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https://github.com/beautiful-atoms/beautiful-atoms
Python module for drawing and rendering beautiful atoms and molecules using Blender.
https://github.com/beautiful-atoms/beautiful-atoms
3d ase atomic atoms blender crystal molecule protein pymatgen python rendering ribbon-diagram
Last synced: 3 days ago
JSON representation
Python module for drawing and rendering beautiful atoms and molecules using Blender.
- Host: GitHub
- URL: https://github.com/beautiful-atoms/beautiful-atoms
- Owner: beautiful-atoms
- License: gpl-3.0
- Created: 2021-10-15T07:13:05.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-10-04T15:48:53.000Z (4 months ago)
- Last Synced: 2025-01-15T01:19:14.894Z (10 days ago)
- Topics: 3d, ase, atomic, atoms, blender, crystal, molecule, protein, pymatgen, python, rendering, ribbon-diagram
- Language: Python
- Homepage: https://beautiful-atoms.readthedocs.io/en/latest/
- Size: 12.7 MB
- Stars: 146
- Watchers: 3
- Forks: 26
- Open Issues: 34
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
## Beautiful Atoms
[](https://github.com/beautiful-atoms/beautiful-atoms/actions/workflows/build_main_image.yml)
[](https://github.com/beautiful-atoms/beautiful-atoms/actions/workflows/unittests.yaml)
[](https://codecov.io/gh/beautiful-atoms/beautiful-atoms)
Batoms is a Python package for editing and rendering atoms and molecule objects using Blender. A Python interface that allows for automating workflows.
Features:
* Model: space-filling, ball-stick, polyhedral, cavity and so on.
* Supported File type: cif, xyz, cube, pdb, json, VASP-out and so on.
* Supported structure: ASE and Pymatgen
* Volumetric data (Isosurface)
* Ribbon diagram for protein
* Site occupancy
* Animation
* GUI
* Support periodic boundary conditions
* Support fetch structures from MaterialProject, Pubchem and RSCB
* ``Flexible``: Python script, run interactively or in the background.
* ``High quality rendering``: 3D models
* ``Free, Open Source``: Easy to download and install.
* ``Cross-platform``: (Linux, Windows, macOS)
## How to use
### **⚠️ Need Blender 4.2.0 or later.**
Please visit the [documentation](https://beautiful-atoms.readthedocs.io/en/latest/) for more information.
## View and edit structure in Jupyter Notebook
Another package, [weas-widget](https://github.com/superstar54/weas-widget), allows users to visualize and edit with atomistic structures in Jupyter Notebook.
## How to contribute
### Extension
One can build the extension locally by following the steps below.
Download wheels for ase and scikit-image:
```
pip download ase scikit-image --dest ./batoms/wheels --only-binary=:all: --python-version=3.11 --platform=manylinux_2_17_x86_64
pip download ase scikit-image --dest ./batoms/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
pip download ase scikit-image --dest ./batoms/wheels --only-binary=:all: --python-version=3.11 --platform=macosx_12_0_arm64
```
Update the wheels in the `batoms/blender_manifest.toml` file.
```console
python scripts/update_wheels.py
```
Build the extension.
```
blender --command extension build --source-dir batoms --output-dir .
```
### Editor
We recommend using [Visual Studio Code](https://code.visualstudio.com/) with the [Blender extension](https://github.com/JacquesLucke/blender_vscode).
In order to develop it inside VSCode, you need at least update the wheel file in the `batoms/blender_manifest.toml` file using the steps above.
### Test
To run the tests, run:
```console
# install pytest
~/apps/blender-4.3.2-linux-x64/4.3/python/bin/python3.11 -m pip install pytest
# run all tests
~/apps/blender-4.3.2-linux-x64/blender -b -P scripts/run_tests.py -- -vv tests
# run a specific test
~/apps/blender-4.3.2-linux-x64/blender -b -P scripts/run_tests.py -- -vv tests/test_batoms.py
```
### Pre-commit
To install the pre-commit hooks, run:
```console
$ pre-commit install
```
## Contact
* Xing Wang