MoleditPy-linux 4.1.2__py3-none-any.whl → 4.1.4__py3-none-any.whl

moleditpy_linux/__init__.py

@@ -8,8 +8,6 @@ Author: Hiromichi Yokoyama
 License: GPL-3.0 license
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
-
-Top-level package for moleditpy_linux.
 """
 
 import importlib.util  # noqa: F401

moleditpy_linux/core/__init__.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""

moleditpy_linux/plugins/plugin_interface.py

@@ -190,11 +190,9 @@ class PluginContext:
         Get or set the current molecule (RDKit Mol object). Shortcut for current_molecule.
         """
         mw = self.get_main_window()
-        return (
-            mw.view_3d_manager.current_mol
-            if mw and hasattr(mw, "view_3d_manager")
-            else None
-        )
+        if mw and hasattr(mw, "view_3d_manager"):
+            return mw.view_3d_manager.current_mol
+        return None
 
     @current_mol.setter
     def current_mol(self, mol: Any) -> None:

moleditpy_linux/plugins/plugin_manager.py

@@ -206,9 +206,10 @@ class PluginManager:
                 shutil.copy2(file_path, dest_path)
                 msg = f"Installed {filename}"
 
-            # Reload plugins after install
+            # Reload plugins after install and rebuild UI immediately
             if self.main_window:
                 self.discover_plugins(self.main_window)
+                self.rebuild_plugin_menus()
             return True, msg
         except (
             AttributeError,
@@ -315,6 +316,13 @@ class PluginManager:
                         stub.__package__ = parent_name
                         sys.modules[parent_name] = stub
 
+            # Purge stale cache so package submodules reload from disk on re-exec
+            for _cached_key in list(sys.modules.keys()):
+                if _cached_key == unique_module_name or _cached_key.startswith(
+                    unique_module_name + "."
+                ):
+                    del sys.modules[_cached_key]
+
             spec = importlib.util.spec_from_file_location(
                 unique_module_name,
                 filepath,
@@ -588,7 +596,8 @@ class PluginManager:
                         selected_atom_ids.add(item.atom_id)
 
                 # Now map these editor IDs to RDKit indices
-                mol = getattr(self.main_window, "current_mol", None)
+                v3d = getattr(self.main_window, "view_3d_manager", None)
+                mol = v3d.current_mol if v3d else None
                 if mol and selected_atom_ids:
                     for i in range(mol.GetNumAtoms()):
                         atom = mol.GetAtomWithIdx(i)

moleditpy_linux/plugins/plugin_manager_window.py

@@ -156,13 +156,12 @@ class PluginManagerWindow(QDialog):
             self.btn_remove.setEnabled(has_selection)
 
     def on_reload(self, silent: bool = False) -> None:
-        """Reload all plugins from disk and refresh the table."""
-        # Trigger reload in main manager
+        """Reload all plugins from disk, rebuild main-window UI, and refresh the table."""
         if self.plugin_manager.main_window:
             self.plugin_manager.discover_plugins(self.plugin_manager.main_window)
+            self.plugin_manager.rebuild_plugin_menus()
             self.refresh_plugin_list()
 
-            # For immediate feedback:
             if not silent:
                 QMessageBox.information(self, "Reloaded", "Plugins have been reloaded.")
         else:

moleditpy_linux/ui/main_window.py

@@ -19,6 +19,7 @@ if TYPE_CHECKING:
     from rdkit import Chem
 
 # PyQt6 Modules
+import copy
 from PyQt6.QtCore import pyqtSignal
 from PyQt6.QtWidgets import QMainWindow, QMessageBox
 
@@ -254,8 +255,6 @@ class MainWindow(QMainWindow):
 
     def save_state_snapshot(self) -> None:
         """Create a deep copy snapshot of the current state for undo/redo comparison."""
-        import copy
-
         try:
             self.state_manager.saved_state = copy.deepcopy(
                 self.state_manager.get_current_state()

moleditpy_linux/ui/move_selected_atoms_dialog.py

@@ -56,6 +56,8 @@ class MoveSelectedAtomsDialog(BasePickingDialog):
         self.mouse_moved_during_drag: bool = False
         self._consume_next_left_release: bool = False
         self.highlight_actor: Optional[pv.Actor] = None
+        self.original_style: Optional[Any] = None
+        self._click_press_pos: Optional[Any] = None
 
         self.widgets: dict[str, Any] = {}
 
@@ -211,6 +213,13 @@ class MoveSelectedAtomsDialog(BasePickingDialog):
     def _init_buttons_ui(self, layout: QVBoxLayout) -> None:
         """Initialize bottom buttons."""
         button_layout = QHBoxLayout()
+
+        box_select_btn = QPushButton("Box Selection: OFF")
+        box_select_btn.setCheckable(True)
+        box_select_btn.clicked.connect(self.toggle_box_selection)
+        self.widgets["box_select_btn"] = box_select_btn
+        button_layout.addWidget(box_select_btn)
+
         clear_btn = QPushButton("Clear Selection")
         clear_btn.clicked.connect(self.clear_selection)
         self.widgets["clear_button"] = clear_btn
@@ -238,6 +247,24 @@ class MoveSelectedAtomsDialog(BasePickingDialog):
 
         e_type = event.type()
 
+        btn = self.widgets.get("box_select_btn")
+        box_selection_on = btn is not None and btn.isChecked()
+
+        if e_type == QEvent.Type.MouseButtonPress:
+            self._click_press_pos = getattr(event, "pos", lambda: None)()
+        elif e_type == QEvent.Type.MouseButtonRelease:
+            if hasattr(self, "_click_press_pos") and self._click_press_pos is not None:
+                pos = getattr(event, "pos", lambda: None)()
+                if pos:
+                    diff = pos - self._click_press_pos
+                    if diff.manhattanLength() < 3:
+                        if box_selection_on:
+                            self.clear_selection()
+            self._click_press_pos = None
+
+        if box_selection_on:
+            return False
+
         if e_type == QEvent.Type.MouseButtonDblClick:
             # Ignore double clicks and reset state
             self.is_dragging_group = False
@@ -645,3 +672,77 @@ class MoveSelectedAtomsDialog(BasePickingDialog):
         self.update_display()
         self.is_dragging_group = False
         self.drag_start_pos = None
+
+    def toggle_box_selection(self, checked: bool) -> None:
+        """Toggle Box Selection mode using PyVista's rectangle picker."""
+        plotter = self.main_window.view_3d_manager.plotter
+        if plotter is None or plotter.interactor is None:
+            return
+
+        btn = self.widgets["box_select_btn"]
+        if checked:
+            btn.setText("Box Selection: ON")
+            # Save original style if not saved
+            if self.original_style is None:
+                self.original_style = plotter.interactor.GetInteractorStyle()
+
+            # Using PyVista's built-in picking which reliably draws the box correctly
+            plotter.enable_rectangle_picking(
+                callback=self.on_rectangle_picked,
+                show_message=False,
+                start=True,
+                color="red",
+            )
+        else:
+            btn.setText("Box Selection: OFF")
+            plotter.disable_picking()
+            # Restore original style
+            if self.original_style is not None:
+                plotter.interactor.SetInteractorStyle(self.original_style)
+
+    def on_rectangle_picked(self, selection: Any) -> None:
+        """Handle PyVista rectangle picking callback."""
+        if not hasattr(selection, "viewport"):
+            return
+
+        x0, y0, x1, y1 = selection.viewport
+        x_min = min(x0, x1)
+        x_max = max(x0, x1)
+        y_min = min(y0, y1)
+        y_max = max(y0, y1)
+
+        # If the drag box is small, treat it as a single click to clear selection
+        if abs(x_max - x_min) < 15 and abs(y_max - y_min) < 15:
+            self.clear_selection()
+            return
+
+        plotter = self.main_window.view_3d_manager.plotter
+        if plotter is None:
+            return
+        renderer = plotter.renderer
+
+        positions = self.main_window.view_3d_manager.atom_positions_3d
+        if positions is not None:
+            added = False
+            for atom_idx, pos in enumerate(positions):
+                renderer.SetWorldPoint(float(pos[0]), float(pos[1]), float(pos[2]), 1.0)
+                renderer.WorldToDisplay()
+                display = renderer.GetDisplayPoint()
+
+                if x_min <= display[0] <= x_max and y_min <= display[1] <= y_max:
+                    if atom_idx not in self.selected_atoms:
+                        self.selected_atoms.add(atom_idx)
+                        added = True
+
+            if added:
+                self.show_atom_labels()
+                self.update_display()
+
+    def reject(self) -> None:
+        """Clean up when dialog closes."""
+        # Ensure we restore the interactor style if it was left in Box Selection mode
+        btn = self.widgets.get("box_select_btn")
+        if btn and btn.isChecked():
+            btn.setChecked(False)
+            self.toggle_box_selection(False)
+        super().reject()

moleditpy_linux/ui/view_3d_logic.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 """
-MoleditPy  EA Python-based molecular editing software
+MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
 License: GPL-3.0 license

{moleditpy_linux-4.1.2.dist-info → moleditpy_linux-4.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.1.2
+Version: 4.1.4
 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-4.1.2.dist-info → moleditpy_linux-4.1.4.dist-info}/RECORD

@@ -1,17 +1,17 @@
-moleditpy_linux/__init__.py,sha256=QkGj1Nbkjg98UGBnaK5MaKZX98Vlb_xhbO2MDRrjvE4,504
+moleditpy_linux/__init__.py,sha256=QYE14Hc9eAwykvTIDIXvur6NXlGcZ0hg2nUZesj6soI,462
 moleditpy_linux/__main__.py,sha256=VHCD-CCX6iKUbmUyRv2BGVXCjHWEaISpmjO7_yh9AaU,654
 moleditpy_linux/main.py,sha256=0QYEi0JEOyjeY9ntLMGJpbxV69MGeog3jRtnkSJK7bI,7221
 moleditpy_linux/assets/file_icon.ico,sha256=yyVj084A7HuMNbV073cE_Ag3Ne405qgOP3Mia1ZqLpE,101632
 moleditpy_linux/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy_linux/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy_linux/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
-moleditpy_linux/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+moleditpy_linux/core/__init__.py,sha256=BEOaCz93HzgTe0FhBzSj6Sfk8MAWxcY9vCDGmOriJx4,267
 moleditpy_linux/core/mol_geometry.py,sha256=GrzQfUZ9RVgwBeJEglQWvKhJMMkMVI6Hc6fUm2BG8UU,21548
 moleditpy_linux/core/molecular_data.py,sha256=QzOnO_qhGp8VqREj89MLnVEgMMzuDoQqKTbuhgIwusc,17834
 moleditpy_linux/plugins/__init__.py,sha256=BEOaCz93HzgTe0FhBzSj6Sfk8MAWxcY9vCDGmOriJx4,267
-moleditpy_linux/plugins/plugin_interface.py,sha256=TMtnSdSVIEcEYLYPqoj9NQEO4LM_KPrg1Gn1eYBiOik,22043
-moleditpy_linux/plugins/plugin_manager.py,sha256=ty9judAFzOF8bErzPM5WE4S8f3Z83zepmwn5EurRUVE,30892
-moleditpy_linux/plugins/plugin_manager_window.py,sha256=5d0VWc5u5G_vsRoFawA5N5jI0q88tbKSzVEG_oAWbl8,13366
+moleditpy_linux/plugins/plugin_interface.py,sha256=nCxmT7EXqL3SrRoltZ-A2d_PES5zggn5I1y28OUkPJ0,22016
+moleditpy_linux/plugins/plugin_manager.py,sha256=46S51i6YpRZSiWgKRHH0CkgBiJ-RPe1lruUelNTlRdg,31364
+moleditpy_linux/plugins/plugin_manager_window.py,sha256=hwJiT33KmoQG7AvGJ-1EM3CoKcVhmvQN2UQ-NiPPARc,13366
 moleditpy_linux/ui/__init__.py,sha256=_BslFbhSM4Ba4GDzH1XpvlqlGgvi4OFkcuU3pPeIz3s,751
 moleditpy_linux/ui/about_dialog.py,sha256=OQgCBR-5cIh_S5VWuBLfiss_xeatju0kGWlIIiEzpzg,4547
 moleditpy_linux/ui/align_plane_dialog.py,sha256=JuAhiw1wFdDRAwOJrtCWAOCRUXZELq2NH19ssOP6L38,11140
@@ -38,13 +38,13 @@ moleditpy_linux/ui/edit_actions_logic.py,sha256=rDtsrEAtBGVCww0Den7er33MjliaDIUX
 moleditpy_linux/ui/export_logic.py,sha256=WWE8WACoW_8s2UMSdLx9580FJguSZ6QgKEE7Vx-f4TE,43113
 moleditpy_linux/ui/geometry_base_dialog.py,sha256=cltYZZEd38j9M5tQTtxzPFh-uKqsBJnM_K8lWAPYXro,4399
 moleditpy_linux/ui/io_logic.py,sha256=45Qb9L0UuENs-ciBiSFL-7S8BXA5L5KZ9vJCmh6ChX4,44724
-moleditpy_linux/ui/main_window.py,sha256=lD4GHOlYvoWNavXBczrDyR1onruoar941YMtW2f43XQ,12491
+moleditpy_linux/ui/main_window.py,sha256=_6Ie539dGrtyJYsKSqx8Y7m0_gufZ6gAsP2FV9RGb4U,12481
 moleditpy_linux/ui/main_window_init.py,sha256=Qz03pjS7IemAL-RhcaqKmiRalV1uHgD-5UnNUz9H878,75833
 moleditpy_linux/ui/mirror_dialog.py,sha256=qcyR9wshVKWs6wvCyZ6ZN09CL_m2oVNWH4U_UyUZpWE,5182
 moleditpy_linux/ui/molecular_scene_handler.py,sha256=4u170Hmu2mJoRi6FjV0uqEfH27Lbyu0TTF5Q5T9D3PU,68511
 moleditpy_linux/ui/molecule_scene.py,sha256=tuvtLNctiXuNSwC7W89nr8kKumoGNJl3brH2TGT3Aew,44004
 moleditpy_linux/ui/move_group_dialog.py,sha256=Lj_kmP5kNvk31sVra0MQ0l71d_n8AaWxLGLU56nsOGM,26777
-moleditpy_linux/ui/move_selected_atoms_dialog.py,sha256=3zAnknQ9bqyyzwoy2YSFdb4UYZuHaQfeMMwoxwDEjbc,25220
+moleditpy_linux/ui/move_selected_atoms_dialog.py,sha256=Pj_em_Bz0sMb4pxkGNeQJq9Y1Q1OAZHBVKni-LQTcUo,29302
 moleditpy_linux/ui/periodic_table_dialog.py,sha256=ZEGreZmfi4p7ihPkuEfJhgq2gD8mMrPWbitrNcJ1h8M,6106
 moleditpy_linux/ui/planarize_dialog.py,sha256=yAG97zoRN_3B01nsy53stHFjV48Qk-L-jqqCxN_Y0YM,7811
 moleditpy_linux/ui/plugin_menu_manager.py,sha256=0NfXBETHMKthI50lrqe63xYzUrLmUP49Apm8g0JuNYQ,18986
@@ -55,7 +55,7 @@ moleditpy_linux/ui/template_preview_view.py,sha256=PM14bgCQHGpmJ_yuJPtkPxCv3QadT
 moleditpy_linux/ui/translation_dialog.py,sha256=ITZr53BWEoEdJZtaS5nPSgNd5TC0Po_fcGbkLD9_BXY,16595
 moleditpy_linux/ui/ui_manager.py,sha256=sMx5-qp5vAr2Am9Du9lHvw93kixG3vBwpRZiHYcAQkc,26070
 moleditpy_linux/ui/user_template_dialog.py,sha256=y-Psn4yIMbwJYNbVDAJGgeV2tf-1MoidT3Bb6BMnuqg,29246
-moleditpy_linux/ui/view_3d_logic.py,sha256=gdc824MWnzr7oqThwm4od5oCxo6m1yiXZg8-lJcWP90,90839
+moleditpy_linux/ui/view_3d_logic.py,sha256=7_jd49EvRmhNqes1xuI7hapf_knhe9mjLwkQ8Xa4P8A,90839
 moleditpy_linux/ui/zoomable_view.py,sha256=5PbSJW3pUCBaEXGhvy6BlqLpKrRpTry2AGwZcSXSgfI,5926
 moleditpy_linux/ui/settings_tabs/__init__.py,sha256=BEOaCz93HzgTe0FhBzSj6Sfk8MAWxcY9vCDGmOriJx4,267
 moleditpy_linux/ui/settings_tabs/settings_2d_tab.py,sha256=QB03CTbHUtTLdJqgCq3_JUa4Ie-yJ94KljvCSFcqhdM,15249
@@ -67,9 +67,9 @@ moleditpy_linux/utils/constants.py,sha256=zG1BY8IkCG-4JJxjvXFXVYlGCW2vWd-mW2faFq
 moleditpy_linux/utils/default_settings.py,sha256=6Q3Gw1vyG7uk-35yBtr1sKeJVnOjb4Sq2Hy8iR3MYK4,2894
 moleditpy_linux/utils/sip_isdeleted_safe.py,sha256=My6IJqDewbYY6SoRYNk6XwFUQ9_yihaR3Ym7EOETuAw,1189
 moleditpy_linux/utils/system_utils.py,sha256=K5c9cJRgMFqtUtLefSu3w2hy2drgxNqfT200bSIFy2k,2325
-moleditpy_linux-4.1.2.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
-moleditpy_linux-4.1.2.dist-info/METADATA,sha256=wXIbmkOuENNKBrmJ48Bhq3kSnsCjqXADcCE6sPVowuU,64017
-moleditpy_linux-4.1.2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-moleditpy_linux-4.1.2.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
-moleditpy_linux-4.1.2.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
-moleditpy_linux-4.1.2.dist-info/RECORD,,
+moleditpy_linux-4.1.4.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+moleditpy_linux-4.1.4.dist-info/METADATA,sha256=92pb0Hcrh7l8bOFe7oIR1hZ7zpvDSPVHCYyhzLCpQ_g,64017
+moleditpy_linux-4.1.4.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+moleditpy_linux-4.1.4.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
+moleditpy_linux-4.1.4.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
+moleditpy_linux-4.1.4.dist-info/RECORD,,