MoleditPy-linux 4.2.1__py3-none-any.whl → 4.2.3__py3-none-any.whl

moleditpy_linux/plugins/plugin_interface.py

@@ -420,8 +420,8 @@ class PluginContext:
             if fn:
                 fn()
 
-    def fit_3d_view(self) -> None:
-        """Zoom and re-center the 3D viewport to fit the current molecule."""
+    def fit_2d_view(self) -> None:
+        """Fit all 2D scene items into the 2D editor viewport."""
         mw = self.get_main_window()
         if mw and hasattr(mw, "view_3d_manager"):
             fit = getattr(mw.view_3d_manager, "fit_to_view", None)

moleditpy_linux/ui/compute_logic.py

@@ -45,6 +45,9 @@ class ComputeManager:
         self.halt_ids: Set[int] = set()
         self.next_conversion_id: int = 1
         self.active_worker_ids: Set[int] = set()
+        # worker_id -> (method_key, plugin_entry) for a plugin optimizer to run
+        # as a post-step once conversion's built-in pre-optimization completes.
+        self._pending_plugin_opt: Dict[int, Tuple[str, Dict[str, Any]]] = {}
 
     def reset_active_threads(self) -> None:
         """Reset active calculation threads list."""
@@ -239,6 +242,25 @@ class ComputeManager:
         self.next_conversion_id = run_id + 1
         self.active_worker_ids.add(run_id)
 
+        # The worker only runs built-in force fields. If the selected method is a
+        # plugin optimizer, pre-optimize with MMFF (RDKit) in the worker (which
+        # auto-falls-back to UFF if MMFF setup fails), then run the plugin
+        # callback as a post-step in on_calculation_finished.
+        effective_method = (
+            optimization_method
+            or self.host.init_manager.optimization_method
+            or "MMFF_RDKIT"
+        ).upper()
+        _reg = getattr(
+            getattr(self.host, "plugin_manager", None), "optimization_methods", None
+        )
+        plugin_entry = _reg.get(effective_method) if isinstance(_reg, dict) else None
+        if plugin_entry:
+            self._pending_plugin_opt[run_id] = (effective_method, plugin_entry)
+            worker_method = "MMFF_RDKIT"
+        else:
+            worker_method = effective_method
+
         # UI Updates
         self.host.init_manager.convert_button.setText("Halt conversion")  # type: ignore[union-attr]
         self._safe_disconnect(self.host.init_manager.convert_button.clicked)  # type: ignore[union-attr]
@@ -267,8 +289,7 @@ class ComputeManager:
         options = {
             "conversion_mode": conversion_mode
             or self.host.init_manager.settings.get("3d_conversion_mode", "fallback"),
-            "optimization_method": optimization_method
-            or self.host.init_manager.optimization_method,
+            "optimization_method": worker_method,
             "optimize_intermolecular_interaction_rdkit": self.host.init_manager.settings.get(
                 "optimize_intermolecular_interaction_rdkit", True
             ),
@@ -285,6 +306,7 @@ class ComputeManager:
         if wids_to_halt:
             self.halt_ids.update(wids_to_halt)
         self.active_worker_ids.clear()
+        self._pending_plugin_opt.clear()
 
         self._restore_button_ui()
         self.host.init_manager.cleanup_button.setEnabled(True)  # type: ignore[union-attr]
@@ -529,6 +551,16 @@ class ComputeManager:
         self.host.view_3d_manager.update_atom_id_menu_text()
         self.host.view_3d_manager.update_atom_id_menu_state()
 
+        # If the selected method was a plugin optimizer, the worker only did the
+        # built-in pre-optimization; run the plugin callback now on the result.
+        pending = (
+            self._pending_plugin_opt.pop(worker_id, None)
+            if worker_id is not None
+            else None
+        )
+        if pending and mol:
+            self._run_plugin_optimization(*pending)
+
     def on_calculation_error(self, message: Union[str, Tuple[int, str]]) -> None:
         """Handle an error or halt signal from the background optimization worker."""
         # Accept either a string or (worker_id, message) tuple from the worker signal
@@ -547,8 +579,10 @@ class ComputeManager:
                     self.host.statusBar().showMessage(  # type: ignore[union-attr]
                         f"Ignored stale worker error: {msg} (ID = {worker_id})"
                     )
+                self._pending_plugin_opt.pop(worker_id, None)
                 return  # stale worker, ignore
             self.active_worker_ids.discard(worker_id)
+            self._pending_plugin_opt.pop(worker_id, None)
         else:
             msg = str(message)
 

moleditpy_linux/ui/main_window_init.py

@@ -1723,6 +1723,13 @@ class MainInitManager:
         self.opt_group.addAction(action)
         self.opt3d_actions[key_upper] = action
 
+        # Plugins register after menu-init, so restore the saved default here
+        # if it names this method (menu-init fell back to MMFF_RDKIT).
+        saved_opt = (self.settings.get("optimization_method") or "").upper()
+        if key_upper == saved_opt:
+            action.setChecked(True)
+            self.optimization_method = key_upper
+
     def _init_help_menu(self, menu_bar: Any) -> None:
         """Initialize the Help menu."""
         help_menu = menu_bar.addMenu("&Help")

moleditpy_linux/ui/plugin_menu_manager.py

@@ -369,14 +369,30 @@ class PluginMenuManager:
                 menu.addAction(a)
 
     def integrate_plugin_optimization_methods(self) -> None:
-        """Inject plugin optimization methods into the 3D Optimization Settings menu."""
-        if not hasattr(self._im.host.plugin_manager, "optimization_methods"):
+        """Inject plugin optimization methods into the 3D Optimization Settings menu.
+
+        Idempotent: previously-added plugin methods are purged first, so a menu
+        rebuild (install/uninstall/reload) re-adds only the currently registered
+        ones. Without this, _clean_menu removes the menu action while
+        opt3d_actions still holds it, and add_optimization_method's dedupe guard
+        would then skip re-adding a still-installed method.
+        """
+        im = self._im
+        methods = getattr(im.host.plugin_manager, "optimization_methods", None)
+        if not isinstance(methods, dict):
             return
 
-        for key, entry in self._im.host.plugin_manager.optimization_methods.items():
-            self._im.add_optimization_method(entry["label"], key)
-            if key in self._im.opt3d_actions:
-                self._im.opt3d_actions[key].setData("plugin_managed")
+        for key, action in list(im.opt3d_actions.items()):
+            if action.data() == "plugin_managed":
+                im.opt_group.removeAction(action)
+                im.optimization_menu.removeAction(action)
+                del im.opt3d_actions[key]
+                im.opt3d_method_labels.pop(key, None)
+
+        for key, entry in methods.items():
+            im.add_optimization_method(entry["label"], key)
+            if key in im.opt3d_actions:
+                im.opt3d_actions[key].setData("plugin_managed")
 
     def integrate_plugin_file_openers(self) -> None:
         """Inject plugin file-opener entries into the File > Import menu."""

{moleditpy_linux-4.2.1.dist-info → moleditpy_linux-4.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.2.1
+Version: 4.2.3
 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_linux-4.2.1.dist-info → moleditpy_linux-4.2.3.dist-info}/RECORD

@@ -9,7 +9,7 @@ moleditpy_linux/core/__init__.py,sha256=BEOaCz93HzgTe0FhBzSj6Sfk8MAWxcY9vCDGmOri
 moleditpy_linux/core/mol_geometry.py,sha256=PzdJGxWs6vXwVyILBG6-6qhiVYuB33YTr8lcHRJVLNE,23933
 moleditpy_linux/core/molecular_data.py,sha256=CboEOZMjtbyRSQ7-f6kj0jngUM0Tw-7L6lU9eDtdycQ,18606
 moleditpy_linux/plugins/__init__.py,sha256=BEOaCz93HzgTe0FhBzSj6Sfk8MAWxcY9vCDGmOriJx4,267
-moleditpy_linux/plugins/plugin_interface.py,sha256=OT3K0yIZQA3HaJlavOj6wlUwS7EnEJaOhWqi1WVjD0M,22066
+moleditpy_linux/plugins/plugin_interface.py,sha256=GGRQsUGSb36RgujErcQWX-dr5pm55dnQ8K75NfviAe0,22054
 moleditpy_linux/plugins/plugin_manager.py,sha256=LeuqJdIkeqYy1SbL8JLJoKDepbdkYXG1SPus4dK15RE,32025
 moleditpy_linux/plugins/plugin_manager_window.py,sha256=ot4ftAR8GA6mn6PMuYYgMGyqqabEmtP7EVYEnxCeDDU,13432
 moleditpy_linux/ui/__init__.py,sha256=_BslFbhSM4Ba4GDzH1XpvlqlGgvi4OFkcuU3pPeIz3s,751
@@ -26,7 +26,7 @@ moleditpy_linux/ui/bond_item.py,sha256=8qm15z3OVflCtkVXRfbPGRtZidAduyZ6Yuxci3-Ed
 moleditpy_linux/ui/bond_length_dialog.py,sha256=lss8J2g_pUK-BCbqWk25JMFsn-g8SxBjiBp8mZrn57I,15930
 moleditpy_linux/ui/calculation_worker.py,sha256=bwrzCW5935Twe5EY7Mtd35YQaWJILvBPwzPIQgmqz98,41849
 moleditpy_linux/ui/color_settings_dialog.py,sha256=RFp8h0R1yC8YwqOxc972Da9xO95Gu-0qywAAEeXMj4E,14224
-moleditpy_linux/ui/compute_logic.py,sha256=7wlouTcU1qYG9srl1YyLIXZLUgxlKqTJvboP2A4aL4E,29454
+moleditpy_linux/ui/compute_logic.py,sha256=kK53dkQQy6LVnnxu5KG7jHPCjdtKirdCOVRy-5QbYRA,31086
 moleditpy_linux/ui/constrained_optimization_dialog.py,sha256=JexsKDqwogdJMKxdDyI-xce3fPq27tsCZdzl2uyXuDc,35980
 moleditpy_linux/ui/custom_interactor_style.py,sha256=8UzJ7tItbsPTSlxe69P8wLB9uOeWG2o1PpJpriRvI3M,44414
 moleditpy_linux/ui/custom_qt_interactor.py,sha256=AZ5TtQjWUs4F5FFg-tBUZQlbk74UHboTjYpBQRUlhvQ,3827
@@ -39,7 +39,7 @@ moleditpy_linux/ui/export_logic.py,sha256=97NrR6lC8U7ChN2EyOuTrl1vHB6g6xuL1BeJmY
 moleditpy_linux/ui/geometry_base_dialog.py,sha256=jj9uI2cexEjC3WxFm8HAlsrGUcTX6lQv-BX70hkSW7o,4472
 moleditpy_linux/ui/io_logic.py,sha256=cGXrECHoCkGIJ7HUZpbm4SrE-Ewmsn6b5nj4V1qsi-M,45975
 moleditpy_linux/ui/main_window.py,sha256=ygYEMJfQQ5Y2-nCMzEym2epOsMRX9JwArB_cyEp3SM4,12551
-moleditpy_linux/ui/main_window_init.py,sha256=hNo2uRcjGhZBHywvE-kuY25QEIyUCAq39gsK88iKwtM,76664
+moleditpy_linux/ui/main_window_init.py,sha256=JoCmrnVg63y-mHioBqaBeCMqwEQZVbfyJ4VVPvbxfOw,77018
 moleditpy_linux/ui/mirror_dialog.py,sha256=iRt5rRVJ4gY2Ha5BlEoYv0D_HJpVXaQz4nqsHPlZ-9c,5210
 moleditpy_linux/ui/molecular_scene_handler.py,sha256=w2TYkJFtsQzQHIfKDQbByoSxmEHOlUrfb5vYvs6-dw4,69793
 moleditpy_linux/ui/molecule_scene.py,sha256=BnYZipB9zZN76mLK3bVro_CroTo166oTz5K7obObYFA,44084
@@ -47,7 +47,7 @@ moleditpy_linux/ui/move_group_dialog.py,sha256=W5Tk2OgKAApXuEqHoB-gY6RsDerRbC3_C
 moleditpy_linux/ui/move_selected_atoms_dialog.py,sha256=NJbYZ8-DHBD7jpqlkyWKNhW7gCYpzfRXjfniPpijC5w,29654
 moleditpy_linux/ui/periodic_table_dialog.py,sha256=yadE1bbJaObAiIfpKwANqiDOBI8R3yOHvDTZYrw1J4Q,6134
 moleditpy_linux/ui/planarize_dialog.py,sha256=qWMokIKDjsuC2KY-s00nrHflIr3uw4XAcwWftNFleek,7951
-moleditpy_linux/ui/plugin_menu_manager.py,sha256=hwp2XWMknQp5R4vsZqwDDXlVk90hvgdVQr1PNhU1qr0,19874
+moleditpy_linux/ui/plugin_menu_manager.py,sha256=Lev1aeWmZInwebnYBe7TpyI01KWYSwl1-etSmDT6Ng4,20592
 moleditpy_linux/ui/settings_dialog.py,sha256=tAw-Ko73oBG5o8jnsiK4MiPar88GxiAkcnE5h6aUlYo,7319
 moleditpy_linux/ui/string_importers.py,sha256=cgsMoIYRKKP-RZZzhcpCdlDqr8KJgmazZdJ7C3GCSaE,8078
 moleditpy_linux/ui/template_preview_item.py,sha256=exJ4r3qmLOCQrEgl9ktNu4zTrgqixZcq82rUb9flWiM,7743
@@ -68,9 +68,9 @@ moleditpy_linux/utils/default_settings.py,sha256=6Q3Gw1vyG7uk-35yBtr1sKeJVnOjb4S
 moleditpy_linux/utils/sip_isdeleted_safe.py,sha256=aXoW_PDHAsu0SkqcvkUZAsWDhl9Ka8-VnzgNE5ub41Y,1215
 moleditpy_linux/utils/suppress_log.py,sha256=EFkN79q6QfYXAuii8g1fBuvFJrnVsio3aFTKMvAmXW4,928
 moleditpy_linux/utils/system_utils.py,sha256=j1RAiiKXg3N-rjpTh7yxKVAYED_kUJy4aVrY-9Hh0Mc,2674
-moleditpy_linux-4.2.1.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
-moleditpy_linux-4.2.1.dist-info/METADATA,sha256=rJnUldrcCJldKgN73wnkjKz54_xuehFDEp1z35l5wuM,64474
-moleditpy_linux-4.2.1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-moleditpy_linux-4.2.1.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
-moleditpy_linux-4.2.1.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
-moleditpy_linux-4.2.1.dist-info/RECORD,,
+moleditpy_linux-4.2.3.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+moleditpy_linux-4.2.3.dist-info/METADATA,sha256=_5QBwFNMIOGE2GTFnPH5fMH8OGzyzB0BnK5MoDAFgMs,64474
+moleditpy_linux-4.2.3.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+moleditpy_linux-4.2.3.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
+moleditpy_linux-4.2.3.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
+moleditpy_linux-4.2.3.dist-info/RECORD,,