jupyterlab-mol-visualizer: A JupyterLab Extension to Visualize Molecular Orbitals

A JupyterLab launcher extension to view the molecular orbitals (MOs). NGL JavaScript package was employed to visualize the MOs. The icon of the extension (bundled as style/molecule.svg) is adapted from SVG Repo.

Features

• Large interactive viewer — the molecular visualization fills the available screen space with a sidebar control panel
• Structure & isosurface loading — load .sdf, .cif, .xyz (structure) and .cube (Gaussian cube) files from the current JupyterLab directory
• Auto-rotate, visibility toggles, camera modes — toggle spin, show/hide structure and positive/negative isosurfaces, and switch between perspective, orthographic, and stereo cameras
• Opacity & isovalue sliders — fine-tune the display with real-time sliders
• Viewer background color controls — choose from 8 preset swatches or use the custom color palette picker
• Auto Centre — re-centre the camera on the molecule with a smooth animation
• Save PNG — export the current view as a high-resolution PNG image
• Ray Trace — render a high-resolution Fresnel image of the structure with positive and negative molecular orbital isosurfaces
• Dark & light theme — adapts to JupyterLab's theme automatically

Try it with Binder

Requirements

• JupyterLab >= 4.0.0

The optional Ray Trace button requires the Glotzer Fresnel path tracer from conda-forge and Python mesh/image helpers:

mamba install -c conda-forge fresnel
pip install jupyterlab_mol_visualizer[render]

Do not install the PyPI package named fresnel; it is unrelated to the path tracer used by this extension.

Install

To install the extension, execute:

pip install jupyterlab_mol_visualizer

Uninstall

To remove the extension, execute:

pip uninstall jupyterlab_mol_visualizer

Contributing

Development install

Note: You will need NodeJS to build the extension package.

The jlpm command is JupyterLab's pinned version of yarn that is installed with JupyterLab. You may use yarn or npm in lieu of jlpm below. For a faster editable install, npm is recommended.

# Clone the repo to your local environment
# Change directory to the jupyterlab_mol_visualizer directory
# Install npm dependencies (only needed first time)
npm install
# Install package in development mode
pip install -e "."

After the first install, subsequent pip install -e . runs are near-instant (the build step is skipped once the labextension exists). To rebuild the extension after making TypeScript changes:

npm run build

You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.

# Watch the source directory in one terminal, automatically rebuilding when needed
npm run watch
# Run JupyterLab in another terminal
jupyter lab

With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).

By default, the build generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:

jupyter lab build --minimize=False

Development uninstall

pip uninstall jupyterlab_mol_visualizer

In development mode, you will also need to remove the symlink created by jupyter labextension develop command. To find its location, you can run jupyter labextension list to figure out where the labextensions folder is located. Then you can remove the symlink named jupyterlab_mol_visualizer within that folder.

Testing the extension

Frontend tests

This extension is using Jest for JavaScript code testing.

To execute them, execute:

npm install
npm test

Integration tests

This extension uses Playwright for the integration tests (aka user level tests). More precisely, the JupyterLab helper Galata is used to handle testing the extension in JupyterLab.

More information are provided within the ui-tests README.

Packaging the extension

See RELEASE

How to cite

When using the content of this repository, please cite the following two articles:

1. D. Du, T. J. Baird, S. Bonella and G. Pizzi, OSSCAR, an open platform for collaborative development of computational tools for education in science, Computer Physics Communications, 282, 108546 (2023). https://doi.org/10.1016/j.cpc.2022.108546

2. D. Du, T. J. Baird, K. Eimre, S. Bonella, G. Pizzi, Jupyter widgets and extensions for education and research in computational physics and chemistry, Computer Physics Communications, 305, 109353 (2024). https://doi.org/10.1016/j.cpc.2024.109353

Acknowledgements

We acknowledge support from the EPFL Open Science Fund via the OSSCAR project.