MoleditPy 3.0.0a5__tar.gz → 3.0.0a7__tar.gz

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a5
+Version: 3.0.0a7
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/README.md

@@ -6,10 +6,10 @@
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a5"
+version = "3.0.0a7"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a5
+Version: 3.0.0a7
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-75%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/core/mol_geometry.py

@@ -12,7 +12,6 @@ DOI: 10.5281/zenodo.17268532
 
 from __future__ import annotations
 import math
-import logging
 from collections import deque
 from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
 
@@ -22,7 +21,11 @@ import numpy as np
 # Primitive geometry helpers
 # ------------------------------------------------------------------
 
-def calc_distance(pos1: Union[np.ndarray, Tuple[float, float, float], List[float]], pos2: Union[np.ndarray, Tuple[float, float, float], List[float]]) -> float:
+
+def calc_distance(
+    pos1: Union[np.ndarray, Tuple[float, float, float], List[float]],
+    pos2: Union[np.ndarray, Tuple[float, float, float], List[float]],
+) -> float:
     """Return the Euclidean distance between two 3-D positions.
 
     Parameters
@@ -78,7 +81,9 @@ def calc_angle_deg(
 # ------------------------------------------------------------------
 
 
-def get_connected_group(mol: Any, start_atom: int, exclude: Optional[int] = None) -> Set[int]:
+def get_connected_group(
+    mol: Any, start_atom: int, exclude: Optional[int] = None
+) -> Set[int]:
     """Return the set of atom indices reachable from *start_atom*
     without passing through *exclude*.
 
@@ -383,7 +388,9 @@ _VALENCE_LIMITS = {
 }
 
 
-def is_problematic_valence(symbol: str, bond_count: Union[int, float], charge: int = 0) -> bool:
+def is_problematic_valence(
+    symbol: str, bond_count: Union[int, float], charge: int = 0
+) -> bool:
     """Return ``True`` if the atom's total bond order exceeds its
     typical maximum valence.
 
@@ -475,7 +482,9 @@ def inject_ez_stereo_to_mol_block(mol_block, rdkit_mol, bonds_data):
     return "\n".join(mol_lines)
 
 
-def identify_valence_problems(atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]) -> List[int]:
+def identify_valence_problems(
+    atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]
+) -> List[int]:
     """Identify atoms with problematic valence.
 
     Parameters

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/core/molecular_data.py

@@ -12,7 +12,7 @@ DOI: 10.5281/zenodo.17268532
 
 from __future__ import annotations
 import logging
-from typing import Any, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, Dict, List, Optional, Tuple, Union
 from rdkit import Chem
 
 try:
@@ -43,7 +43,13 @@ class MolecularData:
         self._next_atom_id = 0
         self.adjacency_list = {}
 
-    def add_atom(self, symbol: str, pos: Union[Any, Tuple[float, float]], charge: int = 0, radical: int = 0) -> int:
+    def add_atom(
+        self,
+        symbol: str,
+        pos: Union[Any, Tuple[float, float]],
+        charge: int = 0,
+        radical: int = 0,
+    ) -> int:
         atom_id = self._next_atom_id
         # Internalize position as raw floats to decouple from UI types (QPointF)
         if hasattr(pos, "x") and hasattr(pos, "y"):
@@ -72,7 +78,9 @@ class MolecularData:
             else:
                 self.atoms[atom_id]["pos"] = PointTuple((float(pos[0]), float(pos[1])))
 
-    def add_bond(self, id1: int, id2: int, order: Union[int, float] = 1, stereo: int = 0) -> Tuple[Tuple[int, int], str]:
+    def add_bond(
+        self, id1: int, id2: int, order: Union[int, float] = 1, stereo: int = 0
+    ) -> Tuple[Tuple[int, int], str]:
         # For stereo bonds, do not sort because ID order determines direction.
         # For non-stereo bonds, sort to normalize the key.
         if stereo == 0:
@@ -457,7 +465,9 @@ class MolecularData:
         mol_block += "M  END\n"
         return mol_block
 
-    def to_template_dict(self, name: str, version: str = "1.0", application_version: str = "") -> Dict[str, Any]:
+    def to_template_dict(
+        self, name: str, version: str = "1.0", application_version: str = ""
+    ) -> Dict[str, Any]:
         """Convert current structure to a dictionary for template storage."""
         import datetime
 

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/main.py

@@ -50,7 +50,6 @@ def setup_logging():
     sys.excepthook = handle_exception
 
 
-
 def main():
     # Setup logging as early as possible
     setup_logging()

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/plugins/plugin_interface.py

@@ -45,6 +45,50 @@ class PluginContext:
             self._plugin_name, path, callback, text, icon, shortcut
         )
 
+    def register_menu_action(
+        self,
+        path: str,
+        text_or_callback: Union[str, Callable],
+        callback: Optional[Callable] = None,
+        icon: Optional[str] = None,
+        shortcut: Optional[str] = None,
+    ):
+        """Backward-compatible alias for add_menu_action.
+        Supports old 3-arg style: register_menu_action(path, text, callback).
+        """
+        if callable(text_or_callback):
+            # New style: (path, callback, ...)
+            self.add_menu_action(path, text_or_callback, None, icon, shortcut)
+        else:
+            # Old style: (path, text, callback)
+            self.add_menu_action(path, callback, text_or_callback, icon, shortcut)
+
+    def add_plugin_menu(
+        self,
+        path: str,
+        callback: Callable,
+        text: Optional[str] = None,
+        icon: Optional[str] = None,
+        shortcut: Optional[str] = None,
+    ):
+        """
+        Register an action nested inside the Plugin menu.
+
+        Equivalent to add_menu_action("Plugin/<path>", ...).
+        Use this instead of add_menu_action when you want your plugin to appear
+        as a nested folder inside the Plugin menu rather than as a top-level menu.
+
+        Args:
+            path: Sub-path within the Plugin menu, e.g. "Utility/My Tool"
+                  results in Plugin > Utility > My Tool.
+            callback: Function to call when triggered.
+            text: Label override (defaults to last part of path).
+            icon: Path to icon (optional).
+            shortcut: Keyboard shortcut (optional).
+        """
+        full_path = f"Plugin/{path.lstrip('/')}"
+        self.add_menu_action(full_path, callback, text, icon, shortcut)
+
     def add_toolbar_action(
         self,
         callback: Callable,
@@ -84,7 +128,7 @@ class PluginContext:
     def push_undo_checkpoint(self) -> None:
         """
         Create an undo checkpoint for the current state.
-        Call this AFTER making modifications to the molecule to ensure the 
+        Call this AFTER making modifications to the molecule to ensure the
         new state is saved to the undo history.
         """
         self._manager.push_undo_checkpoint()
@@ -135,13 +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)
 
@@ -160,7 +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:
@@ -168,7 +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):
         """
@@ -265,6 +309,41 @@ class PluginContext:
         """
         self._manager.register_document_reset_handler(self._plugin_name, callback)
 
+    def get_setting(self, key: str, default: Any = None) -> Any:
+        """
+        Get a plugin-specific persistent setting.
+
+        Settings are stored in the app settings dict under 'plugin.<plugin_name>.<key>'
+        and are persisted across sessions with the application settings.
+
+        Args:
+            key: Setting key name.
+            default: Value to return if the setting is not found.
+        """
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "init_manager") and hasattr(mw.init_manager, "settings"):
+            namespaced = f"plugin.{self._plugin_name}.{key}"
+            return mw.init_manager.settings.get(namespaced, default)
+        return default
+
+    def set_setting(self, key: str, value: Any) -> None:
+        """
+        Save a plugin-specific persistent setting.
+
+        Settings are stored in the app settings dict under 'plugin.<plugin_name>.<key>'
+        and are saved when the application saves its settings.
+
+        Args:
+            key: Setting key name.
+            value: Value to store (must be JSON-serializable).
+        """
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "init_manager") and hasattr(mw.init_manager, "settings"):
+            namespaced = f"plugin.{self._plugin_name}.{key}"
+            mw.init_manager.settings[namespaced] = value
+            if hasattr(mw.init_manager, "settings_dirty"):
+                mw.init_manager.settings_dirty = True
+
 
 class Plugin3DController:
     """Helper to manipulate the 3D scene."""

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/plugins/plugin_manager.py

@@ -18,7 +18,7 @@ import os
 import shutil
 import sys
 import zipfile
-from typing import Any, Callable, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, Callable, Dict, List, Optional, Tuple
 
 from PyQt6.QtCore import QUrl
 from PyQt6.QtGui import QDesktopServices
@@ -30,9 +30,12 @@ except ImportError:
     # Fallback if running as script
     from moleditpy.plugins.plugin_interface import PluginContext
 
+
 class PluginManager:
     def __init__(self, main_window: Any = None) -> None:
-        self.plugin_dir: str = os.path.join(os.path.expanduser("~"), ".moleditpy", "plugins")
+        self.plugin_dir: str = os.path.join(
+            os.path.expanduser("~"), ".moleditpy", "plugins"
+        )
         self.plugins: List[Dict[str, Any]] = []  # List of dicts
         self.main_window: Any = main_window
 
@@ -50,7 +53,9 @@ class PluginManager:
         self.load_handlers: Dict[str, Callable] = {}
         self.custom_3d_styles: Dict[str, Dict[str, Any]] = {}
         self.document_reset_handlers: List[Dict[str, Any]] = []
-        self.plugin_windows: Dict[str, Dict[str, Any]] = {} # Map of plugin_name -> {window_id -> window}
+        self.plugin_windows: Dict[
+            str, Dict[str, Any]
+        ] = {}  # Map of plugin_name -> {window_id -> window}
 
     def get_main_window(self) -> Any:
         return self.main_window
@@ -235,7 +240,9 @@ class PluginManager:
 
         return self.plugins
 
-    def _load_single_plugin(self, filepath: str, module_name: str, category: str) -> None:
+    def _load_single_plugin(
+        self, filepath: str, module_name: str, category: str
+    ) -> None:
         """Common loading logic for both single-file and package plugins."""
         try:
             # Ensure unique module name by including category path
@@ -371,7 +378,15 @@ class PluginManager:
             )
 
     # --- Registration Callbacks ---
-    def register_menu_action(self, plugin_name: str, path: str, callback: Callable, text: str, icon: str, shortcut: str) -> None:
+    def register_menu_action(
+        self,
+        plugin_name: str,
+        path: str,
+        callback: Callable,
+        text: str,
+        icon: str,
+        shortcut: str,
+    ) -> None:
         self.menu_actions.append(
             {
                 "plugin": plugin_name,
@@ -383,7 +398,9 @@ class PluginManager:
             }
         )
 
-    def register_toolbar_action(self, plugin_name: str, callback: Callable, text: str, icon: str, tooltip: str) -> None:
+    def register_toolbar_action(
+        self, plugin_name: str, callback: Callable, text: str, icon: str, tooltip: str
+    ) -> None:
         self.toolbar_actions.append(
             {
                 "plugin": plugin_name,
@@ -394,7 +411,9 @@ class PluginManager:
             }
         )
 
-    def register_drop_handler(self, plugin_name: str, callback: Callable, priority: int) -> None:
+    def register_drop_handler(
+        self, plugin_name: str, callback: Callable, priority: int
+    ) -> None:
         self.drop_handlers.append(
             {"priority": priority, "plugin": plugin_name, "callback": callback}
         )
@@ -470,12 +489,20 @@ class PluginManager:
 
     def refresh_3d_view(self) -> None:
         """Force a re-render of the 3D scene."""
-        if self.main_window and hasattr(self.main_window, "plotter") and self.main_window.plotter:
+        if (
+            self.main_window
+            and hasattr(self.main_window, "plotter")
+            and self.main_window.plotter
+        ):
             self.main_window.plotter.render()
 
     def reset_3d_camera(self) -> None:
         """Reset the 3D camera to fit the current molecule."""
-        if self.main_window and hasattr(self.main_window, "plotter") and self.main_window.plotter:
+        if (
+            self.main_window
+            and hasattr(self.main_window, "plotter")
+            and self.main_window.plotter
+        ):
             self.main_window.plotter.reset_camera()
             self.main_window.plotter.render()
 
@@ -492,7 +519,7 @@ class PluginManager:
             # 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.
             # RDKit molecule atoms have an '_original_atom_id' property.
-            
+
             scene = getattr(self.main_window, "scene", None)
             if scene:
                 selected_items = scene.selectedItems()
@@ -501,7 +528,7 @@ class PluginManager:
                     # Relying on duck-typing for AtomItem
                     if hasattr(item, "atom_id"):
                         selected_atom_ids.add(item.atom_id)
-                
+
                 # Now map these editor IDs to RDKit indices
                 mol = getattr(self.main_window, "current_mol", None)
                 if mol and selected_atom_ids:

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/ui/align_plane_dialog.py

@@ -10,18 +10,14 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import logging
 import numpy as np
-from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
     QHBoxLayout,
     QLabel,
     QMessageBox,
     QPushButton,
     QVBoxLayout,
-    QWidget,
 )
-from rdkit import Geometry
 
 try:
     from .base_picking_dialog import BasePickingDialog
@@ -122,7 +118,7 @@ class AlignPlaneDialog(BasePickingDialog):
                 # fallback to main_window data map
                 self.selected_atoms = (
                     set(self.main_window.state_manager.data.atoms.keys())
-                    if hasattr(self.main_window.state_manager, 'data')
+                    if hasattr(self.main_window.state_manager, "data")
                     else set()
                 )
 

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/ui/alignment_dialog.py

@@ -10,7 +10,6 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import logging
 import numpy as np
 from PyQt6.QtWidgets import (
     QDialog,
@@ -128,9 +127,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         elif len(self.selected_atoms) == 1:
             selected_list = list(self.selected_atoms)
             atom = self.mol.GetAtomWithIdx(selected_list[0])
-            self.selection_label.setText(
-                f"Selected 1 atom: {atom.GetSymbol()}"
-            )
+            self.selection_label.setText(f"Selected 1 atom: {atom.GetSymbol()}")
             self.apply_button.setEnabled(False)
         elif len(self.selected_atoms) == 2:
             selected_list = sorted(list(self.selected_atoms))

{moleditpy-3.0.0a5 → moleditpy-3.0.0a7}/src/moleditpy/ui/angle_dialog.py

@@ -10,7 +10,6 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import logging
 from PyQt6.QtWidgets import (
     QHBoxLayout,
     QLabel,
@@ -23,7 +22,6 @@ from PyQt6.QtWidgets import (
     QMessageBox,
 )
 from PyQt6.QtCore import Qt
-from rdkit import Geometry
 
 try:
     from .geometry_base_dialog import GeometryBaseDialog
@@ -91,7 +89,7 @@ class AngleDialog(GeometryBaseDialog):
         self.angle_slider.setTickPosition(QSlider.TickPosition.TicksBelow)
         self.angle_slider.setTickInterval(45)
         self.angle_slider.setEnabled(False)
-        
+
         # Connect to base class real-time handlers
         self.angle_slider.sliderPressed.connect(self.on_slider_pressed)
         self.angle_slider.sliderMoved.connect(
@@ -101,7 +99,7 @@ class AngleDialog(GeometryBaseDialog):
         self.angle_slider.valueChanged.connect(
             lambda v: self.on_slider_value_changed_click(v, self.angle_input, 1.0)
         )
-        
+
         layout.addLayout(angle_layout)
         layout.addWidget(self.angle_slider)