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Built-in visualizations in openff-toolkit

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