Molecular Representations for Machine Learning Examples

In this GitHub repository, we provide code examples from the ACS In Focus "Molecular Representations for Machine Learning" by Grier M. Jones, Brittany Story, Vasileios Maroulas, and Konstantinos D. Vogiatzis.

Directories

The directories that are relevant for the examples in the book include:

• Chapter_2 : contains examples of graph-based methods
• Chapter_3 : contains examples of topology-based methods
• Chapter_4 : contains examples of physics-based methods
• example_structures : xyz coordinates for 2-benzyloxirane and glycidol

Citation

@book{doi:10.1021/acsinfocus.7e7006,
author = {Jones, Grier M. and Story, Brittany and Maroulas, Vasileios and Vogiatzis, Konstantinos D.},
title = {Molecular Representations for Machine Learning},
publisher = {American Chemical Society},
year = {2023},
doi = {10.1021/acsinfocus.7e7006},
address = {Washington, DC, USA},
edition   = {},
URL = {https://pubs.acs.org/doi/abs/10.1021/acsinfocus.7e7006},
eprint = {https://pubs.acs.org/doi/pdf/10.1021/acsinfocus.7e7006}
}

Setup

These examples require multiple conda env and kernels...

1. Open Gen_Directories.ipynb in Google Colab, which will launch in a Google Drive folder called Colab Notebooks.
2. Generate a personal access token in GitHub. Steps: GitHub Settings > Developer settings > Personal access tokens > Tokens (classic)
3. Once you have launched the Gen_Directories.ipynb, there will be an empty cell with token='' copy your personal access token into the parenthesis
4. The cell containing !git clone https://{token}@github.com/ChemRacer/molecular_representation_examples.git will pull the repo to the directory /content/drive/MyDrive/Colab Notebooks/Molecular_representations/
5. The last cell will generate paths to each example:

for root, dirs, files in os.walk(os.getcwd()):
    for file in files:
        if file.endswith('.ipynb') and 'Chapter_' in root and '.ipynb_checkpoints' not in root:
          if os.path.exists(os.path.join(root,file)):
              print(file.split('.')[0], "https://colab.research.google.com/drive/"+get_id(os.path.join(root,file)))

For help using GitHub in Google Colab.