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

Please visit: https://beautiful-atoms.readthedocs.io/en/latest/

View and edit structure in Jupyter Notebook

Another package, weas-widget, allows users to visualize and edit with atomistic structures in Jupyter Notebook.

How to contribute

Editor

We recommend using Visual Studio Code with the Blender extension.

Test

We recommend using pytest-blender. To run the tests, run:

pip install pytest-blender
blender_python="$(pytest-blender)"
$blender_python -m ensurepip
# Install the development dependencies:
$blender_python -m pip install -r test-requirements.txt
cd tests
pytest

Pre-commit

To install the pre-commit hooks, run:

$ pre-commit install

Contact

• Xing Wang xingwang1991@gmail.com