PR #560 introduced rich representation for the openff.toolkit.topology.Molecule
objects. This means you can visualize them in your Jupyter Notebooks:
We have implemented three backends:
rdkit
openeye
nglview
(requires conformers)
There are two ways to invoke the visualization:
- implicitly, by evaluating the object in a cell
- explicitly, by calling
Molecule.visualize()
This notebook demonstrates all the possible uses.
Note: The content in this notebook demonstrates usage of nglview
with openff-toolkit
.
This can be tricky to get working.
Install with:
conda install -c conda-forge nglview
And configure for use with Jupyter with:
jupyter-nbextension enable nglview --py --sys-prefix
To use with Jupyterlab, configure with:
jupyter labextension install nglview-js-widgets
jupyter-labextension install @jupyter-widgets/jupyterlab-manager