MoleditPy 3.5.2__tar.gz → 3.6.0__tar.gz

{moleditpy-3.5.2 → moleditpy-3.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.5.2
+Version: 3.6.0
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -805,7 +805,7 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     After installation, run this command to create the shortcut in your application menu (e.g., Start Menu or Applications folder).
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### Running the Application
@@ -938,7 +938,7 @@ Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Ze
     インストール後、このコマンドを実行すると、アプリケーションメニュー（スタートメニューやアプリケーションフォルダなど）にショートカットが作成されます。
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### アプリケーションの起動

{moleditpy-3.5.2 → moleditpy-3.6.0}/README.md

@@ -101,7 +101,7 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     After installation, run this command to create the shortcut in your application menu (e.g., Start Menu or Applications folder).
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### Running the Application
@@ -234,7 +234,7 @@ Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Ze
     インストール後、このコマンドを実行すると、アプリケーションメニュー（スタートメニューやアプリケーションフォルダなど）にショートカットが作成されます。
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### アプリケーションの起動

{moleditpy-3.5.2 → moleditpy-3.6.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.5.2"
+version = "3.6.0"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.5.2
+Version: 3.6.0
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -805,7 +805,7 @@ For detailed instructions, please refer to the project [Wiki](https://github.com
     After installation, run this command to create the shortcut in your application menu (e.g., Start Menu or Applications folder).
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### Running the Application
@@ -938,7 +938,7 @@ Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Ze
     インストール後、このコマンドを実行すると、アプリケーションメニュー（スタートメニューやアプリケーションフォルダなど）にショートカットが作成されます。
 
     ```bash
-    moleditpy-installer
+    python -m moleditpy_installer
     ```
 
 #### アプリケーションの起動

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/MoleditPy.egg-info/SOURCES.txt

@@ -53,6 +53,7 @@ src/moleditpy/ui/mirror_dialog.py
 src/moleditpy/ui/molecular_scene_handler.py
 src/moleditpy/ui/molecule_scene.py
 src/moleditpy/ui/move_group_dialog.py
+src/moleditpy/ui/move_selected_atoms_dialog.py
 src/moleditpy/ui/periodic_table_dialog.py
 src/moleditpy/ui/planarize_dialog.py
 src/moleditpy/ui/settings_dialog.py

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/moleditpy/main.py

@@ -148,4 +148,14 @@ def main() -> None:
     app = QApplication([sys.argv[0]] + remaining)
     window = MainWindow(initial_file=args.file, safe_mode=args.safe)
     window.show()
+
+    # Force Windows to refresh taskbar/titlebar icon after event loop starts
+    if sys.platform == "win32":
+        try:
+            from PyQt6.QtCore import QTimer
+
+            QTimer.singleShot(100, lambda: window.setWindowIcon(window.windowIcon()))
+        except Exception:
+            pass
+
     sys.exit(app.exec())

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/moleditpy/ui/custom_interactor_style.py

@@ -22,10 +22,8 @@ from vtkmodules.vtkInteractionStyle import vtkInteractorStyleTrackballCamera  #
 
 
 try:
-    from .move_group_dialog import MoveGroupDialog
     from .atom_picking import pick_atom_index_from_screen
 except ImportError:
-    from moleditpy.ui.move_group_dialog import MoveGroupDialog
     from moleditpy.ui.atom_picking import pick_atom_index_from_screen
 
 from rdkit import Geometry
@@ -107,10 +105,15 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         self._mouse_press_pos = None
 
         # Check Move Group dialog
+        # Check Move Group or Move Selected Atoms dialog
         move_group_dialog = None
         for widget in QApplication.topLevelWidgets():
             try:
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
+                if (
+                    type(widget).__name__
+                    in ("MoveGroupDialog", "MoveSelectedAtomsDialog")
+                    and widget.isVisible()
+                ):
                     move_group_dialog = widget
                     break
             except (AttributeError, RuntimeError, TypeError):
@@ -147,6 +150,20 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                     self._suppress_next_left_button_up = True
                     return  # Disable camera rotation
                 else:
+                    if type(move_group_dialog).__name__ == "MoveSelectedAtomsDialog":
+                        # For MoveSelectedAtomsDialog, we toggle ONLY the clicked atom, no BFS!
+                        def _deferred_toggle(
+                            idx=clicked_atom_idx, dlg=move_group_dialog
+                        ):
+                            try:
+                                dlg.on_atom_picked(idx)
+                            except (AttributeError, RuntimeError):
+                                pass
+
+                        QTimer.singleShot(0, _deferred_toggle)
+                        self._suppress_next_left_button_up = True
+                        return
+
                     # Clicked outside group - Search connected component
                     visited = set()
                     queue = [clicked_atom_idx]
@@ -172,8 +189,14 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
 
                     # Multi-selection with Ctrl
                     is_ctrl_pressed = bool(
-                        QApplication.keyboardModifiers()
-                        & Qt.KeyboardModifier.ControlModifier
+                        (
+                            QApplication.keyboardModifiers()
+                            & Qt.KeyboardModifier.ControlModifier
+                        )
+                        or (
+                            self.GetInteractor()
+                            and self.GetInteractor().GetControlKey()
+                        )
                     )
 
                     if is_ctrl_pressed:
@@ -208,8 +231,10 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                 super(CustomInteractorStyle, self).OnLeftButtonDown()
                 return
 
+        interactor = self.GetInteractor()
         is_temp_mode = bool(
-            QApplication.keyboardModifiers() & Qt.KeyboardModifier.AltModifier
+            (QApplication.keyboardModifiers() & Qt.KeyboardModifier.AltModifier)
+            or (interactor and interactor.GetAltKey())
         )
         is_edit_active = mw.edit_3d_manager.is_3d_edit_mode or is_temp_mode
 
@@ -293,11 +318,15 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         """
         mw = self.main_window
 
-        # Check if Move Group dialog is open
+        # Check if Move Group dialog or Move Selected Atoms dialog is open
         move_group_dialog = None
         try:
             for widget in QApplication.topLevelWidgets():
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
+                if (
+                    type(widget).__name__
+                    in ("MoveGroupDialog", "MoveSelectedAtomsDialog")
+                    and widget.isVisible()
+                ):
                     move_group_dialog = widget
                     break
         except (AttributeError, RuntimeError, TypeError) as e:
@@ -350,11 +379,15 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         """
         mw = self.main_window
 
-        # Move Group drag handling
+        # Move Group / Selected Atoms drag handling
         move_group_dialog = None
         try:
             for widget in QApplication.topLevelWidgets():
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
+                if (
+                    type(widget).__name__
+                    in ("MoveGroupDialog", "MoveSelectedAtomsDialog")
+                    and widget.isVisible()
+                ):
                     move_group_dialog = widget
                     break
         except (AttributeError, RuntimeError, TypeError):
@@ -442,11 +475,15 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         """
         mw = self.main_window
 
-        # Finalize Move Group drag
+        # Finalize Move Group / Selected Atoms drag
         move_group_dialog = None
         try:
             for widget in QApplication.topLevelWidgets():
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
+                if (
+                    type(widget).__name__
+                    in ("MoveGroupDialog", "MoveSelectedAtomsDialog")
+                    and widget.isVisible()
+                ):
                     move_group_dialog = widget
                     break
         except (AttributeError, RuntimeError, TypeError):
@@ -749,11 +786,15 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         """
         mw = self.main_window
 
-        # Finalize Move Group rotation
+        # Finalize Move Group / Selected Atoms rotation
         move_group_dialog = None
         try:
             for widget in QApplication.topLevelWidgets():
-                if isinstance(widget, MoveGroupDialog) and widget.isVisible():
+                if (
+                    type(widget).__name__
+                    in ("MoveGroupDialog", "MoveSelectedAtomsDialog")
+                    and widget.isVisible()
+                ):
                     move_group_dialog = widget
                     break
         except (AttributeError, RuntimeError, TypeError):

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/moleditpy/ui/dialog_logic.py

@@ -18,7 +18,8 @@ import json
 import os
 from typing import Any, List, Literal, Optional, cast
 
-from PyQt6.QtWidgets import QInputDialog, QMessageBox
+from PyQt6.QtWidgets import QInputDialog, QMessageBox, QDialog
+from PyQt6.QtCore import Qt
 
 
 try:
@@ -33,6 +34,7 @@ try:
     from .dihedral_dialog import DihedralDialog
     from .mirror_dialog import MirrorDialog
     from .move_group_dialog import MoveGroupDialog
+    from .move_selected_atoms_dialog import MoveSelectedAtomsDialog
     from .periodic_table_dialog import PeriodicTableDialog
     from .planarize_dialog import PlanarizeDialog
     from .settings_dialog import SettingsDialog
@@ -53,6 +55,7 @@ except ImportError:
     from moleditpy.ui.dihedral_dialog import DihedralDialog
     from moleditpy.ui.mirror_dialog import MirrorDialog
     from moleditpy.ui.move_group_dialog import MoveGroupDialog
+    from moleditpy.ui.move_selected_atoms_dialog import MoveSelectedAtomsDialog
     from moleditpy.ui.periodic_table_dialog import PeriodicTableDialog
     from moleditpy.ui.planarize_dialog import PlanarizeDialog
     from moleditpy.ui.settings_dialog import SettingsDialog
@@ -213,6 +216,13 @@ class DialogManager:
                 self.host, "Error", f"Failed to save template: {str(e)}"
             )
 
+    def _show_modeless_dialog(self, dialog: QDialog) -> None:
+        """Show a modeless dialog on top, especially important for macOS."""
+        dialog.setWindowFlag(Qt.WindowType.WindowStaysOnTopHint, True)
+        dialog.show()
+        dialog.raise_()
+        dialog.activateWindow()
+
     def open_translation_dialog(self) -> None:
         """Open the translation dialog"""
         # Get preselected atoms
@@ -229,8 +239,8 @@ class DialogManager:
             preselected_atoms,
             parent=self.host,
         )
-        self.host.edit_3d_manager.active_3d_dialogs.append(dialog)  # Keep reference
-        dialog.show()  # Use show for modeless display
+        self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage("Translation applied.")
         )
@@ -256,7 +266,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage("Group transformation applied.")
         )
@@ -265,6 +275,34 @@ class DialogManager:
             lambda: self.host.edit_3d_manager.remove_dialog_from_list(dialog)
         )
 
+    def open_move_selected_atoms_dialog(self) -> None:
+        """Open Move Selected Atoms dialog"""
+        # Get preselected atoms
+        preselected_atoms = self._get_preselected_atoms_3d()
+
+        # Disable measurement mode
+        if self.host.edit_3d_manager.measurement_mode:
+            self.host.init_manager.measurement_action.setChecked(False)
+            self.host.edit_3d_manager.toggle_measurement_mode(False)
+
+        dialog = MoveSelectedAtomsDialog(
+            self.host.view_3d_manager.current_mol,
+            self.host,
+            preselected_atoms,
+            parent=self.host,
+        )
+        self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
+        self._show_modeless_dialog(dialog)
+        dialog.accepted.connect(
+            lambda: self.host.statusBar().showMessage(
+                "Selected atoms transformation applied."
+            )
+        )
+        dialog.accepted.connect(self.host.edit_actions_manager.push_undo_state)
+        dialog.finished.connect(
+            lambda: self.host.edit_3d_manager.remove_dialog_from_list(dialog)
+        )
+
     def open_align_plane_dialog(self, plane: str) -> None:
         """Open align dialog"""
         # Get pre-selected atoms
@@ -283,7 +321,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage(
                 f"Atoms aligned to {plane.upper()} plane."
@@ -311,7 +349,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage(
                 "Selection planarized to best-fit plane."
@@ -340,7 +378,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage(
                 f"Atoms aligned to {axis.upper()}-axis."
@@ -368,7 +406,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage("Bond length adjusted.")
         )
@@ -394,7 +432,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage("Angle adjusted.")
         )
@@ -420,7 +458,7 @@ class DialogManager:
             parent=self.host,
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.accepted.connect(
             lambda: self.host.statusBar().showMessage("Dihedral angle adjusted.")
         )
@@ -440,8 +478,18 @@ class DialogManager:
             self.host.init_manager.measurement_action.setChecked(False)
             self.host.edit_3d_manager.toggle_measurement_mode(False)
 
-        dialog = MirrorDialog(self.host.view_3d_manager.current_mol, self.host)
-        dialog.exec()
+        dialog = MirrorDialog(
+            self.host.view_3d_manager.current_mol, self.host, parent=self.host
+        )
+        self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
+        self._show_modeless_dialog(dialog)
+        dialog.accepted.connect(
+            lambda: self.host.statusBar().showMessage("Mirror applied.")
+        )
+        dialog.accepted.connect(self.host.edit_actions_manager.push_undo_state)
+        dialog.finished.connect(
+            lambda: self.host.edit_3d_manager.remove_dialog_from_list(dialog)
+        )
 
     def open_settings_dialog(self) -> None:
         """Open the application settings dialog."""
@@ -468,7 +516,7 @@ class DialogManager:
             self.host.view_3d_manager.current_mol, self.host, parent=self.host
         )
         self.host.edit_3d_manager.active_3d_dialogs.append(dialog)
-        dialog.show()
+        self._show_modeless_dialog(dialog)
         dialog.finished.connect(
             lambda: self.host.edit_3d_manager.remove_dialog_from_list(dialog)
         )

{moleditpy-3.5.2 → moleditpy-3.6.0}/src/moleditpy/ui/main_window_init.py

@@ -1866,6 +1866,14 @@ class MainInitManager:
         edit_3d_menu.addAction(translation_action)
         self.host.translation_action = translation_action
 
+        move_selected_atoms_action = QAction("Move Selected Atoms...", self.host)
+        move_selected_atoms_action.triggered.connect(
+            self.host.dialog_manager.open_move_selected_atoms_dialog
+        )
+        move_selected_atoms_action.setEnabled(False)
+        edit_3d_menu.addAction(move_selected_atoms_action)
+        self.host.move_selected_atoms_action = move_selected_atoms_action
+
         move_group_action = QAction("Move Group...", self.host)
         move_group_action.triggered.connect(
             self.host.dialog_manager.open_move_group_dialog