MoleditPy 2.8.2__tar.gz → 3.0.0__tar.gz

{moleditpy-2.8.2 → moleditpy-3.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.2
+Version: 3.0.0
 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-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![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-8.64%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)
@@ -834,6 +834,7 @@ 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-2.8.2 → moleditpy-3.0.0}/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-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![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-8.64%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)
@@ -130,6 +130,7 @@ 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-2.8.2 → moleditpy-3.0.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.8.2"
+version = "3.0.0"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.8.2 → moleditpy-3.0.0}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.2
+Version: 3.0.0
 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-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![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-8.64%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)
@@ -834,6 +834,7 @@ 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/src/MoleditPy.egg-info/SOURCES.txt

@@ -0,0 +1,82 @@
+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/core/__init__.py
+src/moleditpy/core/mol_geometry.py
+src/moleditpy/core/molecular_data.py
+src/moleditpy/plugins/__init__.py
+src/moleditpy/plugins/plugin_interface.py
+src/moleditpy/plugins/plugin_manager.py
+src/moleditpy/plugins/plugin_manager_window.py
+src/moleditpy/ui/__init__.py
+src/moleditpy/ui/about_dialog.py
+src/moleditpy/ui/align_plane_dialog.py
+src/moleditpy/ui/alignment_dialog.py
+src/moleditpy/ui/analysis_window.py
+src/moleditpy/ui/angle_dialog.py
+src/moleditpy/ui/app_state.py
+src/moleditpy/ui/atom_item.py
+src/moleditpy/ui/base_picking_dialog.py
+src/moleditpy/ui/bond_item.py
+src/moleditpy/ui/bond_length_dialog.py
+src/moleditpy/ui/calculation_worker.py
+src/moleditpy/ui/color_settings_dialog.py
+src/moleditpy/ui/compute_logic.py
+src/moleditpy/ui/constrained_optimization_dialog.py
+src/moleditpy/ui/custom_interactor_style.py
+src/moleditpy/ui/custom_qt_interactor.py
+src/moleditpy/ui/dialog_3d_picking_mixin.py
+src/moleditpy/ui/dialog_logic.py
+src/moleditpy/ui/dihedral_dialog.py
+src/moleditpy/ui/edit_3d_logic.py
+src/moleditpy/ui/edit_actions_logic.py
+src/moleditpy/ui/export_logic.py
+src/moleditpy/ui/geometry_base_dialog.py
+src/moleditpy/ui/io_logic.py
+src/moleditpy/ui/main_window.py
+src/moleditpy/ui/main_window_init.py
+src/moleditpy/ui/mirror_dialog.py
+src/moleditpy/ui/molecular_scene_handler.py
+src/moleditpy/ui/molecule_scene.py
+src/moleditpy/ui/move_group_dialog.py
+src/moleditpy/ui/periodic_table_dialog.py
+src/moleditpy/ui/planarize_dialog.py
+src/moleditpy/ui/settings_dialog.py
+src/moleditpy/ui/sip_isdeleted_safe.py
+src/moleditpy/ui/string_importers.py
+src/moleditpy/ui/template_preview_item.py
+src/moleditpy/ui/template_preview_view.py
+src/moleditpy/ui/translation_dialog.py
+src/moleditpy/ui/ui_manager.py
+src/moleditpy/ui/user_template_dialog.py
+src/moleditpy/ui/view_3d_logic.py
+src/moleditpy/ui/zoomable_view.py
+src/moleditpy/ui/settings_tabs/__init__.py
+src/moleditpy/ui/settings_tabs/settings_2d_tab.py
+src/moleditpy/ui/settings_tabs/settings_3d_tabs.py
+src/moleditpy/ui/settings_tabs/settings_other_tab.py
+src/moleditpy/ui/settings_tabs/settings_tab_base.py
+src/moleditpy/utils/__init__.py
+src/moleditpy/utils/constants.py
+src/moleditpy/utils/default_settings.py
+src/moleditpy/utils/sip_isdeleted_safe.py
+src/moleditpy/utils/system_utils.py

moleditpy-3.0.0/src/moleditpy/__init__.py

@@ -0,0 +1,20 @@
+#!/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
+"""
+
+"""Top-level package for moleditpy."""
+
+import importlib.util
+
+try:
+    OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
+except ImportError:
+    OBABEL_AVAILABLE = False

{moleditpy-2.8.2 → moleditpy-3.0.0}/src/moleditpy/__main__.py

@@ -16,7 +16,7 @@ print("-----------------------------------------------------\n")
 
 try:
     from .main import main
-except Exception:
+except ImportError:
     from main import main
 
 # --- Application Execution ---