MoleditPy 1.18.1__py3-none-any.whl → 2.0.1__py3-none-any.whl

moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.18.1'
+VERSION = '2.0.1'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy/modules/main_window.py

@@ -211,6 +211,10 @@ class MainWindow(QMainWindow):
         # --- MOVED TO main_window_main_init.py ---
         return self.main_window_main_init.init_menu_bar()
 
+    def update_plugin_menu(self, plugin_menu):
+        # --- MOVED TO main_window_main_init.py ---
+        return self.main_window_main_init.update_plugin_menu(plugin_menu)
+
     def init_worker_thread(self):
         # --- MOVED TO main_window_main_init.py ---
         return self.main_window_main_init.init_worker_thread()

moleditpy/modules/main_window_main_init.py

@@ -46,12 +46,16 @@ from PyQt6.QtCore import (
     Qt, QPointF, QRectF, QLineF, QUrl, QTimer
 )
 import platform
-import subprocess
 try:
     import winreg
 except Exception:
     winreg = None
 
+try:
+    from .plugin_manager import PluginManager
+except Exception:
+    from modules.plugin_manager import PluginManager
+
 
 def detect_system_dark_mode():
     """Return True if the OS prefers dark app theme, False if light, or None if unknown.
@@ -253,6 +257,14 @@ class MainWindowMainInit(object):
         # 3D編集ダイアログの参照を保持
         self.active_3d_dialogs = []
         
+
+        # プラグインマネージャーの初期化
+        try:
+            self.plugin_manager = PluginManager()
+        except Exception as e:
+            print(f"Failed to initialize PluginManager: {e}")
+            self.plugin_manager = None
+
         self.init_ui()
         self.init_worker_thread()
         self._setup_3d_picker() 
@@ -286,6 +298,7 @@ class MainWindowMainInit(object):
         self.update_atom_id_menu_text()
         self.update_atom_id_menu_state()
         
+        
         # 初期化完了を設定
         self.initialization_complete = True
         self.update_window_title()  # 初期化完了後にタイトルを更新
@@ -1188,6 +1201,27 @@ class MainWindowMainInit(object):
         edit_3d_menu.addAction(constrained_opt_action)
         self.constrained_opt_action = constrained_opt_action
 
+        # Plugin menu
+        plugin_menu = menu_bar.addMenu("&Plugin")
+        
+        open_plugin_dir_action = QAction("Open Plugin Directory", self)
+        if self.plugin_manager:
+            open_plugin_dir_action.triggered.connect(self.plugin_manager.open_plugin_folder)
+        else:
+            open_plugin_dir_action.setEnabled(False)
+        plugin_menu.addAction(open_plugin_dir_action)
+        
+        reload_plugins_action = QAction("Reload Plugins", self)
+        reload_plugins_action.triggered.connect(lambda: self.update_plugin_menu(plugin_menu))
+        plugin_menu.addAction(reload_plugins_action)
+
+
+        
+        plugin_menu.addSeparator()
+        
+        # Initial population of plugins
+        self.update_plugin_menu(plugin_menu)
+
         settings_menu = menu_bar.addMenu("&Settings")
         # 1) 3D View settings (existing)
         view_settings_action = QAction("3D View Settings...", self)
@@ -1675,3 +1709,41 @@ class MainWindowMainInit(object):
         except Exception as e:
             print(f"Error saving settings: {e}")
 
+    def update_plugin_menu(self, plugin_menu):
+        """Discovers plugins and updates the plugin menu actions."""
+        if not self.plugin_manager:
+            return
+
+        # Clear existing plugin actions
+        plugin_menu.clear()
+        
+        # Re-add static actions
+        open_plugin_dir_action = QAction("Open Plugin Directory", self)
+        open_plugin_dir_action.triggered.connect(self.plugin_manager.open_plugin_folder)
+        plugin_menu.addAction(open_plugin_dir_action)
+        
+        reload_plugins_action = QAction("Reload Plugins", self)
+        reload_plugins_action.triggered.connect(lambda: self.update_plugin_menu(plugin_menu))
+        plugin_menu.addAction(reload_plugins_action)
+
+        explore_plugins_action = QAction("Explore Plugins", self)
+        explore_plugins_action.triggered.connect(
+            lambda: QDesktopServices.openUrl(QUrl("https://github.com/HiroYokoyama/moleditpy-plugins"))
+        )
+        plugin_menu.addAction(explore_plugins_action)
+        
+        plugin_menu.addSeparator()
+        
+        # Add dynamic plugin actions
+        plugins = self.plugin_manager.discover_plugins(self)
+        if not plugins:
+            no_plugin_action = QAction("(No plugins found)", self)
+            no_plugin_action.setEnabled(False)
+            plugin_menu.addAction(no_plugin_action)
+        else:
+            for p in plugins:
+                # Use default param in lambda to capture the current p
+                action = QAction(p['name'], self)
+                action.triggered.connect(lambda checked, mod=p['module']: self.plugin_manager.run_plugin(mod, self.mw if hasattr(self, 'mw') else self)) 
+                plugin_menu.addAction(action)
+

moleditpy/modules/molecule_scene.py

@@ -115,6 +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 = {}
@@ -185,6 +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()
@@ -207,6 +217,7 @@ class MoleculeScene(QGraphicsScene):
                         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):
@@ -233,6 +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()
@@ -342,7 +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())
@@ -384,11 +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:
                     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
@@ -488,6 +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
@@ -512,6 +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()
@@ -635,6 +656,7 @@ class MoleculeScene(QGraphicsScene):
                 
         except Exception as e:
             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'):
         """
@@ -1265,6 +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.
@@ -1536,6 +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) ---
@@ -1561,6 +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
@@ -1581,6 +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
@@ -1610,6 +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
@@ -1688,6 +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]:
@@ -1697,11 +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
@@ -1809,6 +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
@@ -1839,6 +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.")
 
@@ -1973,3 +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/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-1.18.1.dist-info → moleditpy-2.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 1.18.1
+Version: 2.0.1
 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
@@ -759,6 +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
 
@@ -873,6 +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
 

{moleditpy-1.18.1.dist-info → moleditpy-2.0.1.dist-info}/RECORD

@@ -12,20 +12,20 @@ moleditpy/modules/bond_item.py,sha256=eVkEeKvM4igYI67DYxpey3FllqDyt_iWDo4VPYMhaP
 moleditpy/modules/bond_length_dialog.py,sha256=k5x_DhK9Q8CSwouKhEo_kLRRdaYHDaK84KDNmuDNLvY,14868
 moleditpy/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy/modules/constants.py,sha256=BmnH8wNO4QnsenarqQeN9pnaHyIeIo6PJJyT2HFWLfc,4703
+moleditpy/modules/constants.py,sha256=m8tYMuiXp0w4IUeFW1hbSogm6-7g0voDQs5kJygquQA,4702
 moleditpy/modules/constrained_optimization_dialog.py,sha256=IEdNVhFoNSEMeA5ABpUH9Q88-YzDXFloQM2gwnPwnHY,30150
 moleditpy/modules/custom_interactor_style.py,sha256=NjsXE2a43IDNEanZBlcG9eR4ZIERT1MsQC6lbfesapQ,38453
 moleditpy/modules/custom_qt_interactor.py,sha256=MFaTuDh-FPeFBS4303CqxsxmsOIOW4QXUz6USwI8PHQ,2451
 moleditpy/modules/dialog3_d_picking_mixin.py,sha256=2Sut0J5ltXMtrUJ9R3o1oZ4ysed27mdSIqLpWxmGdyM,5037
 moleditpy/modules/dihedral_dialog.py,sha256=rgry7LqyX9JMAR7d82QSroTPoKT3xz18EgKN1GzYZx4,18088
-moleditpy/modules/main_window.py,sha256=bWgYP3EMOAcy1fnjg5DTXHb2d7Xm6zKQtFcleYjg7Ac,35789
+moleditpy/modules/main_window.py,sha256=fXt2QTY7BjTMHEjGcsAb4Z-nu4_hRKayqLq8cA92bKc,35967
 moleditpy/modules/main_window_app_state.py,sha256=ONdjo-ZAPdat1_ToFodzuUep3c8qbKRPX6glnY24c9o,33602
 moleditpy/modules/main_window_compute.py,sha256=DsyMvGD2gnB-9XC6SU-ICuScyyQxubfaDYAk8hkY-vk,51911
 moleditpy/modules/main_window_dialog_manager.py,sha256=S1ROCWqzB2uVSKHY4o5CbTtJAEjSyEXGPC1AgmdVgK4,20065
 moleditpy/modules/main_window_edit_3d.py,sha256=uY203adPg3CLyAdbG2NCThG2Am0WduzPDan9rXAlc14,19841
 moleditpy/modules/main_window_edit_actions.py,sha256=lUFxNFTUQzeXN8CNlb4_4S9j4M1EEq8kpJmh9dCzM3M,64818
 moleditpy/modules/main_window_export.py,sha256=e0HA_jeaokIOBunQqGxUn5QKdniCmE8GrsE1Igy6zm8,38351
-moleditpy/modules/main_window_main_init.py,sha256=Ox6P8MQtEnOw47NWdgOmxNNSAFgR6Vv8My71gNvj8RY,75608
+moleditpy/modules/main_window_main_init.py,sha256=ecRDVqOLMieqRDYTzsCRTjZSqj0fUBuFjqFacbC0lCg,78515
 moleditpy/modules/main_window_molecular_parsers.py,sha256=Ex4-urYsKf6PyHp4XToOhgXzuYWa_n7q--QmHci4OCU,48401
 moleditpy/modules/main_window_project_io.py,sha256=q1vEmWQDqla32HVkmk8-j0OY9ut5TI5NJ4ikahewkEo,17259
 moleditpy/modules/main_window_string_importers.py,sha256=mQVDv2Dj4MwnPgMRe2IqdAAKnB_quE6QfYeAgCjfv28,10892
@@ -34,10 +34,11 @@ moleditpy/modules/main_window_view_3d.py,sha256=MQCW2GnqGUpdJO4-GeR_18z7dS5K8C2G
 moleditpy/modules/main_window_view_loaders.py,sha256=Dbdgv4TY_ZkX8Qyaevwr-mBJYJ59CBzRTEks-U1FiGw,14462
 moleditpy/modules/mirror_dialog.py,sha256=c3v4qY6R4FAljzk4EPaDjL9ZdZMjLQSFLqDMXz2fBUk,4696
 moleditpy/modules/molecular_data.py,sha256=8gE9ByYg3kSBfb1zANsyad_BVBTm6WOLF7NsZIYuG2E,13250
-moleditpy/modules/molecule_scene.py,sha256=Ced3-U_03epwb1yL2QToq9MtILN4qCYDe0qpayHMWAE,94997
+moleditpy/modules/molecule_scene.py,sha256=c5GNL7LrzerXYWshmpY_6Rg-2cBlF7xUt_orxTYC5pQ,96408
 moleditpy/modules/move_group_dialog.py,sha256=65HVXTJSaQ9lp03XFhI1l7OzUsXmH_aqd8OgwjpjfGg,27174
 moleditpy/modules/periodic_table_dialog.py,sha256=ItEZUts1XCietz9paY-spvbzxh6SXak3GnikwqkHZCw,4006
 moleditpy/modules/planarize_dialog.py,sha256=yY8o-SxT8vGEHVWnjDTXecRv5NUaEejEsXH-836Xk8g,8681
+moleditpy/modules/plugin_manager.py,sha256=Qbje9i-b4f81k_gxiDkfH8bv2eNTTya1563L93USQQA,3441
 moleditpy/modules/settings_dialog.py,sha256=Nr7yE8UmYRi3VObWvRlrnv0DnjSjmYXbvqryZ02O12k,65348
 moleditpy/modules/template_preview_item.py,sha256=Ks3C35pYFuLT5G4fsloI7ljE6ESXoYyGvLkM22qcmt0,6673
 moleditpy/modules/template_preview_view.py,sha256=4OCHZDO51BvJpKdfrBWJ4_4WfLfFSKxsVIyf7I-Kj2E,3350
@@ -47,9 +48,9 @@ moleditpy/modules/zoomable_view.py,sha256=hjwljui13QpvjvxJHY4Evot4jMQvxRBQUNH5HU
 moleditpy/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
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