MoleditPy — A Python Molecular Editor
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.
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
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:
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
.pmerawproject format uses Python pickle, which can execute arbitrary code when loaded. Only open.pmerawfiles you created yourself, and use the JSON-based.pmeprjformat for sharing.
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 General Public License v3.0 (GPLv3) - 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.
1 maintainer
Metadata
1 maintainer
Release files for MoleditPy-linux 4.11.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| moleditpy_linux-4.11.2.tar.gz | 883.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| moleditpy_linux-4.11.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.8 MB
Release files / moleditpy_linux-4.11.2.tar.gz
| Download URL | moleditpy_linux-4.11.2.tar.gz |
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| Size | 883.0 kB |
| Tags | Source |
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| Size | 923.0 kB |
| Tags | Python 3 |
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Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
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