PyMOL Python snippet library to edit live Jupyter notebook cells with Visual Studio Code

PyMOL Python snippet library to edit live Jupyter notebook cells with Visual Studio Code using GhostText web browser extension and the GhostText-for-VSCode plugin for Visual Studio Code. The snippets are formatted for the generic VSCode snippet format. You may want to install the BioSyntax package for VSCode for color highlighting that is sensitive to biomolecular structure (e.g., recognizes PDB files).

On Windows 10 or 11

Store the source.python.json file in \Users\\AppData\Roaming\Code\User\snippets\. The folder AppData may be hidden if you use the Windows GUI to move the file. Instead, open the Command Prompt and use the cmv command to move the source.python.json file into the snippets subfolder.

On macOS

Store the source.python.json file in ~/Library/Code/Application Support/Code/User/snippets/source.python.json. If a source.python.json file already exists, copy the contents between the external braces in the PyMOL source.python.json and paste them inside the external braces of the original source.python.json.

Note

Some snippets depend on some pymolshortcuts. Add the pymolshortcuts.py file to working working directory.

Related repositories

• jupyterlabpymolpysnips PyMOL Python snippets for use in JupyterLab with the jupyterlab-snippets extension.
• jupyternbclassicpymolpysnipsplus
• taggedpymolpysnips
• taggedpymolpysnipspymolpysnipsplus
• jupyter-vsc-pymolpysnips
• jupyter-st3-pymolpysnips
• jupyter-emacs-pymolpysnips
• jupyter-ultisnips-pymolpysnips
• jupyter-snipmate-pymolpysnips
• jupyter-neosnippets-pymolpysnips
• jupyter-atom-pymolpysnips

Update History

Version	Changes	Date
Version 0.2	Added badges, funding, and update history	2024 May 18

Sources of funding

• NIH: R01 CA242845
• NIH: R01 AI088011