MoleditPy — A Python Molecular Editor

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 · User manual (日本語) · Plugins · Wiki

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.

See the user manual for every feature and keyboard shortcut.

Installation

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:

moleditpy

The first launch can take a while as RDKit and the other libraries initialize. A Windows installer, a macOS app bundle, and a Docker image 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:

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.

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 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 and binary distribution instructions.