MoleditPy-linux 2.2.4__py3-none-any.whl → 2.2.5__py3-none-any.whl

moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.2.4'
+VERSION = '2.2.5'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux/modules/main_window_app_state.py

@@ -596,8 +596,10 @@ class MainWindowAppState(object):
             json_data["last_successful_optimization_method"] = None
         
         # Plugin State Persistence (Phase 3)
+        # Start with preserved data from missing plugins
+        plugin_data = self._preserved_plugin_data.copy() if self._preserved_plugin_data else {}
+        
         if self.plugin_manager and self.plugin_manager.save_handlers:
-            plugin_data = {}
             for name, callback in self.plugin_manager.save_handlers.items():
                 try:
                     p_state = callback()
@@ -606,8 +608,8 @@ class MainWindowAppState(object):
                 except Exception as e:
                     print(f"Error saving state for plugin {name}: {e}")
             
-            if plugin_data:
-                json_data['plugins'] = plugin_data
+        if plugin_data:
+            json_data['plugins'] = plugin_data
 
         return json_data
 
@@ -629,14 +631,19 @@ class MainWindowAppState(object):
             self.last_successful_optimization_method = None
 
         # Plugin State Restoration (Phase 3)
-        if "plugins" in json_data and self.plugin_manager and self.plugin_manager.load_handlers:
+        self._preserved_plugin_data = {} # Reset preserved data on new load
+        if "plugins" in json_data:
             plugin_data = json_data["plugins"]
             for name, p_state in plugin_data.items():
-                if name in self.plugin_manager.load_handlers:
+                if self.plugin_manager and name in self.plugin_manager.load_handlers:
                     try:
                         self.plugin_manager.load_handlers[name](p_state)
                     except Exception as e:
                         print(f"Error loading state for plugin {name}: {e}")
+                else:
+                    # No handler found (plugin disabled or missing)
+                    # Preserve data so it's not lost on next save
+                    self._preserved_plugin_data[name] = p_state
 
 
         # 2D構造データの復元
@@ -697,7 +704,7 @@ class MainWindowAppState(object):
             for atom in self.data.atoms.values():
                 atom['item'].update_style()
         # 3D構造データの復元
-        if "3d_structure" in json_data:
+        if "3d_structure" in json_data and json_data["3d_structure"] is not None:
             structure_3d = json_data["3d_structure"]
 
             # 制約データの復元 (JSONはタプルをリストとして保存するので、タプルに再変換)

moleditpy_linux/modules/main_window_main_init.py

@@ -264,6 +264,9 @@ class MainWindowMainInit(object):
         except Exception as e:
             print(f"Failed to initialize PluginManager: {e}")
             self.plugin_manager = None
+        
+        # ロードされていないプラグインのデータを保持する辞書
+        self._preserved_plugin_data = {}
 
         self.init_ui()
         self.init_worker_thread()
@@ -1832,6 +1835,14 @@ class MainWindowMainInit(object):
                       if not found_sub:
                           current_menu = current_menu.addMenu(part)
                  
+                 # If last action was NOT from a plugin, insert a separator
+                 actions = current_menu.actions()
+                 if actions:
+                     last_action = actions[-1]
+                     if not last_action.isSeparator() and last_action.data() != PLUGIN_ACTION_TAG:
+                          sep = current_menu.addSeparator()
+                          sep.setData(PLUGIN_ACTION_TAG)
+
                  # Add action
                  action_text = text if text else parts[-1]
                  action = QAction(action_text, self)

moleditpy_linux/modules/plugin_interface.py

@@ -65,6 +65,24 @@ class PluginContext:
         """
         return self._manager.get_main_window()
 
+    @property
+    def current_molecule(self) -> Any:
+        """
+        Get or set the current molecule (RDKit Mol object).
+        """
+        mw = self._manager.get_main_window()
+        if mw:
+            return mw.current_mol
+        return None
+
+    @current_molecule.setter
+    def current_molecule(self, mol: Any):
+        mw = self._manager.get_main_window()
+        if mw:
+            mw.current_mol = mol
+            if hasattr(mw, 'draw_molecule_3d'):
+                 mw.draw_molecule_3d(mol)
+
     def add_export_action(self, label: str, callback: Callable):
         """
         Register a custom export action.

{moleditpy_linux-2.2.4.dist-info → moleditpy_linux-2.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.2.4
+Version: 2.2.5
 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
@@ -706,7 +706,9 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 
-**MoleditPy** is a cross-platform, intuitive molecular editor built in Python. It provides a seamless workflow for drawing 2D molecular structures, visualizing them in 3D, and performing interactive geometric manipulations. Its powerful editing and export capabilities make it an ideal tool for preparing input files for DFT calculation software.
+[🇯🇵 日本語 (Japanese)](#japanese)
+
+**MoleditPy** is a **programmable** and cross-platform molecular editor built in Python. It streamlines the workflow from 2D drawing to 3D visualization, making it an **ideal tool for rapidly preparing input files for DFT calculations**. Designed as an **open platform**, it also allows users to freely extend its capabilities, writing custom Python scripts to manipulate molecular data, automate tasks, or integrate new cheminformatics algorithms seamlessly.
 
 **Author**: HiroYokoyama
 **License**: GPL-v3
@@ -715,7 +717,7 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 -----
 ![](img/icon.png)
 ![](img/screenshot.png)
------
+
 
 ## Overview
 
@@ -760,7 +762,14 @@ 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.
+      * Export 2D and 3D views as high-resolution PNG images.
+
+### 4. Programmable & Extensible
+
+  * **Python Plugin System:** Drop your Python scripts into the plugin folder, and they instantly become part of the application menu.
+  * **Downloadable Plugins:** Explore and download specialized plugins from the [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/).
+  * **Full API Access:** Plugins have direct access to the `MainWindow`, `RDKit` molecule objects, and `PyGraphics` items, allowing for limitless customization.
+  * **Rapid Prototyping:** Ideal for researchers who need to test new algorithms or workflow automations on the fly.
 
 ## Installation and Execution
 
@@ -822,9 +831,11 @@ This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**.
 
 -----
 
+<div id="japanese"></div>
+
 # MoleditPy — A Python Molecular Editor
 
-**MoleditPy**は、Pythonで構築されたクロスプラットフォームかつ直感的な分子エディターです。2Dでの分子描画から3D構造の可視化・編集、さらにはインタラクティブな幾何学的操作まで、シームレスなワークフローを提供します。その強力な編集機能とエクスポート機能により、**DFT計算ソフトウェアのインプット作成に最適なツール**です。
+**MoleditPy**は、Pythonで構築された**機能拡張が自由自在な**分子エディタープラットフォームです。2D描画から3Dへの変換により、**DFT計算用インプットの迅速な作成に最適なツール**であると同時に、**Pythonスクリプトを用いて必要な機能をユーザー自身が手軽に追加・開発できる**柔軟な環境を提供します。
 
 **作者**: HiroYokoyama
 **ライセンス**: GPL-v3
@@ -875,7 +886,14 @@ 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。
+      * 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。
+
+### 4. プログラマブルで拡張可能
+
+  * **Pythonプラグインシステム:** Pythonスクリプトをプラグインフォルダに入れるだけで、即座にアプリケーションメニューの一部として機能します。
+  * **プラグインのダウンロード:** [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/) から特化したプラグインを探索・ダウンロードできます。
+  * **フルAPIアクセス:** プラグインは `MainWindow`、`RDKit` 分子オブジェクト、`PyGraphics` アイテムに直接アクセスでき、無限のカスタマイズが可能です。
+  * **迅速なプロトタイピング:** 新しいアルゴリズムやワークフローの自動化をその場でテストしたい研究者に最適です。
 
 ## インストールと実行
 

{moleditpy_linux-2.2.4.dist-info → moleditpy_linux-2.2.5.dist-info}/RECORD

@@ -12,20 +12,20 @@ moleditpy_linux/modules/bond_item.py,sha256=eVkEeKvM4igYI67DYxpey3FllqDyt_iWDo4V
 moleditpy_linux/modules/bond_length_dialog.py,sha256=k5x_DhK9Q8CSwouKhEo_kLRRdaYHDaK84KDNmuDNLvY,14868
 moleditpy_linux/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy_linux/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy_linux/modules/constants.py,sha256=FZjG-RLZs_Xqn8D7MDAGKZAJY4G44Bh2Nm2qnDTFXm8,4702
+moleditpy_linux/modules/constants.py,sha256=DVxFJrPqhASSlFj9fRpsOe8RiJc2lJqTJMQtmnUCIqg,4702
 moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=IEdNVhFoNSEMeA5ABpUH9Q88-YzDXFloQM2gwnPwnHY,30150
 moleditpy_linux/modules/custom_interactor_style.py,sha256=NjsXE2a43IDNEanZBlcG9eR4ZIERT1MsQC6lbfesapQ,38453
 moleditpy_linux/modules/custom_qt_interactor.py,sha256=MFaTuDh-FPeFBS4303CqxsxmsOIOW4QXUz6USwI8PHQ,2451
 moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=2Sut0J5ltXMtrUJ9R3o1oZ4ysed27mdSIqLpWxmGdyM,5037
 moleditpy_linux/modules/dihedral_dialog.py,sha256=rgry7LqyX9JMAR7d82QSroTPoKT3xz18EgKN1GzYZx4,18088
 moleditpy_linux/modules/main_window.py,sha256=IL8dH3qPx2TkPgO7amuDgjlFoadh5J59xYUEVhlNZqA,36338
-moleditpy_linux/modules/main_window_app_state.py,sha256=DmBfzurTftUIkPZu8465YnxL8Hdx2vHYSbyWdB-kvjs,34757
+moleditpy_linux/modules/main_window_app_state.py,sha256=8YDcGNCSpLTO1NGL9tEvNkXpUcS7JW-uK7TdUGvEqnk,35189
 moleditpy_linux/modules/main_window_compute.py,sha256=ipIkhH_DONXDnPzh7xeym9X-Yfx8EhsvXYOdyxsAj4c,53347
 moleditpy_linux/modules/main_window_dialog_manager.py,sha256=9ZVy5-dlk8SjGU5R6NtbaVZuBQfVK5Nwrc633pEzjq8,19955
 moleditpy_linux/modules/main_window_edit_3d.py,sha256=CUArB5wcsgq1C7LygAEC6URlbnn4RhRYDa5n-Y-etWI,19731
 moleditpy_linux/modules/main_window_edit_actions.py,sha256=-SDLoMQ7S-3u3eBUb-w7BU7OAsFkhQ9ZBjF3Y2jGgZc,64708
 moleditpy_linux/modules/main_window_export.py,sha256=dSVfylsybDDboDuXU9Inotf6YkrKJwgBTqGYSfq1lRE,38241
-moleditpy_linux/modules/main_window_main_init.py,sha256=ZxScNJI-OVx_ki5C37fY4Dmm9IIm5eJWVwd7jIKu8ms,90606
+moleditpy_linux/modules/main_window_main_init.py,sha256=Shxs8_vVa7PhfhVZdHYtPniItLHKJ3i9wcamcVofvso,91172
 moleditpy_linux/modules/main_window_molecular_parsers.py,sha256=KR6vzuqc3nutOcorpYr0QOyX3MFBcxTwDhZX96VgJ9Q,48291
 moleditpy_linux/modules/main_window_project_io.py,sha256=TWwtuKDuvgcvPZ9IGmW8r1EJJOrgxrIJRnxe_f4C1oM,17149
 moleditpy_linux/modules/main_window_string_importers.py,sha256=v47wOd4RtjKYcF-aLP-mogGGdYTpTEo3dDyAu79_5MM,10782
@@ -38,7 +38,7 @@ moleditpy_linux/modules/molecule_scene.py,sha256=khdt7h9Mk_D1cMbYeHGtq7P9aFXo0xG
 moleditpy_linux/modules/move_group_dialog.py,sha256=65HVXTJSaQ9lp03XFhI1l7OzUsXmH_aqd8OgwjpjfGg,27174
 moleditpy_linux/modules/periodic_table_dialog.py,sha256=ItEZUts1XCietz9paY-spvbzxh6SXak3GnikwqkHZCw,4006
 moleditpy_linux/modules/planarize_dialog.py,sha256=yY8o-SxT8vGEHVWnjDTXecRv5NUaEejEsXH-836Xk8g,8681
-moleditpy_linux/modules/plugin_interface.py,sha256=W6Hw1OLqMkcg8XU-S347v2sDBMEoo6iiCSbmL6MjZrA,7639
+moleditpy_linux/modules/plugin_interface.py,sha256=srzPZ3a_aRTx28NAvWNKRVUDYQNfQOTcjzx-5YW2Pb4,8164
 moleditpy_linux/modules/plugin_manager.py,sha256=cxbqIE7Rb_KeBd-cG1vF2ySY2qNx8IJVRXjVPyQMFDc,13457
 moleditpy_linux/modules/plugin_manager_window.py,sha256=UeoPQWTxmckoFIQAuv9jVBzok_9gEKEm9c7JsKRX0P4,10135
 moleditpy_linux/modules/settings_dialog.py,sha256=Nr7yE8UmYRi3VObWvRlrnv0DnjSjmYXbvqryZ02O12k,65348
@@ -47,12 +47,13 @@ moleditpy_linux/modules/template_preview_view.py,sha256=4OCHZDO51BvJpKdfrBWJ4_4W
 moleditpy_linux/modules/translation_dialog.py,sha256=aWlgTR9mtEMbzGIY1SoQhDltsX-01LtCxjqy5NWtGuA,14663
 moleditpy_linux/modules/user_template_dialog.py,sha256=2hARO04DaILgdExx5ubL0GPsxK95VvVRqy7fNfudD_M,30843
 moleditpy_linux/modules/zoomable_view.py,sha256=hjwljui13QpvjvxJHY4Evot4jMQvxRBQUNH5HUlyFOk,5966
+moleditpy_linux/modules/assets/file_icon.ico,sha256=yyVj084A7HuMNbV073cE_Ag3Ne405qgOP3Mia1ZqLpE,101632
 moleditpy_linux/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy_linux/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy_linux/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
-moleditpy_linux-2.2.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-moleditpy_linux-2.2.4.dist-info/METADATA,sha256=dIsDl6OWhQ_BAlFFaYll51SyZqs7Qm4-T0tENUokPbE,59354
-moleditpy_linux-2.2.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-moleditpy_linux-2.2.4.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
-moleditpy_linux-2.2.4.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
-moleditpy_linux-2.2.4.dist-info/RECORD,,
+moleditpy_linux-2.2.5.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+moleditpy_linux-2.2.5.dist-info/METADATA,sha256=OSFWNBWdHFd_AkChJlQU61D4gzMquTUHun4pgffZndU,60708
+moleditpy_linux-2.2.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+moleditpy_linux-2.2.5.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
+moleditpy_linux-2.2.5.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
+moleditpy_linux-2.2.5.dist-info/RECORD,,