XSMILES visualizations in Jupyter Lab

A Custom Jupyter Lab Widget to visualize SMILES-based and atom-based scores.

Please Cite

If you use XSMILES, the use cases, its code, or the generated explanations, please cite our article:

Article in preparation, a preprint should appear mid September!

Heberle, H., Zhao, L., Schmidt, S., Wolf, T., & Heinrich, J. (2022). XSMILES: interactive visualization for molecules, SMILES and XAI scores. Article in preparation.

@article{Heberle2022XSMILES,
author = {Heberle, Henry and Zhao, Linlin and Schmidt, Sebastian and Wolf, Thomas and Heinrich, Julian},
doi = {},
journal = {Article in preparation},
month = {},
number = {},
pages = {},
title = {{XSMILES: interactive visualization for molecules, SMILES and XAI scores}},
volume = {},
year = {2022}
}

Availability and examples

• XSMILES main page

• TBD Demo website

• HOW TO use XSMILES (JupyterLab notebook)

• More examples with JupyterLab

• TBD PiPY repository

• KNIME component? Check the main page

Example Notebook with a how-to

To use XSMILES with Jupyter Lab you need to install the package with pip and have internet connection while using it.

RDKit MinimalLib is downloaded by your browser.

Please check this notebook to see how to use the tool: Notebook

Note that it is only being tested with Jupyter Lab. A reason for you to use Lab is the space available for visualizations, which is much better than in regular Jupyter notebooks. We also had problems with the installation with Jupyter notebooks.

Installation

Quick example - create conda environment and installs xsmiles

conda create --name xsmiles_env python=3.7 -c conda-forge # create conda env with python 3.7

conda activate xsmiles_env # activate the created env

conda install -c conda-forge jupyterlab # install jupyter lab

pip install xsmiles # if xsmiles is not in pip yet, try pip install xsmiles-0.2.2-py2.py3-none-any.whl
# Download the most up to date whl from this repository's releases)

jupyter lab examples/xsmiles_examples.ipynb # run a notebook with jupyter lab

Uninstall

• pip uninstall xsmiles
• rm -r <path-to:>/share/jupyter/labextensions/xsmiles
• jupyter labextension list

Development

Please check the DEVELOPMENT.md file.