MoleditPy 1.18.0__py3-none-any.whl → 2.0.0__py3-none-any.whl

moleditpy/modules/main_window_view_3d.py

@@ -19,6 +19,7 @@ MainWindow (main_window.py) から分離されたモジュール
 
 import numpy as np
 import vtk
+import logging
 
 
 # RDKit imports (explicit to satisfy flake8 and used features)
@@ -58,7 +59,7 @@ if OBABEL_AVAILABLE:
         # If import fails here, disable OBABEL locally; avoid raising
         pybel = None
         OBABEL_AVAILABLE = False
-        print("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
+        logging.warning("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
 else:
     pybel = None
 
@@ -201,7 +202,7 @@ class MainWindowView3d(object):
             resolution = self.settings.get('wireframe_resolution', 6)
             rad = np.array([0.01 for s in sym])  # 極小値（使用されない）
         elif self.current_3d_style == 'stick':
-            atom_radius = self.settings.get('stick_atom_radius', 0.15)
+            atom_radius = self.settings.get('stick_bond_radius', 0.15)  # Use bond radius for atoms
             resolution = self.settings.get('stick_resolution', 16)
             rad = np.array([atom_radius for s in sym])
         else:  # ball_and_stick
@@ -278,7 +279,7 @@ class MainWindowView3d(object):
                                         
                                         # 結合描画と同じ計算
                                         sphere_radius = cyl_radius * radius_factor
-                                    except:
+                                    except Exception:
                                         sphere_radius = 0.09  # デフォルト値
                                         offset_distance = 0.15  # デフォルト値
                                     
@@ -437,7 +438,7 @@ class MainWindowView3d(object):
                         double_radius_factor = self.settings.get('ball_stick_double_bond_radius_factor', 0.8)
                         triple_radius_factor = self.settings.get('ball_stick_triple_bond_radius_factor', 0.75)
                     elif self.current_3d_style == 'wireframe':
-                        double_radius_factor = self.settings.get('wireframe_double_bond_radius_factor', 1.0)
+                        double_radius_factor = self.settings.get('wireframe_double_bond_radius_factor', 0.8)
                         triple_radius_factor = self.settings.get('wireframe_triple_bond_radius_factor', 0.75)
                     elif self.current_3d_style == 'stick':
                         double_radius_factor = self.settings.get('stick_double_bond_radius_factor', 0.60)
@@ -660,7 +661,7 @@ class MainWindowView3d(object):
                     self.plotter.add_mesh(circle_line, color=torus_color, **mesh_props)
                     
             except Exception as e:
-                print(f"Error rendering aromatic circles: {e}")
+                logging.error(f"Error rendering aromatic circles: {e}")
 
         if getattr(self, 'show_chiral_labels', False):
             try:
@@ -820,7 +821,7 @@ class MainWindowView3d(object):
         try:
             # 既存のE/Zラベルを削除
             self.plotter.remove_actor('ez_labels')
-        except:
+        except Exception:
             pass
         
         pts, labels = [], []
@@ -837,7 +838,7 @@ class MainWindowView3d(object):
             # 3D座標からステレオ化学を再計算 (molに対して行う)
             # これにより、2Dでの描画状態に関わらず、現在の3D座標に基づいたE/Z判定が行われる
             Chem.AssignStereochemistry(mol, cleanIt=True, force=True, flagPossibleStereoCenters=True)
-        except:
+        except Exception:
             pass
 
         for bond in mol.GetBonds():
@@ -1171,7 +1172,7 @@ class MainWindowView3d(object):
                 for nm in self.atom_label_legend_names:
                     try:
                         self.plotter.remove_actor(nm)
-                    except:
+                    except Exception:
                         pass
             self.atom_label_legend_names = []
 
@@ -1237,12 +1238,12 @@ class MainWindowView3d(object):
                     for a in list(self.current_atom_info_labels):
                         try:
                             self.plotter.remove_actor(a)
-                        except:
+                        except Exception:
                             pass
                 else:
                     try:
                         self.plotter.remove_actor(self.current_atom_info_labels)
-                    except:
+                    except Exception:
                         pass
         except Exception:
             pass
@@ -1255,7 +1256,7 @@ class MainWindowView3d(object):
                 for nm in list(self.atom_label_legend_names):
                     try:
                         self.plotter.remove_actor(nm)
-                    except:
+                    except Exception:
                         pass
         except Exception:
             pass
@@ -1401,7 +1402,7 @@ class MainWindowView3d(object):
         if renderer and hasattr(renderer, 'SetNumberOfLayers'):
             try:
                 renderer.SetNumberOfLayers(2)  # レイヤー0:3Dオブジェクト、レイヤー1:2Dオーバーレイ
-            except:
+            except Exception:
                 pass  # PyVistaのバージョンによってはサポートされていない場合がある  
 
         # --- 3D軸ウィジェットの設定 ---

moleditpy/modules/main_window_view_loaders.py

@@ -317,7 +317,7 @@ class MainWindowViewLoaders(object):
                             # Keep mol as-is (may lack conformer); downstream code checks for conformers
                         else:
                             raise
-                except:
+                except Exception:
                     self.statusBar().showMessage("Failed to generate 3D coordinates")
                     return
             

moleditpy/modules/molecule_scene.py

@@ -11,6 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import traceback
+import logging
 
 from PyQt6.QtWidgets import (
     QApplication, QGraphicsScene, QGraphicsItem,
@@ -114,6 +115,15 @@ class MoleculeScene(QGraphicsScene):
         }
         self.reinitialize_items()
 
+    
+    def update_all_items(self):
+        """全てのアイテムを強制的に再描画する"""
+        for item in self.items():
+            if isinstance(item, (AtomItem, BondItem)):
+                item.update()
+        if self.views():
+            self.views()[0].viewport().update()
+
     def reinitialize_items(self):
         self.template_preview = TemplatePreviewItem(); self.addItem(self.template_preview)
         self.template_preview.hide(); self.template_preview_points = []; self.template_context = {}
@@ -184,6 +194,7 @@ class MoleculeScene(QGraphicsScene):
                 # Delete the entire rectangular selection
                 data_changed = self.delete_items(set(selected_items))
                 if data_changed:
+                    self.update_all_items()
                     self.window.push_undo_state()
                 self.press_pos = None
                 event.accept()
@@ -203,11 +214,10 @@ class MoleculeScene(QGraphicsScene):
                             self.window.push_undo_state()
                             data_changed = False  # ここでundo済みなので以降で積まない
                     except Exception as e:
-                        print(f"Error clearing E/Z label: {e}")
-                        
-                        traceback.print_exc()
+                        logging.error(f"Error clearing E/Z label: {e}", exc_info=True)
                         if hasattr(self.window, 'statusBar'):
                             self.window.statusBar().showMessage(f"Error clearing E/Z label: {e}", 5000)
+                        self.update_all_items() # エラー時も整合性維持のため再描画
                 # AtomItemは何もしない
             # --- 通常の処理 ---
             elif isinstance(item, AtomItem):
@@ -234,6 +244,7 @@ class MoleculeScene(QGraphicsScene):
                     data_changed = self.delete_items({item})
 
             if data_changed:
+                self.update_all_items()
                 self.window.push_undo_state()
             self.press_pos = None
             event.accept()
@@ -343,7 +354,9 @@ class MoleculeScene(QGraphicsScene):
                 self.data_changed_in_event = True
                 # イベント処理をここで完了させ、下のアイテムが選択されるのを防ぐ
                 self.start_atom=None; self.start_pos = None; self.press_pos = None
-                if self.data_changed_in_event: self.window.push_undo_state()
+                if self.data_changed_in_event:
+                    self.update_all_items()
+                    self.window.push_undo_state()
                 return
 
         released_item = self.itemAt(end_pos, self.views()[0].transform())
@@ -385,13 +398,13 @@ class MoleculeScene(QGraphicsScene):
                         else:  # current_stereo == 4
                             new_stereo = 0  # E -> None
                         self.update_bond_stereo(b, new_stereo)
+                        self.update_all_items() # 強制再描画
                         self.window.push_undo_state()  # ここでUndo stackに積む
                 except Exception as e:
-                    print(f"Error in E/Z stereo toggle: {e}")
-                    
-                    traceback.print_exc()
+                    logging.error(f"Error in E/Z stereo toggle: {e}", exc_info=True)
                     if hasattr(self.window, 'statusBar'):
                         self.window.statusBar().showMessage(f"Error changing E/Z stereochemistry: {e}", 5000)
+                    self.update_all_items() # エラー時も整合性維持のため再描画
                 return # この後の処理は行わない
             elif self.bond_stereo != 0 and b.order == self.bond_order and b.stereo == self.bond_stereo:
                 # 方向性を反転させる
@@ -491,6 +504,10 @@ class MoleculeScene(QGraphicsScene):
             # 原子移動後に測定ラベルの位置を更新
             self.window.update_2d_measurement_labels()
             if self.views(): self.views()[0].viewport().update()
+        
+        if self.data_changed_in_event:
+            self.update_all_items()
+
         self.start_atom=None; self.start_pos = None; self.press_pos = None; self.temp_line = None
         self.template_context = {}
         # Clear user template data when switching modes
@@ -515,6 +532,7 @@ class MoleculeScene(QGraphicsScene):
                 self.data.atoms[item.atom_id]['charge'] = item.charge
                 item.update_style()
 
+            self.update_all_items()
             self.window.push_undo_state()
 
             event.accept()
@@ -610,7 +628,7 @@ class MoleculeScene(QGraphicsScene):
     def create_bond(self, start_atom, end_atom, bond_order=None, bond_stereo=None):
         try:
             if start_atom is None or end_atom is None:
-                print("Error: Cannot create bond with None atoms")
+                logging.error("Error: Cannot create bond with None atoms")
                 return
                 
             exist_b = self.find_bond_between(start_atom, end_atom)
@@ -637,9 +655,8 @@ class MoleculeScene(QGraphicsScene):
                 end_atom.update_style()
                 
         except Exception as e:
-            print(f"Error creating bond: {e}")
-            
-            traceback.print_exc()
+            logging.error(f"Error creating bond: {e}", exc_info=True)
+            self.update_all_items() # エラーリカバリー
 
     def add_molecule_fragment(self, points, bonds_info, existing_items=None, symbol='C'):
         """
@@ -1270,6 +1287,7 @@ class MoleculeScene(QGraphicsScene):
             print(f"Error during delete_items operation: {e}")
             
             traceback.print_exc()
+            self.update_all_items() # エラーリカバリー
             return False
     def purge_deleted_items(self):
         """Purge and release any held deleted-wrapper references.
@@ -1541,6 +1559,7 @@ class MoleculeScene(QGraphicsScene):
                     
                     # 計算した情報を使って、その場にフラグメントを追加
                     self.add_molecule_fragment(points, bonds_info, existing_items=existing_items)
+                    self.update_all_items()
                     self.window.push_undo_state()
 
             # --- 動作2: カーソルが空白領域にある場合 (モード切替) ---
@@ -1566,6 +1585,7 @@ class MoleculeScene(QGraphicsScene):
                     atom.radical = (atom.radical + 1) % 3
                     self.data.atoms[atom.atom_id]['radical'] = atom.radical
                     atom.update_style()
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
@@ -1586,6 +1606,7 @@ class MoleculeScene(QGraphicsScene):
                     atom.charge += delta
                     self.data.atoms[atom.atom_id]['charge'] = atom.charge
                     atom.update_style()
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
@@ -1615,6 +1636,7 @@ class MoleculeScene(QGraphicsScene):
                 for atom in atoms_to_update:
                     atom.update_style()
 
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
@@ -1668,9 +1690,9 @@ class MoleculeScene(QGraphicsScene):
                 elif key == Qt.Key.Key_1 and (bond.order != 1 or bond.stereo != 0):
                     bond.order = 1; bond.stereo = 0
                 elif key == Qt.Key.Key_2 and (bond.order != 2 or bond.stereo != 0):
-                    bond.order = 2; bond.stereo = 0; needs_update = True
+                    bond.order = 2; bond.stereo = 0
                 elif key == Qt.Key.Key_3 and bond.order != 3:
-                    bond.order = 3; bond.stereo = 0; needs_update = True
+                    bond.order = 3; bond.stereo = 0
 
                 # 4. 実際に変更があった場合のみデータモデルを更新
                 if old_order != bond.order or old_stereo != bond.stereo:
@@ -1693,6 +1715,7 @@ class MoleculeScene(QGraphicsScene):
                     bond.update()
 
             if any_bond_changed:
+                self.update_all_items()
                 self.window.push_undo_state()
             
             if key in [Qt.Key.Key_1, Qt.Key.Key_2, Qt.Key.Key_3, Qt.Key.Key_W, Qt.Key.Key_D]:
@@ -1702,11 +1725,13 @@ class MoleculeScene(QGraphicsScene):
         if isinstance(self.hovered_item, BondItem) and self.hovered_item.order == 2:
             if event.key() == Qt.Key.Key_Z:
                 self.update_bond_stereo(self.hovered_item, 3)  # Z-isomer
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
             elif event.key() == Qt.Key.Key_E:
                 self.update_bond_stereo(self.hovered_item, 4)  # E-isomer
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
@@ -1814,6 +1839,7 @@ class MoleculeScene(QGraphicsScene):
                     self.create_bond(start_atom, new_atom_item, bond_order=target_order, bond_stereo=0)
 
                 self.clearSelection()
+                self.update_all_items()
                 self.window.push_undo_state()
                 event.accept()
                 return
@@ -1844,6 +1870,7 @@ class MoleculeScene(QGraphicsScene):
                 items_to_process.add(item_at_cursor)
 
             if self.delete_items(items_to_process):
+                self.update_all_items()
                 self.window.push_undo_state()
                 self.window.statusBar().showMessage("Deleted selected items.")
 
@@ -1978,3 +2005,4 @@ class MoleculeScene(QGraphicsScene):
             traceback.print_exc()
             if hasattr(self.window, 'statusBar'):
                 self.window.statusBar().showMessage(f"Error updating bond stereochemistry: {e}", 5000)
+            self.update_all_items() # エラーリカバリー

moleditpy/modules/planarize_dialog.py

@@ -157,7 +157,7 @@ class PlanarizeDialog(Dialog3DPickingMixin, QDialog):
             for label_actor in self.selection_labels:
                 try:
                     self.main_window.plotter.remove_actor(label_actor)
-                except:
+                except Exception:
                     pass
             self.selection_labels = []
 

moleditpy/modules/plugin_manager.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+plugin_manager.py
+Manages discovery, loading, and execution of external plugins.
+"""
+
+import os
+import sys
+import importlib.util
+import traceback
+from PyQt6.QtGui import QDesktopServices
+from PyQt6.QtCore import QUrl
+from PyQt6.QtWidgets import QMessageBox
+
+class PluginManager:
+    def __init__(self):
+        self.plugin_dir = os.path.join(os.path.expanduser('~'), '.moleditpy', 'plugins')
+        self.plugins = [] # List of {"name": str, "module": module_obj}
+
+    def ensure_plugin_dir(self):
+        """Creates the plugin directory if it creates doesn't exist."""
+        if not os.path.exists(self.plugin_dir):
+            try:
+                os.makedirs(self.plugin_dir)
+            except OSError as e:
+                print(f"Error creating plugin directory: {e}")
+
+    def open_plugin_folder(self):
+        """Opens the plugin directory in the OS file explorer."""
+        self.ensure_plugin_dir()
+        QDesktopServices.openUrl(QUrl.fromLocalFile(self.plugin_dir))
+
+    def discover_plugins(self, parent=None):
+        """
+        Scans the plugin directory for .py files and attempts to import them.
+        Returns a list of valid loaded plugins.
+        """
+        self.ensure_plugin_dir()
+        self.plugins = []
+        
+        if not os.path.exists(self.plugin_dir):
+            return []
+
+        for filename in os.listdir(self.plugin_dir):
+            if filename.endswith(".py") and not filename.startswith("__"):
+                filepath = os.path.join(self.plugin_dir, filename)
+                try:
+                    # Dynamically import the module
+                    spec = importlib.util.spec_from_file_location(filename[:-3], filepath)
+                    if spec and spec.loader:
+                        module = importlib.util.module_from_spec(spec)
+                        sys.modules[spec.name] = module # helper for relative imports if needed
+                        spec.loader.exec_module(module)
+
+                        # Check for required attributes
+                        plugin_name = getattr(module, 'PLUGIN_NAME', filename[:-3])
+                        
+                        # Validate that it has a run function
+                        if hasattr(module, 'run') and callable(module.run):
+                            self.plugins.append({
+                                'name': plugin_name,
+                                'module': module
+                            })
+                        else:
+                            print(f"Plugin {filename} skipped: Missing 'run(main_window)' function.")
+                except Exception as e:
+                    # Robust error handling with user notification
+                    msg = f"Failed to load plugin {filename}:\n{e}"
+                    print(msg)
+                    traceback.print_exc()
+                    if parent:
+                        QMessageBox.warning(parent, "Plugin Load Error", msg)
+        
+        return self.plugins
+
+    def run_plugin(self, module, main_window):
+        """Executes the plugin's run method."""
+        try:
+            module.run(main_window)
+        except Exception as e:
+            QMessageBox.critical(main_window, "Plugin Error", f"Error running plugin '{getattr(module, 'PLUGIN_NAME', 'Unknown')}':\n{e}")
+            traceback.print_exc()
+

moleditpy/modules/settings_dialog.py

@@ -53,7 +53,6 @@ class SettingsDialog(QDialog):
             'wireframe_bond_radius': 0.01,
             'wireframe_resolution': 6,
             # Stick model parameters
-            'stick_atom_radius': 0.15,
             'stick_bond_radius': 0.15,
             'stick_resolution': 16,
             # Multiple bond offset parameters (per-model)
@@ -278,8 +277,8 @@ class SettingsDialog(QDialog):
         # Aromatic torus thickness factor
         self.aromatic_torus_thickness_slider = QSlider(Qt.Orientation.Horizontal)
         self.aromatic_torus_thickness_slider.setRange(10, 300)  # 0.1x to 3.0x
-        self.aromatic_torus_thickness_slider.setValue(100)  # Default 1.0x
-        self.aromatic_torus_thickness_label = QLabel("1.0")
+        self.aromatic_torus_thickness_slider.setValue(60)  # Default 0.6x
+        self.aromatic_torus_thickness_label = QLabel("0.6")
         self.aromatic_torus_thickness_slider.valueChanged.connect(
             lambda v: self.aromatic_torus_thickness_label.setText(f"{v/100:.1f}")
         )
@@ -564,17 +563,7 @@ class SettingsDialog(QDialog):
         info_label.setStyleSheet("color: #666; font-style: italic; margin-top: 10px;")
         form_layout.addRow(info_label)
         
-        # 原子半径
-        self.stick_atom_radius_slider = QSlider(Qt.Orientation.Horizontal)
-        self.stick_atom_radius_slider.setRange(5, 50)  # 0.05 ~ 0.5
-        self.stick_atom_radius_label = QLabel("0.15")
-        self.stick_atom_radius_slider.valueChanged.connect(lambda v: self.stick_atom_radius_label.setText(f"{v/100:.2f}"))
-        atom_radius_layout = QHBoxLayout()
-        atom_radius_layout.addWidget(self.stick_atom_radius_slider)
-        atom_radius_layout.addWidget(self.stick_atom_radius_label)
-        form_layout.addRow("Atom Radius:", atom_radius_layout)
-        
-        # ボンド半径
+        # ボンド半径（原子半径も同じ値を使用）
         self.stick_bond_radius_slider = QSlider(Qt.Orientation.Horizontal)
         self.stick_bond_radius_slider.setRange(5, 50)  # 0.05 ~ 0.5
         self.stick_bond_radius_label = QLabel("0.15")
@@ -673,7 +662,7 @@ class SettingsDialog(QDialog):
                 'display_kekule_3d': self.default_settings.get('display_kekule_3d', False),
                 'always_ask_charge': self.default_settings.get('always_ask_charge', False),
                 'display_aromatic_circles_3d': self.default_settings.get('display_aromatic_circles_3d', False),
-                'aromatic_torus_thickness_factor': self.default_settings.get('aromatic_torus_thickness_factor', 1.0),
+                'aromatic_torus_thickness_factor': self.default_settings.get('aromatic_torus_thickness_factor', 0.6),
             },
             "Ball & Stick": {
                 'ball_stick_atom_scale': self.default_settings['ball_stick_atom_scale'],
@@ -700,7 +689,6 @@ class SettingsDialog(QDialog):
                 'wireframe_triple_bond_radius_factor': self.default_settings.get('wireframe_triple_bond_radius_factor', 0.75)
             },
             "Stick": {
-                'stick_atom_radius': self.default_settings['stick_atom_radius'],
                 'stick_bond_radius': self.default_settings['stick_bond_radius'],
                 'stick_resolution': self.default_settings['stick_resolution'],
                 'stick_double_bond_offset_factor': self.default_settings.get('stick_double_bond_offset_factor', 1.5),
@@ -844,7 +832,6 @@ class SettingsDialog(QDialog):
             'wireframe_bond_radius': self.wf_bond_radius_slider.value() / 100.0,
             'wireframe_resolution': self.wf_resolution_slider.value(),
             # Stick settings
-            'stick_atom_radius': self.stick_atom_radius_slider.value() / 100.0,
             'stick_bond_radius': self.stick_bond_radius_slider.value() / 100.0,
             'stick_resolution': self.stick_resolution_slider.value(),
             # Multi-bond settings (per-model)
@@ -944,10 +931,6 @@ class SettingsDialog(QDialog):
         self.wf_resolution_label.setText(str(settings_dict.get('wireframe_resolution', self.default_settings['wireframe_resolution'])))
         
         # Stick設定
-        stick_atom_radius = int(settings_dict.get('stick_atom_radius', self.default_settings['stick_atom_radius']) * 100)
-        self.stick_atom_radius_slider.setValue(stick_atom_radius)
-        self.stick_atom_radius_label.setText(f"{stick_atom_radius/100:.2f}")
-        
         stick_bond_radius = int(settings_dict.get('stick_bond_radius', self.default_settings['stick_bond_radius']) * 100)
         self.stick_bond_radius_slider.setValue(stick_bond_radius)
         self.stick_bond_radius_label.setText(f"{stick_bond_radius/100:.2f}")
@@ -1019,7 +1002,7 @@ class SettingsDialog(QDialog):
         self.always_ask_charge_checkbox.setChecked(settings_dict.get('always_ask_charge', self.default_settings.get('always_ask_charge', False)))
         # Aromatic ring circle display and torus thickness factor
         self.aromatic_circle_checkbox.setChecked(settings_dict.get('display_aromatic_circles_3d', self.default_settings.get('display_aromatic_circles_3d', False)))
-        thickness_factor = float(settings_dict.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 1.0)))
+        thickness_factor = float(settings_dict.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 0.6)))
         try:
             self.aromatic_torus_thickness_slider.setValue(int(thickness_factor * 100))
             self.aromatic_torus_thickness_label.setText(f"{thickness_factor:.1f}")
@@ -1060,7 +1043,6 @@ class SettingsDialog(QDialog):
             'wireframe_bond_radius': self.wf_bond_radius_slider.value() / 100.0,
             'wireframe_resolution': self.wf_resolution_slider.value(),
             # Stick settings
-            'stick_atom_radius': self.stick_atom_radius_slider.value() / 100.0,
             'stick_bond_radius': self.stick_bond_radius_slider.value() / 100.0,
             'stick_resolution': self.stick_resolution_slider.value(),
             # Multiple bond offset settings (per-model)

moleditpy/modules/user_template_dialog.py

@@ -23,6 +23,7 @@ except Exception:
     from modules.constants import VERSION, CPK_COLORS
 import os
 import json
+import logging
 
 class UserTemplateDialog(QDialog):
     """ユーザーテンプレート管理ダイアログ"""
@@ -106,7 +107,7 @@ class UserTemplateDialog(QDialog):
                         elif hasattr(child, 'refit_view'):
                             child.refit_view()
         except Exception as e:
-            print(f"Warning: Failed to refit template previews: {e}")
+            logging.warning(f"Warning: Failed to refit template previews: {e}")
     
     def showEvent(self, event):
         """ダイアログ表示時にプレビューを適切にフィット"""
@@ -136,7 +137,7 @@ class UserTemplateDialog(QDialog):
                         template_data['filepath'] = filepath
                         self.user_templates.append(template_data)
         except Exception as e:
-            print(f"Error loading user templates: {e}")
+            logging.error(f"Error loading user templates: {e}")
         
         self.update_template_grid()
     
@@ -146,7 +147,7 @@ class UserTemplateDialog(QDialog):
             with open(filepath, 'r', encoding='utf-8') as f:
                 return json.load(f)
         except Exception as e:
-            print(f"Error loading template file {filepath}: {e}")
+            logging.error(f"Error loading template file {filepath}: {e}")
             return None
     
     def save_template_file(self, filepath, template_data):
@@ -156,7 +157,7 @@ class UserTemplateDialog(QDialog):
                 json.dump(template_data, f, indent=2, ensure_ascii=False)
             return True
         except Exception as e:
-            print(f"Error saving template file {filepath}: {e}")
+            logging.error(f"Error saving template file {filepath}: {e}")
             return False
     
     def update_template_grid(self):
@@ -253,7 +254,7 @@ class UserTemplateDialog(QDialog):
             if view and not rect.isEmpty():
                 view.fitInView(rect, Qt.AspectRatioMode.KeepAspectRatio)
         except Exception as e:
-            print(f"Warning: Failed to fit preview view: {e}")
+            logging.warning(f"Warning: Failed to fit preview view: {e}")
     
     def draw_template_preview(self, scene, template_data, view_size=None):
         """テンプレートプレビューを描画 - fitInView縮小率に基づく動的スケーリング"""
@@ -303,7 +304,7 @@ class UserTemplateDialog(QDialog):
                 scale_factor = 4.0
             
             # Debug info (can be removed in production)
-            # print(f"Mol size: {mol_size:.1f}, Fit scale: {fit_scale:.3f}, Scale factor: {scale_factor:.2f}")
+            # logging.debug(f"Mol size: {mol_size:.1f}, Fit scale: {fit_scale:.3f}, Scale factor: {scale_factor:.2f}")
         else:
             scale_factor = 1.0
         
@@ -481,7 +482,7 @@ class UserTemplateDialog(QDialog):
             except Exception:
                 pass
         except Exception as e:
-            print(f"Warning: Failed to switch main window to template mode: {e}")
+            logging.warning(f"Warning: Failed to switch main window to template mode: {e}")
     
     def use_template(self, template_data):
         """テンプレートを使用（エディタに適用）"""
@@ -518,7 +519,7 @@ class UserTemplateDialog(QDialog):
                 # Mark selected and keep dialog open
                 self.selected_template = template_data
             except Exception as e:
-                print(f"Warning: Failed to switch main window to template mode: {e}")
+                logging.warning(f"Warning: Failed to switch main window to template mode: {e}")
 
             # Don't close dialog - keep it open for easy template switching
             # self.accept()

{moleditpy-1.18.0.dist-info → moleditpy-2.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 1.18.0
+Version: 2.0.0
 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
@@ -684,7 +684,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -760,6 +759,7 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
       * Import structures from **MOL/SDF** files or **SMILES** strings.
       * Export 3D structures to **MOL** or **XYZ** formats, which are compatible with most DFT calculation software.
       * Export 2D and 3D views as high-resolution PNG images.
+  * **Plugin System:** Extend functionality with Python scripts. Place custom scripts in `~/.moleditpy/plugins` to add new features to the "Plugin" menu.
 
 ## Installation and Execution
 
@@ -874,6 +874,7 @@ This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**.
       * **MOL/SDF**ファイルや**SMILES**文字列から構造をインポートできます。
       * 3D構造を**MOL**または**XYZ**形式でエクスポートでき、これらは多くのDFT計算ソフトウェアと互換性があります。
       * 2Dおよび3Dビューを高解像度のPNG画像としてエクスポートできます。
+  * **プラグインシステム:** Pythonスクリプトで機能を拡張できます。`~/.moleditpy/plugins` にスクリプトを配置することで、「Plugin」メニューに独自の機能を追加できます。
 
 ## インストールと実行