Demonstration of Open Chemistry integration of Avogadro 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)

The oc.load method can accept a cjson dict directly

In [3]:

# Get the electron count, demonstrate querying the JSON
print("electronCount = ", cjson['orbitals']['electronCount'])
mol = oc.load(cjson)

electronCount =  102

Show the orbital, note that this is calculated using the Avogadro 2 libraries from the output in the CJSON file. You can use numeric orbital numbers, or homo/lumo.

In [4]:

mol.structure.show()

<jupyterlab_cjson.CJSON object>

In [5]:

mol.orbitals.show(mo=20, iso=0.005)

<jupyterlab_cjson.CJSON object>

In [6]:

mol.orbitals.show(mo='homo', iso=0.005)

<jupyterlab_cjson.CJSON object>