Demonstration of Open Chemistry integration of Avogadro in JupyterLab¶

In [1]:

import avogadro as avo
import openchemistry as oc

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

In [2]:

# Get the Avogadro classes necessary to open a file.
m = avo.core.Molecule()
f = avo.io.FileFormatManager()
# Read a file using Avogadro's wrapped file format API
f.read_file(m, 'h2o-restricted.fchk')

Out[2]:

True

The oc.load method can accept an avogadro Molecule directly

In [3]:

mol = oc.load(m)

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='lumo', iso=0.05)

<jupyterlab_cjson.CJSON object>

In [6]:

mol.orbitals.show(mo='homo', iso=0.05)

<jupyterlab_cjson.CJSON object>