Python module for drawing and rendering atoms and molecules objects using X3DOM. X3dase can be used as a viewer for the molecule structure in the Jupyter notebook.

Functions:

• Support all file-formats using by ASE, including cif, xyz, cube, pdb, json, VASP-out and so on.
• Ball & stick
• Space filling
• Polyhedral
• Isosurface
• Show element and index
• Measure distance and angle
• Animation

For the introduction of ASE , please visit https://wiki.fysik.dtu.dk/ase/index.html

• Xing Wang [email protected]

• Python
• ASE
• Skimage

pip install --upgrade --user x3dase

You can get the source using git:

git clone https://github.com/superstar54/x3dase.git

Then add it to your PYTHONPATH and PATH. On windows, you can edit the system environment variables.

export PYTHONPATH=/path-to-x3dase:$PYTHONPATH

Using Ctrl + click to select atoms.

images = [atoms1, atoms2, atoms3]
X3D(images)