,
+                160,
+                Qt.AspectRatioMode.KeepAspectRatio,
+                Qt.TransformationMode.SmoothTransformation,
+            )
         else:
             # Fallback: create a simple placeholder if icon.png not found
             pixmap = QPixmap(160, 160)
@@ -50,35 +56,36 @@ 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))
-        except Exception:
-            pass
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
         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
@@ -100,5 +107,6 @@ class AboutDialog(QDialog): # pragma: no cover
         except Exception:
             try:
                 event.ignore()
-            except Exception:
-                pass
+            except Exception:  # pragma: no cover
+                import traceback
+                traceback.print_exc()

{moleditpy-2.6.0 → moleditpy-2.6.2}/src/moleditpy/modules/align_plane_dialog.py

@@ -10,18 +10,24 @@ 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
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
 
-class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
+
+class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
     def __init__(self, mol, main_window, plane, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -29,47 +35,51 @@ 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'}
+        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 = 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.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 +88,35 @@ 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:
+        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:
@@ -115,28 +125,36 @@ 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:
             # Prefer RDKit molecule if available
-            if hasattr(self, 'mol') and self.mol is not None:
+            if hasattr(self, "mol") and self.mol is not None:
                 try:
                     n = self.mol.GetNumAtoms()
                     # create a set of indices [0..n-1]
                     self.selected_atoms = set(range(n))
                 except Exception:
                     # fallback to main_window data map
-                    self.selected_atoms = set(self.main_window.data.atoms.keys()) if hasattr(self.main_window, 'data') else set()
+                    self.selected_atoms = (
+                        set(self.main_window.data.atoms.keys())
+                        if hasattr(self.main_window, "data")
+                        else set()
+                    )
             else:
                 # fallback to main_window data map
-                self.selected_atoms = set(self.main_window.data.atoms.keys()) if hasattr(self.main_window, 'data') else set()
+                self.selected_atoms = (
+                    set(self.main_window.data.atoms.keys())
+                    if hasattr(self.main_window, "data")
+                    else set()
+                )
 
             # Update labels and display
             self.show_atom_labels()
@@ -144,42 +162,49 @@ 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)
         if count == 0:
-            self.selection_label.setText("Click atoms to select for align (minimum 3 required)")
+            self.selection_label.setText(
+                "Click atoms to select for align (minimum 3 required)"
+            )
             self.apply_button.setEnabled(False)
         else:
             atom_list = sorted(self.selected_atoms)
             atom_display = []
             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)}")
+                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:
             sorted_atoms = sorted(self.selected_atoms)
-            pairs = [(idx, f"#{i+1}") for i, idx in enumerate(sorted_atoms)]
-            self.show_atom_labels_for(pairs, color='blue')
+            pairs = [(idx, f"#{i + 1}") for i, idx in enumerate(sorted_atoms)]
+            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:
-            QMessageBox.warning(self, "Warning", "Please select at least 3 atoms for align.")
+            QMessageBox.warning(
+                self, "Warning", "Please select at least 3 atoms for align."
+            )
             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()
+            selected_positions = self.main_window.atom_positions_3d[
+                selected_indices
+            ].copy()
 
             # 重心を計算
             centroid = np.mean(selected_positions, axis=0)
@@ -196,12 +221,14 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
             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':
+            if self.plane == "xy":
                 target_normal = np.array([0, 0, 1])  # Z軸方向
-            elif self.plane == 'xz':
+            elif self.plane == "xz":
                 target_normal = np.array([0, 1, 0])  # Y軸方向
-            elif self.plane == 'yz':
+            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:
@@ -221,7 +248,11 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
                 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)
+                    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()
@@ -229,7 +260,9 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
                     current_pos = np.array(conf.GetAtomPosition(i))
                     # 重心基準で回転
                     centered_pos = current_pos - centroid
-                    rotated_pos = rodrigues_rotation(centered_pos, rotation_axis, rotation_angle)
+                    rotated_pos = rodrigues_rotation(
+                        centered_pos, rotation_axis, rotation_angle
+                    )
                     new_pos = rotated_pos + centroid
                     conf.SetAtomPosition(i, new_pos.tolist())
                     self.main_window.atom_positions_3d[i] = new_pos
@@ -245,19 +278,19 @@ 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()