MoleditPy 4.13.0__tar.gz → 5.0.0a2__tar.gz

moleditpy-5.0.0a2/DISTRIBUTION.md

@@ -0,0 +1,29 @@
+# Distribution, source, and replacing libraries
+
+MoleditPy is LGPL-3.0-or-later. Read `LICENSE` together with `COPYING`. Recipients may inspect and modify the program, replace LGPL libraries, and reverse engineer for debugging their modifications. No warranty is provided.
+
+## Source distributions and installed Python packages
+
+The corresponding MoleditPy source, tests, build specifications and release workflows are in https://github.com/HiroYokoyama/python_molecular_editor. Each frozen build includes `licenses/build-manifest.json` with its exact source commit and dependency versions. Release archives must accompany or link the exact corresponding source and build instructions. The wheel and source archive include both GNU license texts and these notices.
+
+For a Python installation, create a virtual environment, install `moleditpy` and substitute compatible PySide6-Essentials/Shiboken6 wheels in that environment with pip. Running from source uses those installed shared libraries directly. Example:
+
+```sh
+python -m venv .venv
+# Activate .venv with the command for your shell.
+python -m pip install -e ./moleditpy
+python -m pip install --force-reinstall /path/to/modified/shiboken6.whl /path/to/modified/PySide6_Essentials.whl
+python -m moleditpy --safe
+```
+
+## Frozen Windows and macOS applications
+
+The application is an unpacked PyInstaller directory / `.app` bundle, with Qt and PySide6 shared libraries stored outside the executable archive. It does not statically link those libraries into MoleditPy. Keep a backup, close the application, and replace a compatible set of Qt libraries and matching PySide6/Shiboken6 bindings. Use the architecture, Qt ABI and versions recorded in `licenses/build-manifest.json`.
+
+On Windows the files are normally below `MoleditPy/_internal/PySide6/` (Qt6Core.dll, Qt6Gui.dll, Qt6Widgets.dll and associated bindings), with Shiboken6 below `_internal/shiboken6/`. Replace the corresponding files and plugin directories while preserving the layout. On macOS inspect `MoleditPy.app/Contents/Frameworks/PySide6/` and `Contents/Frameworks/`; replace matching `.framework`, `.dylib` and binding files and retain relative paths. Bundled paths vary with PyInstaller versions; locate the external `QtCore`/`Qt6Core` shared library first. macOS may require ad-hoc signing of a locally modified bundle: `codesign --force --deep --sign - MoleditPy.app`. This is a local platform requirement; MoleditPy does not require the publisher's signature.
+
+A reliable alternative to file replacement is to rebuild with modified dependencies: check out the manifest commit, install the modified compatible wheels in a clean environment, install `moleditpy` and PyInstaller, then run `pyinstaller --clean --noconfirm windows-installer/script/MoleditPy.spec` or `macos-installer/script/MoleditPy.spec` from the repository root. The build uses normal dynamic Qt libraries and does not impose a signature or activation lock.
+
+## Corresponding dependency source
+
+The manifest records installed versions and upstream source locations. Obtain Qt/PySide6 sources matching those versions from https://download.qt.io/official_releases/QtForPython/ and https://download.qt.io/official_releases/qt/, or their matching tags at https://code.qt.io/pyside/pyside-setup.git and https://code.qt.io/qt/qt5.git. Follow that version's upstream build instructions and preserve its third-party source notices. Distribution of modified libraries also requires their modified corresponding source under their applicable licenses. Release distributors must make required corresponding source available alongside the binaries, or use another compliant LGPL/GPL source-delivery method; an upstream project link alone is not a substitute for that obligation.

moleditpy-5.0.0a2/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
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+  2. Conveying Modified Versions.
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+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
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+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
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+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
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+   document.
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+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
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+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
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+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
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+
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+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
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+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

moleditpy-5.0.0a2/LICENSING.md

@@ -0,0 +1,11 @@
+# Licensing and independently developed plugins
+
+MoleditPy 5.0.0a1 and later is licensed under the GNU Lesser General Public License, version 3 or (at your option) any later version (LGPL-3.0-or-later). `LICENSE` contains LGPLv3's additional permissions; `COPYING` contains the incorporated GPLv3 terms. Earlier releases keep their original license.
+
+Copyright holder permission: independently developed plugins that use MoleditPy's documented plugin API may be distributed under any license, including proprietary licenses. Their authors choose their license and retain their copyright. This permission does not relicense copied or modified MoleditPy code, or code/libraries belonging to third parties. Those components retain their own licenses and obligations. Existing plugins retain their current licenses unless their authors explicitly change them.
+
+Modifications to MoleditPy itself remain subject to the LGPL. Distribution terms must allow users to modify the covered components and reverse engineer for debugging their modifications as required by LGPLv3. No separate activation, signature check, or plugin restriction blocks modified builds.
+
+This migration was authorized by the project owner. The repository attribution audit (`git shortlog -sne`) identifies Hiromichi Yokoyama/HiroYokoyama identities, automation bots, and CodexSandboxOffline under the owner's email. Third-party code is excluded from the relicensing grant.
+
+See [distribution and library replacement instructions](DISTRIBUTION.md) and [third-party notices](THIRD_PARTY_NOTICES.md).

moleditpy-5.0.0a2/PKG-INFO

@@ -0,0 +1,97 @@
+Metadata-Version: 2.4
+Name: MoleditPy
+Version: 5.0.0a2
+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-Expression: LGPL-3.0-or-later
+Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor
+Project-URL: Issues, https://github.com/HiroYokoyama/python_molecular_editor/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: COPYING
+License-File: THIRD_PARTY_NOTICES.md
+License-File: DISTRIBUTION.md
+License-File: LICENSING.md
+Requires-Dist: numpy
+Requires-Dist: pyside6-essentials<6.10,>=6.9; python_version < "3.10"
+Requires-Dist: pyside6-essentials<6.12,>=6.10; python_version >= "3.10"
+Requires-Dist: pyvista<0.50
+Requires-Dist: pyvistaqt<0.14
+Requires-Dist: rdkit<2026.4
+Dynamic: license-file
+
+# MoleditPy — A Python Molecular Editor
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+[![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
+[![License: LGPL v3+](https://img.shields.io/badge/License-LGPLv3%2B-blue.svg)](https://www.gnu.org/licenses/lgpl-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)
+[![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
+[![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)
+[![](https://img.shields.io/static/v1?label=Sponsor&message=%E2%9D%A4&logo=GitHub&color=%23fe8e86)](https://github.com/sponsors/HiroYokoyama)
+
+**MoleditPy** is a programmable, cross-platform molecular editor built with PySide6, RDKit, and PyVista. It takes you from a 2D sketch to an editable 3D structure and out to input files for DFT calculations, and it can be extended with plain Python plugins.
+
+**[Website](https://hiroyokoyama.github.io/python_molecular_editor/)** · **[User manual](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual)** ([日本語](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual-JP)) · **[Plugins](https://hiroyokoyama.github.io/moleditpy-plugins/)** · **[Wiki](https://github.com/HiroYokoyama/python_molecular_editor/wiki)**
+
+![MoleditPy screenshot](https://hiroyokoyama.github.io/python_molecular_editor/img/screenshot.png)
+
+## Features
+
+- **2D drawing** — atoms, bonds, ring templates, alkyl chains, charges, radicals, stereo bonds, and the full periodic table.
+- **3D editing** — 2D-to-3D conversion, dragging atoms in the 3D view, exact bond lengths, angles, and dihedrals, and MMFF94/UFF optimization with constraints.
+- **Analysis and export** — molecular properties, R/S labels, MOL/SDF/XYZ/SMILES/InChI import and export, PNG/SVG images, and STL/OBJ for 3D printing.
+- **Plugins** — drop a Python file into the plugin folder to add menu actions and tools. Browse the official collection in the [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/).
+
+See the [user manual](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual) for every feature and keyboard shortcut.
+
+## Installation
+
+```bash
+python -m pip install moleditpy-installer
+python -m moleditpy_installer
+```
+
+The first command installs MoleditPy and the shortcut helper; the second creates shortcuts and file associations. The same `moleditpy` package is used on Windows, macOS, and Linux. MoleditPy 5 requires Python 3.9–3.14. For an existing environment, uninstall `moleditpy-linux` and `openbabel-wheel` before upgrading. The core uses PySide6-Essentials and does not require Open Babel. Start the app from the shortcut or with:
+
+```bash
+moleditpy
+```
+
+The first launch can take a while as RDKit and the other libraries initialize. A [Windows installer](https://hiroyokoyama.github.io/python_molecular_editor/windows-installer/windows_installer), a [macOS app bundle](https://hiroyokoyama.github.io/python_molecular_editor/macos-installer/macos_installer), and a [Docker image](https://github.com/HiroYokoyama/python_molecular_editor_docker) are also available.
+
+> **Security note:** the legacy `.pmeraw` project format uses Python pickle, which can execute arbitrary code when loaded. Only open `.pmeraw` files you created yourself, and use the JSON-based `.pmeprj` format for sharing.
+
+To install the application directly without the shortcut helper:
+
+```bash
+python -m pip install MoleditPy
+```
+
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
+Please also cite the plugins you used; see [Citation in the plugin collection](https://github.com/HiroYokoyama/moleditpy-plugins#citation).
+
+## License & Disclaimer
+
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/README.md

@@ -3,13 +3,13 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
 [![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.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)
+[![License: LGPL v3+](https://img.shields.io/badge/License-LGPLv3%2B-blue.svg)](https://www.gnu.org/licenses/lgpl-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)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
 [![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)
 [![](https://img.shields.io/static/v1?label=Sponsor&message=%E2%9D%A4&logo=GitHub&color=%23fe8e86)](https://github.com/sponsors/HiroYokoyama)
 
-**MoleditPy** is a programmable, cross-platform molecular editor built with PyQt6, RDKit, and PyVista. It takes you from a 2D sketch to an editable 3D structure and out to input files for DFT calculations, and it can be extended with plain Python plugins.
+**MoleditPy** is a programmable, cross-platform molecular editor built with PySide6, RDKit, and PyVista. It takes you from a 2D sketch to an editable 3D structure and out to input files for DFT calculations, and it can be extended with plain Python plugins.
 
 **[Website](https://hiroyokoyama.github.io/python_molecular_editor/)** · **[User manual](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual)** ([日本語](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual-JP)) · **[Plugins](https://hiroyokoyama.github.io/moleditpy-plugins/)** · **[Wiki](https://github.com/HiroYokoyama/python_molecular_editor/wiki)**
 
@@ -27,11 +27,11 @@ See the [user manual](https://hiroyokoyama.github.io/python_molecular_editor/man
 ## Installation
 
 ```bash
-pip install moleditpy-installer
+python -m pip install moleditpy-installer
 python -m moleditpy_installer
 ```
 
-The first command installs the right package for your platform (`moleditpy`, or `moleditpy-linux` on Linux); the second creates an application shortcut. Start the app from the shortcut or with:
+The first command installs MoleditPy and the shortcut helper; the second creates shortcuts and file associations. The same `moleditpy` package is used on Windows, macOS, and Linux. MoleditPy 5 requires Python 3.9–3.14. For an existing environment, uninstall `moleditpy-linux` and `openbabel-wheel` before upgrading. The core uses PySide6-Essentials and does not require Open Babel. Start the app from the shortcut or with:
 
 ```bash
 moleditpy
@@ -41,6 +41,12 @@ The first launch can take a while as RDKit and the other libraries initialize. A
 
 > **Security note:** the legacy `.pmeraw` project format uses Python pickle, which can execute arbitrary code when loaded. Only open `.pmeraw` files you created yourself, and use the JSON-based `.pmeprj` format for sharing.
 
+To install the application directly without the shortcut helper:
+
+```bash
+python -m pip install MoleditPy
+```
+
 ## Citation
 
 If you use this software in your work, please cite it as follows:
@@ -53,4 +59,6 @@ Please also cite the plugins you used; see [Citation in the plugin collection](h
 
 ## License & Disclaimer
 
-This project is licensed under the GNU General Public License v3.0 (GPLv3) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).

moleditpy-5.0.0a2/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,20 @@
+# Third-party notices
+
+MoleditPy is LGPL-3.0-or-later. Its license does not replace third-party licenses.
+
+| Component | License / source |
+| --- | --- |
+| PySide6-Essentials and Shiboken6 | LGPL-3.0 (or other terms offered by Qt); https://code.qt.io/pyside/pyside-setup.git |
+| Qt Core, GUI, Widgets, SVG and required support libraries | LGPL-3.0 (or other terms offered by Qt); https://code.qt.io/qt/qtbase.git and https://code.qt.io/qt/qtsvg.git |
+| RDKit | BSD-3-Clause; https://github.com/rdkit/rdkit |
+| PyVista and pyvistaqt | MIT; https://github.com/pyvista/pyvista and https://github.com/pyvista/pyvistaqt |
+| VTK | BSD-3-Clause; https://gitlab.kitware.com/vtk/vtk |
+| NumPy | BSD-3-Clause and bundled notices; https://github.com/numpy/numpy |
+| Python | PSF license and included notices; https://github.com/python/cpython |
+| PyInstaller bootloader | GPL-2.0-or-later with the PyInstaller exception; https://github.com/pyinstaller/pyinstaller |
+
+Dependency wheels and frozen distributions include additional libraries (for example image codecs, numerical libraries, and platform support). Preserve their accompanying license and copyright notices. Build archives include installed dependency license directories under `licenses/third-party` and a version/source manifest.
+
+The core does not depend on or bundle Open Babel. Optional plugins and their dependencies carry independent license notices. The frozen build deliberately excludes unused Qt modules, including GPL-only add-on modules; installing arbitrary Qt add-ons can change a distributor's obligations.
+
+Official Qt licensing information: https://doc.qt.io/qt-6/licensing.html and https://doc.qt.io/qtforpython-6/licenses.html. GNU license texts: https://www.gnu.org/licenses/lgpl-3.0.html and https://www.gnu.org/licenses/gpl-3.0.html.

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/pyproject.toml

@@ -1,13 +1,14 @@
 [build-system]
-requires = ["setuptools>=61.0"]
+requires = ["setuptools>=77.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "MoleditPy"
 
-version = "4.13.0"
+version = "5.0.0a2"
 
-license = {file = "LICENSE"}
+license = "LGPL-3.0-or-later"
+license-files = ["LICENSE", "COPYING", "THIRD_PARTY_NOTICES.md", "DISTRIBUTION.md", "LICENSING.md"]
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },
@@ -34,12 +35,11 @@ classifiers = [
 
 dependencies = [
   "numpy",
-  "pyqt6 < 6.10; python_version == '3.9'",
-  "pyqt6 < 6.12; python_version != '3.9'",
+  "pyside6-essentials >= 6.9, < 6.10; python_version < '3.10'",
+  "pyside6-essentials >= 6.10, < 6.12; python_version >= '3.10'",
   "pyvista < 0.50",
   "pyvistaqt < 0.14",
-  "rdkit < 2026.4",
-  "openbabel-wheel < 3.2"
+  "rdkit < 2026.4"
 ]
 
 [project.urls]

moleditpy-5.0.0a2/src/MoleditPy.egg-info/PKG-INFO

@@ -0,0 +1,97 @@
+Metadata-Version: 2.4
+Name: MoleditPy
+Version: 5.0.0a2
+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-Expression: LGPL-3.0-or-later
+Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor
+Project-URL: Issues, https://github.com/HiroYokoyama/python_molecular_editor/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: COPYING
+License-File: THIRD_PARTY_NOTICES.md
+License-File: DISTRIBUTION.md
+License-File: LICENSING.md
+Requires-Dist: numpy
+Requires-Dist: pyside6-essentials<6.10,>=6.9; python_version < "3.10"
+Requires-Dist: pyside6-essentials<6.12,>=6.10; python_version >= "3.10"
+Requires-Dist: pyvista<0.50
+Requires-Dist: pyvistaqt<0.14
+Requires-Dist: rdkit<2026.4
+Dynamic: license-file
+
+# MoleditPy — A Python Molecular Editor
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+[![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
+[![License: LGPL v3+](https://img.shields.io/badge/License-LGPLv3%2B-blue.svg)](https://www.gnu.org/licenses/lgpl-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)
+[![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
+[![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)
+[![](https://img.shields.io/static/v1?label=Sponsor&message=%E2%9D%A4&logo=GitHub&color=%23fe8e86)](https://github.com/sponsors/HiroYokoyama)
+
+**MoleditPy** is a programmable, cross-platform molecular editor built with PySide6, RDKit, and PyVista. It takes you from a 2D sketch to an editable 3D structure and out to input files for DFT calculations, and it can be extended with plain Python plugins.
+
+**[Website](https://hiroyokoyama.github.io/python_molecular_editor/)** · **[User manual](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual)** ([日本語](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual-JP)) · **[Plugins](https://hiroyokoyama.github.io/moleditpy-plugins/)** · **[Wiki](https://github.com/HiroYokoyama/python_molecular_editor/wiki)**
+
+![MoleditPy screenshot](https://hiroyokoyama.github.io/python_molecular_editor/img/screenshot.png)
+
+## Features
+
+- **2D drawing** — atoms, bonds, ring templates, alkyl chains, charges, radicals, stereo bonds, and the full periodic table.
+- **3D editing** — 2D-to-3D conversion, dragging atoms in the 3D view, exact bond lengths, angles, and dihedrals, and MMFF94/UFF optimization with constraints.
+- **Analysis and export** — molecular properties, R/S labels, MOL/SDF/XYZ/SMILES/InChI import and export, PNG/SVG images, and STL/OBJ for 3D printing.
+- **Plugins** — drop a Python file into the plugin folder to add menu actions and tools. Browse the official collection in the [Plugin Explorer](https://hiroyokoyama.github.io/moleditpy-plugins/explorer/).
+
+See the [user manual](https://hiroyokoyama.github.io/python_molecular_editor/manual/manual) for every feature and keyboard shortcut.
+
+## Installation
+
+```bash
+python -m pip install moleditpy-installer
+python -m moleditpy_installer
+```
+
+The first command installs MoleditPy and the shortcut helper; the second creates shortcuts and file associations. The same `moleditpy` package is used on Windows, macOS, and Linux. MoleditPy 5 requires Python 3.9–3.14. For an existing environment, uninstall `moleditpy-linux` and `openbabel-wheel` before upgrading. The core uses PySide6-Essentials and does not require Open Babel. Start the app from the shortcut or with:
+
+```bash
+moleditpy
+```
+
+The first launch can take a while as RDKit and the other libraries initialize. A [Windows installer](https://hiroyokoyama.github.io/python_molecular_editor/windows-installer/windows_installer), a [macOS app bundle](https://hiroyokoyama.github.io/python_molecular_editor/macos-installer/macos_installer), and a [Docker image](https://github.com/HiroYokoyama/python_molecular_editor_docker) are also available.
+
+> **Security note:** the legacy `.pmeraw` project format uses Python pickle, which can execute arbitrary code when loaded. Only open `.pmeraw` files you created yourself, and use the JSON-based `.pmeprj` format for sharing.
+
+To install the application directly without the shortcut helper:
+
+```bash
+python -m pip install MoleditPy
+```
+
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
+Please also cite the plugins you used; see [Citation in the plugin collection](https://github.com/HiroYokoyama/moleditpy-plugins#citation).
+
+## License & Disclaimer
+
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/src/MoleditPy.egg-info/SOURCES.txt

@@ -1,5 +1,9 @@
+COPYING
+DISTRIBUTION.md
 LICENSE
+LICENSING.md
 README.md
+THIRD_PARTY_NOTICES.md
 pyproject.toml
 src/MoleditPy.egg-info/PKG-INFO
 src/MoleditPy.egg-info/SOURCES.txt
@@ -52,6 +56,7 @@ 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/menu_utils.py
 src/moleditpy/ui/mirror_dialog.py
 src/moleditpy/ui/molecular_scene_handler.py
 src/moleditpy/ui/molecule_scene.py

moleditpy-5.0.0a2/src/MoleditPy.egg-info/requires.txt

@@ -0,0 +1,10 @@
+numpy
+pyvista<0.50
+pyvistaqt<0.14
+rdkit<2026.4
+
+[:python_version < "3.10"]
+pyside6-essentials<6.10,>=6.9
+
+[:python_version >= "3.10"]
+pyside6-essentials<6.12,>=6.10

moleditpy-5.0.0a2/src/moleditpy/__init__.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: LGPL-3.0-or-later
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+import os
+
+# qtpy/pyvistaqt must use the same binding as the application's native widgets,
+# including when an older installation left QT_API=pyqt6 in the environment.
+os.environ["QT_API"] = "pyside6"
+
+from .utils.constants import VERSION as __version__  # noqa: E402, F401

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/src/moleditpy/__main__.py

@@ -5,7 +5,7 @@
 MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
-License: GPL-3.0 license
+License: LGPL-3.0-or-later
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """

{moleditpy-4.13.0/src/moleditpy/ui/settings_tabs → moleditpy-5.0.0a2/src/moleditpy/core}/__init__.py

@@ -5,7 +5,7 @@
 MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
-License: GPL-3.0 license
+License: LGPL-3.0-or-later
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/src/moleditpy/core/mol_geometry.py

@@ -5,7 +5,7 @@
 MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
-License: GPL-3.0 license
+License: LGPL-3.0-or-later
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/src/moleditpy/core/molecular_data.py

@@ -5,7 +5,7 @@
 MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
-License: GPL-3.0 license
+License: LGPL-3.0-or-later
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """

{moleditpy-4.13.0 → moleditpy-5.0.0a2}/src/moleditpy/core/stereo_check.py

@@ -5,7 +5,7 @@
 MoleditPy — A Python-based molecular editing software
 
 Author: Hiromichi Yokoyama
-License: GPL-3.0 license
+License: LGPL-3.0-or-later
 Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """