MoleditPy-linux 4.1.2__tar.gz → 4.1.4__tar.gz

{moleditpy_linux-4.1.2 → moleditpy_linux-4.1.4}/PKG-INFO

@@ -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 → moleditpy_linux-4.1.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.1.2"
+version = "4.1.4"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.1.2 → moleditpy_linux-4.1.4}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -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 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.2 → moleditpy_linux-4.1.4}/src/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-4.1.4/src/moleditpy_linux/utils/__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
+"""