MoleditPy-linux 4.3.0__py3-none-any.whl → 4.3.2__py3-none-any.whl

moleditpy_linux/ui/constrained_optimization_dialog.py

@@ -65,6 +65,8 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         self.constraints: list[Any] = []  # (type, atoms_indices, value)
         self.constraint_labels: list[Any] = []  # 3D label actors
         self._opt_thread: Any = None
+        # Closed dialogs must discard late optimization-thread results
+        self._closed = False
         self.init_ui()
         self.enable_picking()
 
@@ -599,6 +601,11 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             self.optimize_button.setEnabled(True)
 
     def _on_optimization_error(self, err_msg: str) -> None:
+        if self._closed:
+            logging.warning(
+                "Constrained optimization failed after dialog close: %s", err_msg
+            )
+            return
         self.optimize_button.setEnabled(True)
         status_bar = self.main_window.statusBar()
         if status_bar is not None:
@@ -606,6 +613,9 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         QMessageBox.critical(self, "Error", f"Optimization error: {err_msg}")
 
     def _on_optimization_finished(self, ff_name: str, conf: Any) -> None:
+        if self._closed:
+            logging.info("Discarding constrained optimization result after close.")
+            return
         self.optimize_button.setEnabled(True)
         try:
             # Apply optimized coordinates to the main window's numpy array
@@ -619,25 +629,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                         pos.z,
                     ]
 
-            # Update 3D view
-            self.main_window.view_3d_manager.draw_molecule_3d(self.mol)
-            self.main_window.view_3d_manager.update_chiral_labels()
-            self.main_window.edit_actions_manager.push_undo_state()
-            status_bar = self.main_window.statusBar()
-            if status_bar is not None:
-                status_bar.showMessage("Constrained optimization finished.")
-
-            try:
-                constrained_method_name = f"Constrained_{ff_name}"
-                self.main_window.compute_manager.last_successful_optimization_method = (
-                    constrained_method_name
-                )
-            except (AttributeError, RuntimeError, ValueError, TypeError) as e:
-                logging.warning(
-                    "Failed to set last_successful_optimization_method: %s", e
-                )
-
-            # Save constraints list to MainWindow on success (same logic as reject)
+            # Sync constraints to MainWindow before push_undo_state so the snapshot records them
             try:
                 # Save as list for JSON compatibility
                 json_safe_constraints = []
@@ -669,6 +661,24 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             except (AttributeError, RuntimeError, ValueError, TypeError) as e:
                 logging.warning("Failed to save constraints post-optimization: %s", e)
 
+            # Update 3D view
+            self.main_window.view_3d_manager.draw_molecule_3d(self.mol)
+            self.main_window.view_3d_manager.update_chiral_labels()
+            self.main_window.edit_actions_manager.push_undo_state()
+            status_bar = self.main_window.statusBar()
+            if status_bar is not None:
+                status_bar.showMessage("Constrained optimization finished.")
+
+            try:
+                constrained_method_name = f"Constrained_{ff_name}"
+                self.main_window.compute_manager.last_successful_optimization_method = (
+                    constrained_method_name
+                )
+            except (AttributeError, RuntimeError, ValueError, TypeError) as e:
+                logging.warning(
+                    "Failed to set last_successful_optimization_method: %s", e
+                )
+
         except (AttributeError, RuntimeError, ValueError, TypeError) as e:
             logging.exception("Optimization failed: %s", e)
 
@@ -679,6 +689,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
 
     def reject(self) -> None:
         """Clear labels, disable picking, and save constraints before closing."""
+        self._closed = True
         self.clear_constraint_labels()
         self.clear_selection_labels()
         self.disable_picking()
@@ -706,6 +717,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                     True  # Mark as unsaved changes
                 )
                 self.main_window.state_manager.update_window_title()
+                self.main_window.edit_actions_manager.push_undo_state()
 
         except (AttributeError, RuntimeError, ValueError, TypeError) as e:
             logging.warning("Failed to save constraints to main window: %s", e)

moleditpy_linux/ui/custom_interactor_style.py

@@ -159,9 +159,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                             try:
                                 move_group_dialog.on_atom_picked(clicked_atom_idx)
                             except (AttributeError, RuntimeError):
-                                # Safe defensive fallback catching AttributeError, RuntimeError
-                                logging.debug(
-                                    "Suppressed non-critical error", exc_info=True
+                                logging.warning(
+                                    "Move-dialog atom toggle failed", exc_info=True
                                 )
 
                         QTimer.singleShot(0, _deferred_toggle)
@@ -273,9 +272,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                                         closest_atom_idx
                                     )
                                 except (AttributeError, RuntimeError):
-                                    # Safe defensive fallback catching AttributeError, RuntimeError
-                                    logging.debug(
-                                        "Suppressed non-critical error", exc_info=True
+                                    logging.warning(
+                                        "Measurement selection failed", exc_info=True
                                     )
 
                             QTimer.singleShot(0, _deferred_measure)
@@ -383,6 +381,54 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         # Standard right-click
         super().OnRightButtonDown()
 
+    def _heal_stuck_pointer_state(self, move_group_dialog: Any) -> None:
+        """Self-heal drag/rotate state whose release event was lost.
+
+        A release can be lost mid-gesture (e.g. pyvista temporarily swapping
+        the interactor style, a dialog grabbing events), leaving this style or
+        a Move Group dialog in a permanent drag/rotate state that blocks
+        interaction. Verify against the real button state on every move and
+        reset when the button is not actually held.
+        """
+        try:
+            buttons = QApplication.mouseButtons()
+            left_held = bool(buttons & Qt.MouseButton.LeftButton)
+            right_held = bool(buttons & Qt.MouseButton.RightButton)
+            any_held = buttons != Qt.MouseButton.NoButton
+        except (AttributeError, RuntimeError, TypeError):
+            return
+
+        if self._is_dragging_atom and not left_held:
+            self.reset_interactor_state()
+
+        if not any_held:
+            try:
+                if self.GetState() != 0:  # stuck ROTATE/PAN/etc. without a button
+                    self.reset_interactor_state()
+            except (AttributeError, RuntimeError, TypeError):
+                # Safe defensive fallback catching AttributeError, RuntimeError, TypeError
+                logging.debug("Suppressed non-critical error", exc_info=True)
+
+        if move_group_dialog is not None:
+            try:
+                if (
+                    getattr(move_group_dialog, "is_dragging_group_vtk", False)
+                    and not left_held
+                ):
+                    move_group_dialog.is_dragging_group_vtk = False
+                    move_group_dialog.drag_start_pos_vtk = None
+                    move_group_dialog.mouse_moved_vtk = False
+                if (
+                    getattr(move_group_dialog, "is_rotating_group_vtk", False)
+                    and not right_held
+                ):
+                    move_group_dialog.is_rotating_group_vtk = False
+                    move_group_dialog.rotation_start_pos = None
+                    move_group_dialog.rotation_mouse_moved = False
+            except (AttributeError, RuntimeError, TypeError):
+                # Safe defensive fallback catching AttributeError, RuntimeError, TypeError
+                logging.debug("Suppressed non-critical error", exc_info=True)
+
     def on_mouse_move(self, obj: Any, event: Any) -> None:
         """
         Handle mouse move (drag vs camera/hover).
@@ -402,6 +448,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     break
         except (AttributeError, RuntimeError, TypeError):
             logging.warning("Caught exception in " + __file__, exc_info=True)
+
+        self._heal_stuck_pointer_state(move_group_dialog)
         if move_group_dialog and getattr(
             move_group_dialog, "is_dragging_group_vtk", False
         ):

moleditpy_linux/ui/custom_qt_interactor.py

@@ -10,9 +10,11 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import time
+import logging
 from typing import Any, Optional
 
+from PyQt6.QtCore import QEvent
+from PyQt6.QtGui import QMouseEvent
 from pyvistaqt import QtInteractor
 
 
@@ -27,9 +29,6 @@ class CustomQtInteractor(QtInteractor):
     ) -> None:
         super().__init__(parent, **kwargs)
         self.main_window = main_window
-        self._last_click_time = 0.0
-        self._click_count = 0
-        self._ignore_next_release = False
 
     def wheelEvent(self, event: Any) -> None:
         """
@@ -45,61 +44,32 @@ class CustomQtInteractor(QtInteractor):
     def mouseReleaseEvent(self, event: Any) -> None:
         """
         Override the Qt mouse release event to return focus to the 2D view after
-        all 3D view operations. Also filters out "Ghost Release" (release without
-        a corresponding press).
+        all 3D view operations.
         """
-        if self._ignore_next_release:
-            self._ignore_next_release = False
-            event.accept()
-            return
-
         super().mouseReleaseEvent(event)  # Process parent class event first
         if self.main_window and hasattr(self.main_window.init_manager, "view_2d"):
             self.main_window.init_manager.view_2d.setFocus()
 
-    def mousePressEvent(self, event: Any) -> None:
-        """
-        Custom mouse press handling to track accumulated clicks and filter out
-        triple-clicks.
-        """
-        current_time = time.time()
-        # Reset count if too much time has passed (0.5s is standard double-click time)
-        if current_time - self._last_click_time > 0.5:
-            self._click_count = 0
-
-        self._click_count += 1
-        self._last_click_time = current_time
-
-        # If this is the 3rd click (or more), swallow it to prevent
-        # the internal state desync that happens with rapid clicking sequences.
-        if self._click_count >= 3:
-            self._ignore_next_release = True
-            event.accept()
-            return
-
-        super().mousePressEvent(event)
-
     def mouseDoubleClickEvent(self, event: Any) -> None:
-        """Ignore mouse double-clicks on the 3D widget to avoid accidental actions.
+        """Re-dispatch double-clicks as plain presses so fast clicking works.
 
-        Swallow the double-click event so it doesn't trigger selection, editing,
-        or camera jumps. We intentionally do not call the superclass handler.
-        Crucially, we also flag the NEXT release event to be swallowed, preventing
-        a "Ghost Release" (Release without Press) from reaching VTK.
+        Qt turns every second fast click into a double-click event. Forwarding
+        it unchanged would reach VTK with a repeat count and be dropped by the
+        interactor style, so the click would be lost (e.g. when rapidly
+        selecting atoms in measurement mode). Synthesizing a normal press keeps
+        press/release pairing intact and makes each fast click act as a click.
         """
-        current_time = time.time()
-        self._last_click_time = current_time
-        # Set to 2 to ensure the next click counts as 3rd
-        if current_time - self._last_click_time < 0.5:
-            self._click_count = 2
-        else:
-            self._click_count = 2  # Force sync
-
-        self._ignore_next_release = True
-
         try:
-            # Accept the event to mark it handled and prevent further processing.
+            synthetic_press = QMouseEvent(
+                QEvent.Type.MouseButtonPress,
+                event.position(),
+                event.globalPosition(),
+                event.button(),
+                event.buttons(),
+                event.modifiers(),
+            )
+            super().mousePressEvent(synthetic_press)
             event.accept()
         except (AttributeError, RuntimeError, TypeError):
-            # If event doesn't support accept for some reason, just return.
-            return
+            # Safe defensive fallback catching AttributeError, RuntimeError, TypeError
+            logging.debug("Suppressed non-critical error", exc_info=True)

moleditpy_linux/ui/dialog_3d_picking_mixin.py

@@ -82,9 +82,8 @@ class Dialog3DPickingMixin:
                             try:
                                 self.on_atom_picked(int(closest_atom_idx))
                             except (AttributeError, RuntimeError):
-                                # Safe defensive fallback catching AttributeError, RuntimeError
-                                logging.debug(
-                                    "Suppressed non-critical error", exc_info=True
+                                logging.warning(
+                                    "Dialog atom pick failed", exc_info=True
                                 )
 
                         from PyQt6.QtCore import QTimer

moleditpy_linux/ui/edit_actions_logic.py

@@ -21,6 +21,7 @@ from typing import Any, Dict, List, Optional, TYPE_CHECKING
 import numpy as np
 
 from ..core.mol_geometry import identify_valence_problems
+from .app_state import _serialize_constraints
 
 # RDKit imports (explicit to satisfy flake8 and used features)
 from PyQt6.QtCore import QByteArray, QMimeData, QPointF, Qt, QTimer
@@ -116,6 +117,15 @@ class EditActionsManager:
         self.redo_stack.clear()
         self.push_undo_state()
 
+    def _constraints_for_comparison(self) -> List[Any]:
+        """Current 3D constraints in the serialized form stored in snapshots."""
+        constraints = getattr(
+            getattr(self.host, "edit_3d_manager", None), "constraints_3d", None
+        )
+        if not isinstance(constraints, list):
+            return []
+        return _serialize_constraints(constraints)
+
     def push_undo_state(self) -> None:
         """Saves current molecular state to undo stack for history tracking."""
         if getattr(self.host, "is_restoring_state", False):
@@ -150,6 +160,7 @@ class EditActionsManager:
             ]
             if self.host.view_3d_manager.current_mol
             else None,
+            "constraints_3d": self._constraints_for_comparison(),
         }
 
         last_state_for_comparison = None
@@ -174,6 +185,7 @@ class EditActionsManager:
                 "_next_atom_id": last_state.get("_next_atom_id"),
                 "mol_3d": last_state.get("mol_3d", None),
                 "mol_3d_atom_ids": last_state.get("mol_3d_atom_ids", None),
+                "constraints_3d": last_state.get("constraints_3d") or [],
             }
 
         if (

moleditpy_linux/ui/export_logic.py

@@ -116,8 +116,8 @@ class ExportManager:
             if not file_path.lower().endswith(".obj"):
                 file_path += ".obj"
 
-            # Save as OBJ+MTL with material per object
-            mtl_path = file_path.replace(".obj", ".mtl")
+            # splitext, not str.replace: ".OBJ" must not make mtl_path collide with file_path
+            mtl_path = os.path.splitext(file_path)[0] + ".mtl"
 
             self.create_multi_material_obj(meshes_with_colors, file_path, mtl_path)
 

moleditpy_linux/ui/io_logic.py

@@ -242,6 +242,14 @@ class IOManager:
             final_mol.xyz_atom_data = atoms_data
         return final_mol
 
+    def _report_load_error(self, title: str, message: str) -> None:
+        """Report a load failure on the status bar and, in GUI mode, a dialog."""
+        status_bar = self.host.statusBar()
+        if status_bar is not None:
+            status_bar.showMessage(message)
+        if not os.environ.get("MOLEDITPY_HEADLESS"):
+            QMessageBox.warning(self.host, title, message)
+
     def load_xyz_file(self, file_path: str) -> Optional[Any]:
         """Load XYZ file and create RDKit Mol with charge prompt and bond determination."""
         if not self.host.state_manager.check_unsaved_changes():
@@ -349,6 +357,19 @@ class IOManager:
             # Unreachable via OK (validated inline)
             return 0, True, False
 
+    @staticmethod
+    def _covalent_radius(symbol: str, atomic_num: int) -> float:
+        """Covalent radius from the local table, RDKit's periodic table for
+        elements the table lacks (it stops at V), or 1.0 as a last resort."""
+        radius = COVALENT_RADII.get(symbol)
+        if radius:
+            return radius
+        try:
+            radius = Chem.GetPeriodicTable().GetRcovalent(atomic_num)
+        except (ValueError, RuntimeError):
+            radius = 0.0
+        return radius if radius > 0.0 else 1.0
+
     def estimate_bonds_from_distances(self, mol: Chem.RWMol) -> int:
         """Estimate bonds based on interatomic distances using covalent radii."""
         conf = mol.GetConformer()
@@ -364,8 +385,8 @@ class IOManager:
                 distance = rdMolTransforms.GetBondLength(conf, i, j)
                 symbol_i = atom_i.GetSymbol()
                 symbol_j = atom_j.GetSymbol()
-                radius_i = COVALENT_RADII.get(symbol_i, 1.0)
-                radius_j = COVALENT_RADII.get(symbol_j, 1.0)
+                radius_i = self._covalent_radius(symbol_i, atom_i.GetAtomicNum())
+                radius_j = self._covalent_radius(symbol_j, atom_j.GetAtomicNum())
                 expected = radius_i + radius_j
                 tolerance = 1.2 if (symbol_i == "H" or symbol_j == "H") else 1.3
                 if expected * 0.5 <= distance <= expected * tolerance:
@@ -493,8 +514,9 @@ class IOManager:
         elif file_path.lower().endswith(".pmeraw"):
             self.load_raw_data(file_path)
         else:
-            self.host.statusBar().showMessage(
-                "Error: Unable to determine file format or file corrupted."
+            self._report_load_error(
+                "Project Load Error",
+                "Error: Unable to determine file format or file corrupted.",
             )
 
     def save_as_json(self) -> None:
@@ -592,14 +614,23 @@ class IOManager:
             QTimer.singleShot(100, self.host.view_3d_manager.fit_to_view)
 
         except FileNotFoundError:
-            self.host.statusBar().showMessage(f"File not found: {file_path}")
+            self._report_load_error(
+                "Project Load Error", f"File not found: {file_path}"
+            )
         except json.JSONDecodeError as e:
-            self.host.statusBar().showMessage(f"Invalid JSON format: {e}")
+            self._report_load_error("Project Load Error", f"Invalid JSON format: {e}")
         except (OSError, IOError) as e:
-            self.host.statusBar().showMessage(f"File I/O error: {e}")
-        except (TypeError, ValueError, RuntimeError, AttributeError, KeyError) as e:
-            self.host.statusBar().showMessage(
-                f"Data corruption in PME Project file: {e}"
+            self._report_load_error("Project Load Error", f"File I/O error: {e}")
+        except (
+            TypeError,
+            ValueError,
+            RuntimeError,
+            AttributeError,
+            KeyError,
+            IndexError,
+        ) as e:
+            self._report_load_error(
+                "Project Load Error", f"Data corruption in PME Project file: {e}"
             )
 
     def save_raw_data(self) -> None:
@@ -757,7 +788,7 @@ class IOManager:
             AttributeError,
             KeyError,
         ) as e:
-            self.host.statusBar().showMessage(f"Error loading file: {e}")
+            self._report_load_error("MOL Import Error", f"Error loading file: {e}")
 
     def save_as_mol(self) -> None:
         """Save current 2D structure as MOL file."""
@@ -842,8 +873,7 @@ class IOManager:
             self.host.set_has_unsaved_changes(False)
             self.host.state_manager.update_window_title()
         except (OSError, IOError, ValueError, RuntimeError, AttributeError) as e:
-            if self.host.statusBar():
-                self.host.statusBar().showMessage(f"XYZ Load failed: {e}")
+            self._report_load_error("XYZ Load Error", f"XYZ Load failed: {e}")
 
     def load_mol_file_for_3d_viewing(self, file_path: Optional[str] = None) -> None:
         """Open MOL/SDF file in 3D viewer."""
@@ -897,7 +927,7 @@ class IOManager:
             self.host.set_has_unsaved_changes(False)
             self.host.state_manager.update_window_title()
         except (OSError, IOError, ValueError, RuntimeError, AttributeError) as e:
-            self.host.statusBar().showMessage(f"3D MOL Load failed: {e}")
+            self._report_load_error("3D MOL Load Error", f"3D MOL Load failed: {e}")
 
     def save_3d_as_mol(self) -> None:
         """Save current 3D structure as MOL file."""
@@ -1031,13 +1061,26 @@ class IOManager:
             QTimer.singleShot(100, self._plotter_render)
 
         except FileNotFoundError:
-            self.host.statusBar().showMessage(f"File not found: {file_path}")
+            self._report_load_error(
+                "Project Load Error", f"File not found: {file_path}"
+            )
         except (OSError, IOError) as e:
-            self.host.statusBar().showMessage(f"File I/O error: {e}")
-        except pickle.UnpicklingError as e:
-            self.host.statusBar().showMessage(f"Invalid project file format: {e}")
-        except (TypeError, ValueError, RuntimeError, AttributeError) as e:
-            self.host.statusBar().showMessage(f"Error loading project file: {e}")
+            self._report_load_error("Project Load Error", f"File I/O error: {e}")
+        except (pickle.UnpicklingError, EOFError, ImportError) as e:
+            self._report_load_error(
+                "Project Load Error", f"Invalid project file format: {e}"
+            )
+        except (
+            TypeError,
+            ValueError,
+            RuntimeError,
+            AttributeError,
+            KeyError,
+            IndexError,
+        ) as e:
+            self._report_load_error(
+                "Project Load Error", f"Error loading project file: {e}"
+            )
 
     def _set_mol_prop(self, mol: Chem.Mol, prop_name: str, value: Any) -> None:
         """Set an RDKit molecule property safely."""

moleditpy_linux/ui/main_window_init.py

@@ -202,7 +202,8 @@ class MainInitManager:
         self.host.edit_actions_manager.update_edit_menu_actions()
 
         if initial_file:
-            self.load_command_line_file(initial_file)
+            # Deferred: a load-error dialog raised in the constructor would block the window from showing
+            QTimer.singleShot(0, lambda: self.load_command_line_file(initial_file))
 
         QTimer.singleShot(0, self.apply_initial_settings)
         # Camera initialization flag (permits reset only during the first draw)
@@ -1195,6 +1196,7 @@ class MainInitManager:
 
         file_menu.addSeparator()
         quit_action = QAction("Quit", self.host)
+        quit_action.setShortcut("Ctrl+Q")
         quit_action.triggered.connect(self.host.close)
         file_menu.addAction(quit_action)
 

moleditpy_linux/ui/molecular_scene_handler.py

@@ -1099,11 +1099,13 @@ class KeyboardMixin:
                     # 3. Update BondItem properties based on key
                     if key == Qt.Key.Key_W:
                         if bond.stereo == 1:
+                            # Flip mutates the model without changing order/stereo, so set the undo flag here
                             bond_data = self.data.bonds.pop(current_key)
                             new_key = (current_key[1], current_key[0])
                             self.data.bonds[new_key] = bond_data
                             bond.atom1, bond.atom2 = bond.atom2, bond.atom1
                             bond.update_position()
+                            any_bond_changed = True
                         else:
                             bond.order = 1
                             bond.stereo = 1
@@ -1115,6 +1117,7 @@ class KeyboardMixin:
                             self.data.bonds[new_key] = bond_data
                             bond.atom1, bond.atom2 = bond.atom2, bond.atom1
                             bond.update_position()
+                            any_bond_changed = True
                         else:
                             bond.order = 1
                             bond.stereo = 2

moleditpy_linux/ui/move_selected_atoms_dialog.py

@@ -696,9 +696,13 @@ class MoveSelectedAtomsDialog(BasePickingDialog):
         else:
             btn.setText("Box Selection: OFF")
             plotter.disable_picking()
-            # Restore original style
+            # Restore original style via pyvista's bookkeeping so its
+            # update_style() re-asserts ours instead of RubberBandPick
             if self.original_style is not None:
-                plotter.interactor.SetInteractorStyle(self.original_style)
+                try:
+                    plotter.iren.style = self.original_style
+                except AttributeError:
+                    plotter.interactor.SetInteractorStyle(self.original_style)
 
     def on_rectangle_picked(self, selection: Any) -> None:
         """Handle PyVista rectangle picking callback."""

moleditpy_linux/ui/plugin_menu_manager.py

@@ -143,6 +143,20 @@ class PluginMenuManager:
         except Exception:
             logging.warning("Plugin rebuild: menu cleanup error", exc_info=True)
 
+        # Drop tagged (plugin-created) top-level menus the clean pass emptied
+        try:
+            menu_bar = self._im.host.menuBar()
+            for top_action in list(menu_bar.actions()):
+                if top_action.data() != self._PLUGIN_ACTION_TAG:
+                    continue
+                submenu = top_action.menu()
+                if submenu is None or not any(
+                    not a.isSeparator() for a in submenu.actions()
+                ):
+                    menu_bar.removeAction(top_action)
+        except Exception:
+            logging.warning("Plugin rebuild: menubar cleanup error", exc_info=True)
+
         self._im.plugin_menubar_separator_added = False
 
         for method, label in [
@@ -182,9 +196,11 @@ class PluginMenuManager:
 
             if not current_menu:
                 if not self._im.plugin_menubar_separator_added:
-                    self._im.host.menuBar().addSeparator()
+                    sep = self._im.host.menuBar().addSeparator()
+                    sep.setData(self._PLUGIN_ACTION_TAG)
                     self._im.plugin_menubar_separator_added = True
                 current_menu = self._im.host.menuBar().addMenu(top_level_title)
+                current_menu.menuAction().setData(self._PLUGIN_ACTION_TAG)
 
             for part in parts[1:-1]:
                 sub = next(

moleditpy_linux/ui/ui_manager.py

@@ -322,9 +322,51 @@ class UIManager(QObject):
         style = CustomInteractorStyle(self.host)
 
         # Set interactor style
-        self.host.view_3d_manager.plotter.interactor.SetInteractorStyle(style)
+        self._install_interactor_style(style)
         self.host.view_3d_manager.plotter.interactor.Initialize()
 
+        # Watchdog: if anything silently replaces the custom style (observed as
+        # "rotation works but pick/select is dead"), report it and reinstall.
+        self._expected_style = style
+        self._style_watchdog = QTimer(self)
+        self._style_watchdog.setInterval(2000)
+        self._style_watchdog.timeout.connect(self._check_interactor_style)
+        self._style_watchdog.start()
+
+    def _install_interactor_style(self, style: Any) -> None:
+        """Install *style* through pyvista's bookkeeping, not raw VTK.
+
+        pyvista's RenderWindowInteractor re-asserts its own ``_style_class``
+        via ``update_style()`` whenever its built-in double-click chart
+        handler fires (fast clicks!). Installing through the ``iren.style``
+        property keeps that bookkeeping pointing at our style so the
+        re-assert is a no-op instead of an eviction.
+        """
+        plotter = self.host.view_3d_manager.plotter
+        try:
+            plotter.iren.style = style
+        except AttributeError:
+            plotter.interactor.SetInteractorStyle(style)
+
+    def _check_interactor_style(self) -> None:
+        """Reinstall CustomInteractorStyle if it was silently replaced."""
+        try:
+            interactor = self.host.view_3d_manager.plotter.interactor
+            current = interactor.GetInteractorStyle()
+            if current is self._expected_style:
+                return
+            name = type(current).__name__
+            if "RubberBand" in name:  # legitimate temporary box-selection style
+                return
+            logging.debug(
+                "3D interactor style was replaced by %s — reinstalling "
+                "CustomInteractorStyle",
+                name,
+            )
+            self._install_interactor_style(self._expected_style)
+        except (AttributeError, RuntimeError):
+            logging.debug("Style watchdog check failed", exc_info=True)
+
     def handle_drag_enter_event(self, event: QDragEnterEvent) -> None:
         """Internal handler for drag enter event (bypasses PyQt type checks in tests)."""
         mime_data = event.mimeData()

{moleditpy_linux-4.3.0.dist-info → moleditpy_linux-4.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.3.0
+Version: 4.3.2
 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
@@ -770,16 +770,17 @@ This application combines a modern GUI built with **PyQt6**, powerful cheminform
   * **Stereochemistry Display:** Automatically identifies and displays R/S labels for chiral centers in the 3D view after conversion.
   * **File I/O:**
       * Save and load entire sessions, including 2D/3D data and constraints, with the native `.pmeprj` project file.
-      * Import structures from **MOL/SDF** files or **SMILES** strings.
+      * Import structures from **MOL/SDF/XYZ** files or **SMILES/InChI** 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.
+      * Export 2D views as high-resolution PNG or SVG images, and 3D views as PNG images.
+      * Export the 3D model as **STL** or **OBJ/MTL** files for 3D printing and rendering.
       * **Security note on `.pmeraw`:** the legacy `.pmeraw` project format uses Python pickle, which can execute arbitrary code when loaded. Only open `.pmeraw` files that you created yourself; prefer the JSON-based `.pmeprj` format for sharing.
 
 ### 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.
+  * **Full API Access:** Plugins have direct access to the `MainWindow`, `RDKit` molecule objects, and the Qt graphics items of the 2D scene, allowing for limitless customization.
   * **Rapid Prototyping:** Ideal for researchers who need to test new algorithms or workflow automations on the fly.
 
 ## Installation and Execution
@@ -835,7 +836,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
-  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The `MainWindow` acts as a composition hub that delegates all work to specialized manager objects (state, I/O, 3D view, dialogs), ensuring long-term maintainability and easier verification.
 
 ## License & Disclaimer
 
@@ -905,16 +906,17 @@ Additionally, please cite the plugins you used.
   * **立体化学表示:** 3D変換後、キラル中心を自動的に認識し、R/Sラベルを3Dビューに表示します。
   * **ファイル入出力:**
       * 2D/3Dデータや制約情報を含むセッション全体を、独自のプロジェクトファイル (`.pmeprj`) として保存・読み込みできます。
-      * **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。
+      * **MOL/SDF/XYZ**ファイルや**SMILES/InChI**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。
+      * 2Dビューを高解像度のPNG・SVG画像として、3DビューをPNG画像としてエクスポートできます。
+      * 3Dモデルを**STL**または**OBJ/MTL**ファイルとしてエクスポートでき、3Dプリントやレンダリングに利用できます。
       * **`.pmeraw` に関するセキュリティ上の注意:** 旧形式の `.pmeraw` プロジェクトは Python の pickle を使用しており、読み込み時に任意のコードが実行される可能性があります。自分で作成した `.pmeraw` ファイルのみを開き、共有には JSON ベースの `.pmeprj` 形式を使用してください。
 
 ### 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。
+  * **フルAPIアクセス:** プラグインは `MainWindow`、`RDKit` 分子オブジェクト、2D シーンの Qt グラフィックス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
@@ -970,6 +972,7 @@ moleditpy
   * **GUIと2D描画 (PyQt6):** `QGraphicsScene`上にカスタムの`AtomItem`（原子）と`BondItem`（結合）を配置し、対話的に操作します。Undo/Redo機能は、アプリケーションの状態をシリアライズしてスタックに保存することで実現しています。
   * **化学計算 (RDKit / Open Babel):** 2DデータからRDKit分子オブジェクトを生成し、3D座標生成や分子特性計算を実行します。RDKitでの3D座標生成が失敗した際は、Open Babelにフォールバックします。重い計算処理は別スレッド (`QThread`) で実行し、GUIの応答性を維持しています。
   * **3D可視化 (PyVista / pyvistaqt):** RDKitのコンフォーマ座標からPyVistaのメッシュ（球や円柱）を生成して描画します。カスタムの`vtkInteractorStyle`を実装し、3Dビュー内での原子の直接的なドラッグ＆ドロップ編集を可能にしています。
+  * **モジュラーアーキテクチャ:** コードベースは `core` ロジック、`ui` コンポーネント、`utils` の専用パッケージに整理されています。`MainWindow` は、状態管理・ファイル入出力・3D ビュー・ダイアログなどを専門のマネージャーオブジェクトに委譲するコンポジションハブとして機能し、長期的な保守性と検証の容易さを確保しています。
 
 ## ライセンス & 免責事項
 

{moleditpy_linux-4.3.0.dist-info → moleditpy_linux-4.3.2.dist-info}/RECORD

@@ -27,33 +27,33 @@ moleditpy_linux/ui/bond_length_dialog.py,sha256=lss8J2g_pUK-BCbqWk25JMFsn-g8SxBj
 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=DIPmqzlQv-g-MK8EllAD_soG0tk8PMoW5oxEl-uvsJA,31216
-moleditpy_linux/ui/constrained_optimization_dialog.py,sha256=Adz27xAMZJrfN3e118Z6h6VMvdmCNcuRyYl755YBSDE,35824
-moleditpy_linux/ui/custom_interactor_style.py,sha256=zbZCmAZAR1ywuENDIb_guIhu09IUn_kjeopr6FT2t2s,44529
-moleditpy_linux/ui/custom_qt_interactor.py,sha256=AZ5TtQjWUs4F5FFg-tBUZQlbk74UHboTjYpBQRUlhvQ,3827
-moleditpy_linux/ui/dialog_3d_picking_mixin.py,sha256=lH7NS7zF_TxhXEIr_mEPg-9LpI1AqpsZzMFAue33AIA,10705
+moleditpy_linux/ui/constrained_optimization_dialog.py,sha256=rc3YK6DOJdIbhriwsM2jOAW9j_-3PvFz1XtFHpGw4E4,36346
+moleditpy_linux/ui/custom_interactor_style.py,sha256=p48f1BD8OK36lyAimK69lXbITjuXRg7QO8aSwk4ogtI,46791
+moleditpy_linux/ui/custom_qt_interactor.py,sha256=76L0Jpbg09VXzHOzJs9kG260Vs9qcwbt8Chn0iOopDg,2820
+moleditpy_linux/ui/dialog_3d_picking_mixin.py,sha256=nsZQ27PYZrO9s_w5EXxxluVfOOmNKcv0vvm89IWN7mU,10604
 moleditpy_linux/ui/dialog_logic.py,sha256=KCz3ZPJap4K_tiNDjCzGqQHYxdEsvcUG6Lws2tDhvx4,19617
 moleditpy_linux/ui/dihedral_dialog.py,sha256=0-EeJZG6YCehCWwqCEOougzZjF-zyzKEHCUC_cls7GE,18833
 moleditpy_linux/ui/edit_3d_logic.py,sha256=DcdZZwPRkJ0RIReyTyvelkZILYG-vggop92dz2hkYSY,19192
-moleditpy_linux/ui/edit_actions_logic.py,sha256=QE2w90Lo_0JI78X9Og1qVgX-woZLipxna3aOD0g-j1Y,66080
-moleditpy_linux/ui/export_logic.py,sha256=97NrR6lC8U7ChN2EyOuTrl1vHB6g6xuL1BeJmYyy7p8,43720
+moleditpy_linux/ui/edit_actions_logic.py,sha256=no8SM7munZv7Nb5tEEaRr9vCIiDgYCns9wK4QZ1Tq4c,66656
+moleditpy_linux/ui/export_logic.py,sha256=lZnzTLIEy_UWHiZpJ5Decr1-fy1JFMVjJNgXXc2cs2o,43765
 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/io_logic.py,sha256=a5ER4P6NCFfIv4nRiDiclCJ3_9F_OjZkqVUEw26AS8w,47427
 moleditpy_linux/ui/main_window.py,sha256=qVSN2XclGCBsRCRtC10xBUn5VdzPer0rzMPHOuYw2ZU,12553
-moleditpy_linux/ui/main_window_init.py,sha256=I4CmwH7E_xzKmHWYbooarKek2bhznXySViB3lkBJfJ4,77064
+moleditpy_linux/ui/main_window_init.py,sha256=94_Sf_E5ZTtkyQvSIURWXbuXxabg46L0AxOMsVPKHf8,77244
 moleditpy_linux/ui/mirror_dialog.py,sha256=Tsc2O9Ktjz0zzJWB_YkVgkqgDhytQ7ksN_PwpcY9vJI,5169
-moleditpy_linux/ui/molecular_scene_handler.py,sha256=WJ8LM88e5RMLRojClaS2_GC2zsJrN5LgtHK9J1FSRvA,69818
+moleditpy_linux/ui/molecular_scene_handler.py,sha256=Y53CceA2cbtPdY-n7mcnYsfRl2MgQT55R9xCMQ4m18o,70035
 moleditpy_linux/ui/molecule_scene.py,sha256=ZUZBaCyWaNEAITHI4JmJ__gQcI9kgttj8qBP6dgF6LU,44090
 moleditpy_linux/ui/move_group_dialog.py,sha256=3jfj8zmKrYs0N9537o3g0V3f0UOnr0pj8uNT0qvUlPM,27063
-moleditpy_linux/ui/move_selected_atoms_dialog.py,sha256=6Q43RXKL8Fmkf93emxUJYeel-QqMQ_lCyzeq8Bj6PV4,29656
+moleditpy_linux/ui/move_selected_atoms_dialog.py,sha256=7_Krz69LDx71_pBr9_bP55UhT97SJZU-W6OEN59waDg,29889
 moleditpy_linux/ui/periodic_table_dialog.py,sha256=yadE1bbJaObAiIfpKwANqiDOBI8R3yOHvDTZYrw1J4Q,6134
 moleditpy_linux/ui/planarize_dialog.py,sha256=PvEXAx27iO3d9OWrr0kL4WTeNI2eMIx-FRZaFWW-cao,7936
-moleditpy_linux/ui/plugin_menu_manager.py,sha256=fxo8osB3AsPWvetJa5skZLymYTEVvgVMyvgxzpuusAs,21317
+moleditpy_linux/ui/plugin_menu_manager.py,sha256=EXju-Bcy-Wxg_MpJLsV2nUgjlwVpyqZBVU5VohzUk5w,22101
 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
 moleditpy_linux/ui/template_preview_view.py,sha256=XMJ5tg4CdF2QA_6Yt0DMXAMWFugmiOadhIEvLpclsbo,3817
 moleditpy_linux/ui/translation_dialog.py,sha256=jAEHOCICixT1TcsQHnW-8h1o1HMxPC8Mw3_qYrUaoI0,16663
-moleditpy_linux/ui/ui_manager.py,sha256=7NbTQOdabHmmurReDdJTVPSZbwJzZb9FkHnYZWZApjw,26635
+moleditpy_linux/ui/ui_manager.py,sha256=cljxqBlvlz98n5uiie1auKJdenGAeRIVF9e21R1hkDA,28568
 moleditpy_linux/ui/user_template_dialog.py,sha256=ZKGMyhqzS14CKor51YiEcHUXe8bNvughRDTG9-Pc-d0,29198
 moleditpy_linux/ui/view_3d_logic.py,sha256=fuXQKAQFH8e_Xm6e8mG2y4EN2EnBqFxJRqsloilBU9c,92757
 moleditpy_linux/ui/zoomable_view.py,sha256=Kpr9SaIYAKH-Fexm5-gi3cswsiT5V7g7yTk7acutZjA,6239
@@ -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-4.3.0.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
-moleditpy_linux-4.3.0.dist-info/METADATA,sha256=lkQg-9e6L8dbr3cKWRE8fMVlrCqTICB6_JtYR90VMI4,64474
-moleditpy_linux-4.3.0.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
-moleditpy_linux-4.3.0.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
-moleditpy_linux-4.3.0.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
-moleditpy_linux-4.3.0.dist-info/RECORD,,
+moleditpy_linux-4.3.2.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+moleditpy_linux-4.3.2.dist-info/METADATA,sha256=IE2cOdceTHiUxPeNUczyD4YL3fsLiSZyZwxYa1JwuXQ,65372
+moleditpy_linux-4.3.2.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
+moleditpy_linux-4.3.2.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
+moleditpy_linux-4.3.2.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
+moleditpy_linux-4.3.2.dist-info/RECORD,,