Drawing and rendering atoms and molecules objects using X3DOM. X3dase can be used as a viewer for the molecule structure in the Jupyter notebook.
Project description
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 xingwang1991@gmail.com
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
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)
Project details
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Source Distribution
x3dase-1.1.0.tar.gz
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x3dase-1.1.0-py3-none-any.whl
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