moleditpy 3.0.0__tar.gz → 3.0.0a2__tar.gz

{moleditpy-3.0.0 → moleditpy-3.0.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0
+Version: 3.0.0a2
 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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%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)
@@ -834,7 +834,6 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
-  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0 → moleditpy-3.0.0a2}/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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%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)
@@ -130,7 +130,6 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
-  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0 → moleditpy-3.0.0a2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0"
+version = "3.0.0a2"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0 → moleditpy-3.0.0a2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0
+Version: 3.0.0a2
 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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%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)
@@ -834,7 +834,6 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
-  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

moleditpy-3.0.0a2/src/MoleditPy.egg-info/SOURCES.txt

@@ -0,0 +1,72 @@
+LICENSE
+README.md
+pyproject.toml
+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/__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
+src/moleditpy/assets/icon.png
+src/moleditpy/modules/__init__.py
+src/moleditpy/modules/about_dialog.py
+src/moleditpy/modules/align_plane_dialog.py
+src/moleditpy/modules/alignment_dialog.py
+src/moleditpy/modules/analysis_window.py
+src/moleditpy/modules/angle_dialog.py
+src/moleditpy/modules/atom_item.py
+src/moleditpy/modules/bond_item.py
+src/moleditpy/modules/bond_length_dialog.py
+src/moleditpy/modules/calculation_worker.py
+src/moleditpy/modules/color_settings_dialog.py
+src/moleditpy/modules/constants.py
+src/moleditpy/modules/constrained_optimization_dialog.py
+src/moleditpy/modules/custom_interactor_style.py
+src/moleditpy/modules/custom_qt_interactor.py
+src/moleditpy/modules/dialog_3d_picking_mixin.py
+src/moleditpy/modules/dihedral_dialog.py
+src/moleditpy/modules/main_window.py
+src/moleditpy/modules/main_window_app_state.py
+src/moleditpy/modules/main_window_compute.py
+src/moleditpy/modules/main_window_dialog_manager.py
+src/moleditpy/modules/main_window_edit_3d.py
+src/moleditpy/modules/main_window_edit_actions.py
+src/moleditpy/modules/main_window_export.py
+src/moleditpy/modules/main_window_main_init.py
+src/moleditpy/modules/main_window_molecular_parsers.py
+src/moleditpy/modules/main_window_project_io.py
+src/moleditpy/modules/main_window_string_importers.py
+src/moleditpy/modules/main_window_ui_manager.py
+src/moleditpy/modules/main_window_view_3d.py
+src/moleditpy/modules/main_window_view_loaders.py
+src/moleditpy/modules/mirror_dialog.py
+src/moleditpy/modules/mol_geometry.py
+src/moleditpy/modules/molecular_data.py
+src/moleditpy/modules/molecular_scene_handler.py
+src/moleditpy/modules/molecule_scene.py
+src/moleditpy/modules/move_group_dialog.py
+src/moleditpy/modules/periodic_table_dialog.py
+src/moleditpy/modules/planarize_dialog.py
+src/moleditpy/modules/plugin_interface.py
+src/moleditpy/modules/plugin_manager.py
+src/moleditpy/modules/plugin_manager_window.py
+src/moleditpy/modules/settings_dialog.py
+src/moleditpy/modules/sip_isdeleted_safe.py
+src/moleditpy/modules/system_utils.py
+src/moleditpy/modules/template_preview_item.py
+src/moleditpy/modules/template_preview_view.py
+src/moleditpy/modules/translation_dialog.py
+src/moleditpy/modules/user_template_dialog.py
+src/moleditpy/modules/zoomable_view.py

{moleditpy-3.0.0/src/moleditpy/utils → moleditpy-3.0.0a2/src/moleditpy}/__init__.py

@@ -9,3 +9,7 @@ License: GPL-3.0 license
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
+
+"""Top-level package for moleditpy.
+
+"""

{moleditpy-3.0.0 → moleditpy-3.0.0a2}/src/moleditpy/main.py

@@ -14,41 +14,23 @@ import ctypes
 import sys
 import argparse
 import logging
-import os
 
 from PyQt6.QtWidgets import QApplication
 
 try:
-    from .ui.main_window import MainWindow
+    from .modules.main_window import MainWindow
 except ImportError:
-    # Add the parent directory (src) to sys.path so 'moleditpy.*' imports work
-    src_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
-    if src_dir not in sys.path:
-        sys.path.insert(0, src_dir)
-    from moleditpy.ui.main_window import MainWindow
+    from modules.main_window import MainWindow
 
 
 def setup_logging():
+    """Configure global logging to standard output."""
     logging.basicConfig(
         level=logging.INFO,
-        format="%(asctime)s [%(levelname)s] %(name)s (%(pathname)s:%(lineno)d): %(message)s",
+        format="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
         stream=sys.stdout,
-        force=True,
     )
 
-    def handle_exception(exc_type, exc_value, exc_traceback):
-        """Log unhandled exceptions using the configured logging system."""
-        if issubclass(exc_type, KeyboardInterrupt):
-            # Allow keyboard interrupt to exit normally
-            sys.__excepthook__(exc_type, exc_value, exc_traceback)
-            return
-
-        logging.error(
-            "Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)
-        )
-
-    sys.excepthook = handle_exception
-
 
 def main():
     # Setup logging as early as possible

moleditpy-3.0.0/src/moleditpy/ui/sip_isdeleted_safe.py → moleditpy-3.0.0a2/src/moleditpy/modules/__init__.py

@@ -1,35 +1,41 @@
-#!/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
-"""
-
-try:
-    from PyQt6 import sip as _sip  # type: ignore
-
-    _sip_isdeleted = getattr(_sip, "isdeleted", None)
-except (AttributeError, RuntimeError, TypeError, ImportError):
-    _sip = None
-    _sip_isdeleted = None
-
-
-def sip_isdeleted_safe(obj) -> bool:
-    """Return True if sip reports the given wrapper object as deleted.
-
-    This function is conservative: if SIP isn't available or any error
-    occurs while checking, it returns False (i.e. not deleted) so that the
-    caller can continue other lightweight guards (like checking scene()).
-    """
-    try:
-        if _sip_isdeleted is None:
-            return False
-        # Ensure we return a boolean value
-        return bool(_sip_isdeleted(obj))
-    except (AttributeError, RuntimeError, TypeError):
-        return False
+#!/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
+"""
+
+try:
+    import importlib.util
+
+    OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
+except ImportError:
+    OBABEL_AVAILABLE = False
+
+try:
+    from PyQt6 import sip as _sip  # type: ignore
+
+    _sip_isdeleted = getattr(_sip, "isdeleted", None)
+except ImportError:
+    _sip = None
+    _sip_isdeleted = None
+
+
+def sip_isdeleted_safe(obj) -> bool:
+    """Return True if sip reports the given wrapper object as deleted.
+
+    This function is conservative: if SIP isn't available or any error
+    occurs while checking, it returns False (i.e. not deleted) so that the
+    caller can continue other lightweight guards (like checking scene()).
+    """
+    try:
+        if _sip_isdeleted is None:
+            return False
+        return bool(_sip_isdeleted(obj))
+    except (AttributeError, RuntimeError, TypeError):
+        return False

{moleditpy-3.0.0/src/moleditpy/ui → moleditpy-3.0.0a2/src/moleditpy/modules}/about_dialog.py

@@ -1,3 +1,4 @@
+import logging
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
@@ -10,8 +11,6 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
-import logging
-
 import os
 
 from PyQt6.QtCore import Qt
@@ -19,9 +18,9 @@ from PyQt6.QtGui import QCursor, QPainter, QPen, QPixmap
 from PyQt6.QtWidgets import QDialog, QHBoxLayout, QLabel, QPushButton, QVBoxLayout
 
 try:
-    from ..utils.constants import VERSION
+    from .constants import VERSION
 except ImportError:
-    from moleditpy.utils.constants import VERSION
+    from modules.constants import VERSION
 
 
 class AboutDialog(QDialog):
@@ -92,10 +91,10 @@ class AboutDialog(QDialog):
     def image_clicked(self, event):
         """Easter egg: Clear all and load bipyrimidine from SMILES"""
         # Clear the current scene
-        self.main_window.edit_actions_manager.clear_all()
+        self.main_window.clear_all()
 
         bipyrimidine_smiles = "C1=CN=C(N=C1)C2=NC=CC=N2"
-        self.main_window.string_importer_manager.load_from_smiles(bipyrimidine_smiles)
+        self.main_window.load_from_smiles(bipyrimidine_smiles)
 
         # Close the dialog
         self.accept()