MoleditPy-linux 3.0.0__tar.gz → 3.0.1__tar.gz

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.0
+Version: 3.0.1
 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-3.0.0 → moleditpy_linux-3.0.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.0.0"
+version = "3.0.1"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.0
+Version: 3.0.1
 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-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -173,6 +173,14 @@ 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.
+        """
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "ui_manager"):
+            mw.ui_manager.update_status_bar(message)
+
     @property
     def current_mol(self) -> Any:
         """
@@ -186,8 +194,7 @@ class PluginContext:
         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:
@@ -214,6 +221,30 @@ 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_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/io_logic.py

@@ -502,6 +502,7 @@ class IOManager:
                 50, lambda: self.host.view_3d_manager.plotter.view_isometric()
             )
             QTimer.singleShot(100, lambda: self.host.view_3d_manager.plotter.render())
+            QTimer.singleShot(100, self.host.view_3d_manager.fit_to_view)
 
         except FileNotFoundError:
             self.host.statusBar().showMessage(f"File not found: {file_path}")
@@ -670,6 +671,7 @@ class IOManager:
                 50, lambda: self.host.view_3d_manager.plotter.view_isometric()
             )
             QTimer.singleShot(100, lambda: self.host.view_3d_manager.plotter.render())
+            QTimer.singleShot(100, self.host.view_3d_manager.fit_to_view)
         except Exception as e:
             self.host.statusBar().showMessage(f"Error loading file: {e}")
 

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/main_window.py

@@ -73,28 +73,33 @@ class MainWindow(QMainWindow):
             self, initial_file=initial_file, safe_mode=safe_mode
         )
 
-    # --- Core Proxy Properties ---
+    # --- Core Proxy Properties (Legacy Plugin Support Only. Bypassed by Core Logics) ---
     @property
     def current_mol(self):
+        """Proxy for current molecule. Not for core logic use."""
         return self.view_3d_manager.current_mol
 
     @current_mol.setter
     def current_mol(self, value):
+        """Proxy for current molecule setter. Not for core logic use."""
         self.view_3d_manager.current_mol = value
 
     @property
     def plotter(self):
+        """Proxy for 3D plotter. Not for core logic use."""
         return self.view_3d_manager.plotter
 
     @property
     def data(self):
+        """Proxy for state data. Not for core logic use."""
         return self.state_manager.data
 
     @property
     def scene(self):
+        """Proxy for 2D scene. Not for core logic use."""
         return self.init_manager.scene
 
     def draw_molecule_3d(self, mol):
+        """Proxy for 3D rendering. Not for core logic use."""
         self.current_mol = mol
         self.view_3d_manager.draw_molecule_3d(mol)
-

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/main_window_init.py

@@ -289,6 +289,7 @@ class MainInitManager:
             self.host.io_manager.load_xyz_for_3d_viewing(file_path)
         elif file_ext in ["pmeraw", "pmeprj"]:
             self.host.io_manager.open_project_file(file_path=file_path)
+            QTimer.singleShot(100, self.host.view_3d_manager.fit_to_view)
         else:
             self.host.statusBar().showMessage(f"Unsupported file type: {file_ext}")
 
@@ -489,8 +490,8 @@ class MainInitManager:
                 logging.error("REPORT ERROR: Missing attribute 'conv_actions' on self")
 
             # Intermolecular interaction
-            if hasattr(self, "intermolecular_rdkit_action"):
-                self.intermolecular_rdkit_action.setChecked(
+            if hasattr(self.host, "intermolecular_rdkit_action"):
+                self.host.intermolecular_rdkit_action.setChecked(
                     self.host.init_manager.settings.get(
                         "optimize_intermolecular_interaction_rdkit", True
                     )
@@ -524,6 +525,8 @@ class MainInitManager:
                 self.host.init_manager.scene.setBackgroundBrush(QBrush(QColor(bg_c)))
                 for item in self.host.init_manager.scene.items():
                     with contextlib.suppress(AttributeError, RuntimeError, TypeError):
+                        if type(item).__name__ not in ("AtomItem", "BondItem"):
+                            continue
                         if hasattr(item, "update_style"):
                             item.update_style()
                         else:  # [REPORT ERROR MISSING ATTRIBUTE]
@@ -1316,12 +1319,7 @@ class MainInitManager:
                 action.setChecked(True)
             action.triggered.connect(
                 lambda checked=False, k=key: (
-                    self.host.view_3d_manager.set_3d_style(k),
-                    self.host.view_3d_manager.draw_molecule_3d(
-                        self.host.view_3d_manager.current_mol
-                    )
-                    if getattr(self.host.view_3d_manager, "current_mol", None)
-                    else None,
+                    self.host.view_3d_manager.set_3d_style(k)
                 )
             )
             style_menu.addAction(action)
@@ -1334,12 +1332,7 @@ class MainInitManager:
                     action = QAction(style_name, self.host, checkable=True)
                     action.triggered.connect(
                         lambda checked=False, s=style_name: (
-                            self.host.view_3d_manager.set_3d_style(s),
-                            self.host.view_3d_manager.draw_molecule_3d(
-                                self.host.view_3d_manager.current_mol
-                            )
-                            if getattr(self.host.view_3d_manager, "current_mol", None)
-                            else None,
+                            self.host.view_3d_manager.set_3d_style(s)
                         )
                     )
                     style_menu.addAction(action)

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/settings_dialog.py

@@ -3,7 +3,11 @@
 
 """
 MoleditPy — A Python-based molecular editing software
-Refactored SettingsDialog (Phase 2)
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
 """
 
 import logging  # [REPORT ERROR MISSING ATTRIBUTE]

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/settings_tabs/settings_3d_tabs.py

@@ -225,8 +225,7 @@ class SettingsModelTab(SettingsTabBase):
             val = settings_dict.get(f"{p}_atom_scale", 1.0)
             self.atom_scale_slider.setValue(int(val * 100))
         if p in ["ball_stick", "wireframe", "stick"]:
-            prefix = "wf" if p == "wireframe" else p
-            val = settings_dict.get(f"{prefix}_bond_radius", 0.1)
+            val = settings_dict.get(f"{p}_bond_radius", 0.1)
             self.bond_radius_slider.setValue(int(val * 100))
 
             self.db_offset_slider.setValue(
@@ -261,8 +260,7 @@ class SettingsModelTab(SettingsTabBase):
         if p in ["ball_stick", "cpk"]:
             s[f"{p}_atom_scale"] = self.atom_scale_slider.value() / 100.0
         if p in ["ball_stick", "wireframe", "stick"]:
-            prefix = "wireframe" if p == "wireframe" else p
-            s[f"{prefix}_bond_radius"] = self.bond_radius_slider.value() / 100.0
+            s[f"{p}_bond_radius"] = self.bond_radius_slider.value() / 100.0
             s[f"{p}_double_bond_offset_factor"] = self.db_offset_slider.value() / 100.0
             s[f"{p}_triple_bond_offset_factor"] = self.tr_offset_slider.value() / 100.0
             s[f"{p}_double_bond_radius_factor"] = self.db_radius_slider.value() / 100.0

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/ui/view_3d_logic.py

@@ -549,7 +549,7 @@ class View3DManager:
             # Set bond radius and resolution based on style
             if current_style == "wireframe":
                 cyl_radius = self.host.init_manager.settings.get(
-                    "wireframe_bond_radius", 0.01
+                    "wireframe_bond_radius", 0.02
                 )
                 bond_resolution = self.host.init_manager.settings.get(
                     "wireframe_resolution", 6
@@ -935,7 +935,7 @@ class View3DManager:
                         )
                     elif current_style == "wireframe":
                         bond_radius = self.host.init_manager.settings.get(
-                            "wireframe_bond_radius", 0.01
+                            "wireframe_bond_radius", 0.02
                         )
                     else:
                         bond_radius = 0.1  # Default

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/utils/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "3.0.0"
+VERSION = "3.0.1"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-3.0.0 → moleditpy_linux-3.0.1}/src/moleditpy_linux/utils/default_settings.py

@@ -35,7 +35,7 @@ DEFAULT_SETTINGS = {
     "cpk_resolution": 32,
     "cpk_colors": {},
     # --- 3D Model Parameters (Wireframe) ---
-    "wireframe_bond_radius": 0.01,
+    "wireframe_bond_radius": 0.02,
     "wireframe_resolution": 6,
     "wireframe_double_bond_offset_factor": 3.0,
     "wireframe_triple_bond_offset_factor": 3.0,