MoleditPy 3.0.0b1__tar.gz → 3.0.2__tar.gz

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0b1
+Version: 3.0.2
 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

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0b1"
+version = "3.0.2"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0b1
+Version: 3.0.2
 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

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/src/MoleditPy.egg-info/SOURCES.txt

@@ -10,12 +10,6 @@ src/MoleditPy.egg-info/top_level.txt
 src/moleditpy/__init__.py
 src/moleditpy/__main__.py
 src/moleditpy/main.py
-src/moleditpy.egg-info/PKG-INFO
-src/moleditpy.egg-info/SOURCES.txt
-src/moleditpy.egg-info/dependency_links.txt
-src/moleditpy.egg-info/entry_points.txt
-src/moleditpy.egg-info/requires.txt
-src/moleditpy.egg-info/top_level.txt
 src/moleditpy/assets/file_icon.ico
 src/moleditpy/assets/icon.icns
 src/moleditpy/assets/icon.ico

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/src/moleditpy/plugins/plugin_interface.py

@@ -119,12 +119,6 @@ class PluginContext:
         """
         return Plugin3DController(self._manager.get_main_window())
 
-    def show_status_message(self, message: str, timeout: int = 3000) -> None:
-        """
-        Display a message in the application status bar.
-        """
-        self._manager.show_status_message(message, timeout)
-
     def push_undo_checkpoint(self) -> None:
         """
         Create an undo checkpoint for the current state.
@@ -133,18 +127,6 @@ class PluginContext:
         """
         self._manager.push_undo_checkpoint()
 
-    def refresh_3d_view(self) -> None:
-        """
-        Force a refresh (re-render) of the 3D scene.
-        """
-        self._manager.refresh_3d_view()
-
-    def reset_3d_camera(self) -> None:
-        """
-        Resets the 3D camera to fit the current molecule.
-        """
-        self._manager.reset_3d_camera()
-
     def get_selected_atom_indices(self) -> List[int]:
         """
         Returns a list of RDKit atom indices currently selected in the 2D or 3D view.
@@ -173,21 +155,30 @@ class PluginContext:
         """
         return self._manager.get_main_window()
 
+    def show_status_message(self, message: str, timeout: int = 3000) -> None:
+        """
+        Display a temporary message in the status bar of the main window.
+        """
+        self._manager.show_status_message(message, timeout)
+
     @property
     def current_mol(self) -> Any:
         """
         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
+        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 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)
+            mw.view_3d_manager.draw_molecule_3d(mol)
 
     @property
     def current_molecule(self) -> Any:
@@ -204,7 +195,11 @@ class PluginContext:
         Returns the PyVista plotter from the MainWindow.
         """
         mw = self.get_main_window()
-        return mw.view_3d_manager.plotter if mw and hasattr(mw, "view_3d_manager") else None
+        return (
+            mw.view_3d_manager.plotter
+            if mw and hasattr(mw, "view_3d_manager")
+            else None
+        )
 
     @property
     def scene(self) -> Any:
@@ -214,6 +209,33 @@ class PluginContext:
         mw = self.get_main_window()
         return mw.init_manager.scene if mw and hasattr(mw, "init_manager") else None
 
+    def draw_molecule_3d(self, mol: Any) -> None:
+        """Draw a molecule in the 3D scene (Direct manager call)."""
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "view_3d_manager"):
+            mw.view_3d_manager.draw_molecule_3d(mol)
+
+    def refresh_3d_view(self) -> None:
+        """Force the 3D window to redraw using the current molecule."""
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "view_3d_manager"):
+            mol = getattr(mw.view_3d_manager, "current_mol", None)
+            if mol:
+                mw.view_3d_manager.draw_molecule_3d(mol)
+            else:
+                # Also redraw/clear plotter if no molecule
+                if (
+                    hasattr(mw.view_3d_manager, "plotter")
+                    and mw.view_3d_manager.plotter
+                ):
+                    mw.view_3d_manager.plotter.render()
+
+    def reset_3d_camera(self) -> None:
+        """Zoom in and re-center the 3D viewport to fit the current molecule."""
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "view_3d_manager") and mw.view_3d_manager.plotter:
+            mw.view_3d_manager.plotter.reset_camera()
+
     def add_export_action(self, label: str, callback: Callable):
         """
         Register a custom export action.

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/src/moleditpy/plugins/plugin_manager.py

@@ -514,7 +514,6 @@ class PluginManager:
 
         # Check 2D selection
         try:
-            from .plugin_interface import PluginContext
             # We need to access the scene items.
             # In MoleditPy, atoms in the scene are AtomItem objects which have an 'atom_id'.
             # These atom_ids map to entries in state_manager.data.atoms.

{moleditpy-3.0.0b1 → moleditpy-3.0.2}/src/moleditpy/plugins/plugin_manager_window.py

@@ -10,9 +10,9 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import os
-import shutil
-import hashlib
+import os
+import shutil
+import hashlib
 
 from PyQt6.QtCore import Qt, QUrl
 from PyQt6.QtGui import QDesktopServices, QDragEnterEvent, QDropEvent
@@ -258,10 +258,10 @@ class PluginManagerWindow(QDialog):
                 is_valid = True
                 is_folder = True
 
-            if is_valid:
-                sha256_value = self._compute_sha256(file_path)
-                # 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",
@@ -281,15 +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)}\n"
-                    f"SHA-256: {sha256_value}"
-                )
+                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,
@@ -310,43 +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)
-
-    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"
+            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"