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https://github.com/superstar54/x3dase
X3D for Atomic Simulation Environment
https://github.com/superstar54/x3dase
Last synced: 23 days ago
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X3D for Atomic Simulation Environment
- Host: GitHub
- URL: https://github.com/superstar54/x3dase
- Owner: superstar54
- License: gpl-3.0
- Created: 2020-10-21T14:52:09.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2020-11-08T19:18:22.000Z (about 4 years ago)
- Last Synced: 2024-10-10T17:45:53.020Z (3 months ago)
- Language: HTML
- Size: 24.8 MB
- Stars: 10
- Watchers: 4
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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
## Dependencies
* Python
* ASE
* Skimage
## Installation using pip
```sh
pip install --upgrade --user x3dase
```
## Installation from source
You can get the source using git:
``` sh
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.
``` sh
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
``` python
images = [atoms1, atoms2, atoms3]
X3D(images)
```