superstar54 / x3dase

X3D for Atomic Simulation Environment

x3dase

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

Author

• Xing Wang [e-mail]

Dependencies

• Python
• ASE
• Skimage

Installation using pip

pip install --upgrade --user x3dase

Installation from source

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

Examples

Draw molecule in Jupyter notebooks

<iframe src="examples/c2h6so.html" style="width:100%; height:300px;" ></iframe>

Shortcut

key	function
b	ball-and-stick model
s	spacefilling model
p	polyhedra model
1	view top
2	view front
3	view right
4	view element
5	view index

Show different models

Measure distance and angle between atoms

Using Ctrl + click to select atoms.

Selection	measurement
single atom	xyz position and atomic symbol
two atoms	interatomic distance
three atoms	three internal angles

Polyhedra for crystal

Isosurface for electron density

Animation

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