jupyterlab-mol-visualizer: A JupyterLab Launcher to Visualize Molecular Orbital and Structure

!Github Actions Status

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A JupyterLab launcher extension to view the molecular orbitals.

!demo

Requirements

* JupyterLab >= 3.0

Install

To install the extension, execute:

``bash
pip install jupyterlab-mol-visualizer
`
or

`bash
jupyter labextension install jupyterlab-mol-visualizer
`

Uninstall

To remove the extension, execute:

`bash
pip uninstall jupyterlab-mol-visualizer
`

Contributing

$3

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.

`bash


Clone the repo to your local environment

Change directory to the jupyterlab_mol_visualizer directory

Install package in development mode

pip install -e .

Link your development version of the extension with JupyterLab

jupyter labextension develop . --overwrite

Rebuild extension Typescript source after making changes

jlpm 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.

`bash


Watch the source directory in one terminal, automatically rebuilding when needed

jlpm 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 jlpm run build command 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:

`bash
jupyter lab build --minimize=False
`

$3

`bash
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.

Acknowledgements

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