MoleditPy 3.0.0a6__tar.gz → 3.0.0a8__tar.gz

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a6
+Version: 3.0.0a8
 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-3.0.0a6 → moleditpy-3.0.0a8}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a6"
+version = "3.0.0a8"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a6
+Version: 3.0.0a8
 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-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/plugins/plugin_interface.py

@@ -179,13 +179,13 @@ class PluginContext:
         Get or set the current molecule (RDKit Mol object). Shortcut for current_molecule.
         """
         mw = self.get_main_window()
-        return mw.current_mol if mw else None
+        return mw.view_3d_manager.current_mol if mw and hasattr(mw, "view_3d_manager") else None
 
     @current_mol.setter
     def current_mol(self, mol: Any):
         mw = self.get_main_window()
-        if mw:
-            mw.current_mol = mol
+        if mw and hasattr(mw, "view_3d_manager"):
+            mw.view_3d_manager.current_mol = mol
             if hasattr(mw.view_3d_manager, "draw_molecule_3d"):
                 mw.view_3d_manager.draw_molecule_3d(mol)
 
@@ -204,7 +204,7 @@ class PluginContext:
         Returns the PyVista plotter from the MainWindow.
         """
         mw = self.get_main_window()
-        return mw.plotter if mw else None
+        return mw.view_3d_manager.plotter if mw and hasattr(mw, "view_3d_manager") else None
 
     @property
     def scene(self) -> Any:
@@ -212,7 +212,7 @@ class PluginContext:
         Returns the 2D MoleculeScene from the MainWindow.
         """
         mw = self.get_main_window()
-        return mw.scene if mw else None
+        return mw.init_manager.scene if mw and hasattr(mw, "init_manager") else None
 
     def add_export_action(self, label: str, callback: Callable):
         """

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/plugins/plugin_manager_window.py

@@ -10,8 +10,9 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import os
-import shutil
+import os
+import shutil
+import hashlib
 
 from PyQt6.QtCore import Qt, QUrl
 from PyQt6.QtGui import QDesktopServices, QDragEnterEvent, QDropEvent
@@ -257,9 +258,10 @@ class PluginManagerWindow(QDialog):
                 is_valid = True
                 is_folder = True
 
-            if is_valid:
-                # Extract info and confirm
-                info = {
+            if is_valid:
+                sha256_value = self._compute_sha256(file_path)
+                # Extract info and confirm
+                info = {
                     "name": os.path.basename(file_path),
                     "version": "Unknown",
                     "author": "Unknown",
@@ -279,14 +281,15 @@ class PluginManagerWindow(QDialog):
                 elif file_path.endswith(".py"):
                     info = self.plugin_manager.get_plugin_info_safe(file_path)
 
-                msg = (
-                    f"Do you want to install this plugin?\n\n"
-                    f"Name: {info['name']}\n"
-                    f"Author: {info['author']}\n"
-                    f"Version: {info['version']}\n"
-                    f"Description: {info['description']}\n\n"
-                    f"File: {os.path.basename(file_path)}"
-                )
+                msg = (
+                    f"Do you want to install this plugin?\n\n"
+                    f"Name: {info['name']}\n"
+                    f"Author: {info['author']}\n"
+                    f"Version: {info['version']}\n"
+                    f"Description: {info['description']}\n\n"
+                    f"File: {os.path.basename(file_path)}\n"
+                    f"SHA-256: {sha256_value}"
+                )
 
                 reply = QMessageBox.question(
                     self,
@@ -307,7 +310,43 @@ class PluginManagerWindow(QDialog):
             summary = ""
             if files_installed:
                 summary += "Installed:\n" + "\n".join(files_installed) + "\n\n"
-            if errors:
-                summary += "Errors:\n" + "\n".join(errors)
-
-            QMessageBox.information(self, "Plugin Installation", summary)
+            if errors:
+                summary += "Errors:\n" + "\n".join(errors)
+
+            QMessageBox.information(self, "Plugin Installation", summary)
+
+    def _compute_sha256(self, path):
+        if os.path.isfile(path):
+            return self._sha256_for_file(path)
+        if os.path.isdir(path):
+            return self._sha256_for_directory(path)
+        return "N/A"
+
+    def _sha256_for_file(self, path):
+        hasher = hashlib.sha256()
+        try:
+            with open(path, "rb") as f:
+                for chunk in iter(lambda: f.read(8192), b""):
+                    hasher.update(chunk)
+            return hasher.hexdigest()
+        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
+            return "N/A"
+
+    def _sha256_for_directory(self, dir_path):
+        hasher = hashlib.sha256()
+        try:
+            root = os.path.abspath(dir_path)
+            for current_root, _dirs, files in os.walk(root):
+                rel_root = os.path.relpath(current_root, root)
+                for filename in sorted(files):
+                    file_path = os.path.join(current_root, filename)
+                    rel_path = os.path.normpath(os.path.join(rel_root, filename))
+                    hasher.update(rel_path.encode("utf-8", errors="replace"))
+                    hasher.update(b"\0")
+                    with open(file_path, "rb") as f:
+                        for chunk in iter(lambda: f.read(8192), b""):
+                            hasher.update(chunk)
+                    hasher.update(b"\0")
+            return hasher.hexdigest()
+        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
+            return "N/A"

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/ui/io_logic.py

@@ -175,32 +175,44 @@ class IOManager:
                 _set_prop(final_mol, "_xyz_skip_checks", 1)
             else:
                 final_mol = None
-                while True:
-                    prompt_fn = getattr(self, "prompt_for_charge", None)
-                    if callable(prompt_fn):
-                        result = prompt_fn()
-                        if isinstance(result, tuple) and len(result) == 3:
-                            charge_val, ok, skip_flag = result
+                settings = getattr(self.host.init_manager, "settings", {}) or {}
+                # First try with charge 0 (per user's 'first try with 0 then ask' requirement)
+                # but only if "Always ask" is not explicitly enabled in settings.
+                if not settings.get("always_ask_charge", False):
+                    try:
+                        final_mol = _process(0, use_rd_determine=True)
+                    except (RuntimeError, ValueError, TypeError):
+                        final_mol = None
+
+                # If still no final_mol (because always_ask is True, or charge 0 failed)
+                if final_mol is None:
+                    while True:
+                        prompt_fn = getattr(self, "prompt_for_charge", None)
+                        if callable(prompt_fn):
+                            result = prompt_fn()
+                            if isinstance(result, tuple) and len(result) == 3:
+                                charge_val, ok, skip_flag = result
+                            else:
+                                charge_val, ok, skip_flag = 0, True, False
                         else:
                             charge_val, ok, skip_flag = 0, True, False
-                    else:
-                        charge_val, ok, skip_flag = 0, True, False
-
-                    if not ok:
-                        return None
-                    if skip_flag:
-                        final_mol = _process(0, use_rd_determine=False)
-                        _set_prop(final_mol, "_xyz_skip_checks", 1)
-                        break
-                    try:
-                        final_mol = _process(charge_val, use_rd_determine=True)
-                        break
-                    except (RuntimeError, ValueError, TypeError) as e:
-                        self.host.statusBar().showMessage(
-                            f"Chemistry failed for charge {charge_val}: {e}. Try a different charge or skip."
-                        )
-                        if not callable(prompt_fn):
-                            raise e
+
+                        if not ok:
+                            return None
+                        if skip_flag:
+                            final_mol = _process(0, use_rd_determine=False)
+                            _set_prop(final_mol, "_xyz_skip_checks", 1)
+                            break
+                        try:
+                            final_mol = _process(charge_val, use_rd_determine=True)
+                            break
+                        except (RuntimeError, ValueError, TypeError) as e:
+                            if hasattr(self.host, "statusBar") and self.host.statusBar():
+                                self.host.statusBar().showMessage(
+                                    f"Chemistry failed for charge {charge_val}: {e}. Try a different charge or skip."
+                                )
+                            if not callable(prompt_fn):
+                                raise e
 
                 if final_mol:
                     final_mol._xyz_atom_data = atoms_data

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/ui/main_window.py

@@ -86,14 +86,15 @@ class MainWindow(QMainWindow):
     def plotter(self):
         return self.view_3d_manager.plotter
 
+    @property
+    def data(self):
+        return self.state_manager.data
+
     @property
     def scene(self):
         return self.init_manager.scene
 
-    def dragEnterEvent(self, event):
-        """Delegate drag enter event to UI manager."""
-        self.ui_manager.dragEnterEvent(event)
+    def draw_molecule_3d(self, mol):
+        self.current_mol = mol
+        self.view_3d_manager.draw_molecule_3d(mol)
 
-    def dropEvent(self, event):
-        """Delegate drop event to UI manager."""
-        self.ui_manager.dropEvent(event)

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/ui/ui_manager.py

@@ -200,11 +200,20 @@ class UIManager(QObject):
         ):
             self.host.init_manager.view_2d.setFocus()
 
-        # Handle Window Close via event filter
-        if obj is self.host and event.type() == QEvent.Type.Close:
-            if not self.handle_close_event(event):
-                event.ignore()
-                return True  # Stop propagation
+        if obj is self.host:
+            # Handle Drag and Drop via event filter
+            if event.type() == QEvent.Type.DragEnter:
+                self.handle_drag_enter_event(event)
+                return True
+            if event.type() == QEvent.Type.Drop:
+                self.handle_drop_event(event)
+                return True
+
+            # Handle Window Close via event filter
+            if event.type() == QEvent.Type.Close:
+                if not self.handle_close_event(event):
+                    event.ignore()
+                    return True  # Stop propagation
 
         return super().eventFilter(obj, event)
 
@@ -310,9 +319,6 @@ class UIManager(QObject):
         self.host.view_3d_manager.plotter.interactor.SetInteractorStyle(style)
         self.host.view_3d_manager.plotter.interactor.Initialize()
 
-    def dragEnterEvent(self, event):
-        """Handle drag enter event."""
-        self.handle_drag_enter_event(event)
 
     def handle_drag_enter_event(self, event):
         """Internal handler for drag enter event (bypasses PyQt type checks in tests)."""
@@ -338,9 +344,6 @@ class UIManager(QObject):
 
         event.ignore()
 
-    def dropEvent(self, event):
-        """Handle file drop event."""
-        self.handle_drop_event(event)
 
     def handle_drop_event(self, event):
         """Internal handler for file drop event (bypasses PyQt type checks in tests)."""

{moleditpy-3.0.0a6 → moleditpy-3.0.0a8}/src/moleditpy/utils/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "3.0.0a6"
+VERSION = "3.0.0a8"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5