# 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
```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

<img src="x3dase/images/jupyter.png" width="600"/>

<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
<img src="x3dase/images/models.png" width="500"/>

### 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
<img src="x3dase/images/polyhedra.png" width="300"/>


### Isosurface for electron density
<img src="x3dase/images/isosurface.png" width="300"/>

### Animation
``` python
images = [atoms1, atoms2, atoms3]
X3D(images)
```




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

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x3dase

superstar54

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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

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

x3dase

x3dase

Author

Dependencies

Installation using pip

Installation from source

Examples

Draw molecule in Jupyter notebooks

Shortcut

Show different models

Measure distance and angle between atoms

Polyhedra for crystal

Isosurface for electron density

Animation

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