Volume Rendering Demonstration in JupyterLab¶

In [1]:

import openchemistry as oc
import json

Once you have imported the basic Python modules we load a file

In [2]:

with open('caffeine.cjson') as f:
    cjson = json.load(f)
mol = oc.load(cjson)

Set up the transfer function used to render the orbital volume, by setting the color and opacity nodes

In [3]:

transfer_function = {
    'colormap': {
        'colors': [
            [1, 0, 0],
            [0.5, 0.5, 0],
            [1, 0, 1],
            [0, 0.5, 0.5],
            [0,0,1]
        ],
        'points': [
            -0.1,
            -0.03,
            0,
            0.03,
            0.1
        ]
    },
    'opacitymap': {
        'opacities': [
            1,
            0.75,
            0,
            0,
            0.75,
            1
        ],
        'points': [
            -0.3,
            -0.2,
            -0.0001,
            0.0001,
            0.2,
            0.3
        ]
    }
}

NOTE: Only the vtkjs viewer is capable of volume rendering.

In [4]:

mol.orbitals.show(
    mo='homo',
    viewer='vtkjs',
    isosurface=False,
    volume=True,
    transfer_function=transfer_function
)

<jupyterlab_cjson.CJSON object>