AutomatedSeriesClassification

This is code for automated chemical series classification

Original article

Automated Identification of Chemical Series: Classifying like a Medicinal Chemist https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00204

First, you should have RDKit installed. Then, the code can be downloaded and installed with:

git clone https://github.com/rdkit/AutomatedSeriesClassification
cd AutomatedSeriesClassification
pip install -e .

The -e flag means it gets installed in editable mode.

The following script will download chembl27.sdf.gz and make substructurefingerprint library. If you want to use an alternate version of chembl, specify the --chebml-version flag. You can run python -m automated_series_classification.dataprep --help in your shell to see all options.

$ python -m automated_series_classification.dataprep  # it'll take ~30 or more minutes on my PC

Then launch jupyter notebook, the notebook use same dataset as original articles. But you'll get different results compared to the article. This is because I used more newer version of ChEMBL for this code. If you would like to use same dataset to original article it is easy, just changing download link of chembl

Any comments, requests and suggestions will be greatly appreciated.