This is code for automated chemical series classification
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-versionflag. You can runpython -m automated_series_classification.dataprep --helpin 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
- Greg Landrum
Any comments, requests and suggestions will be greatly appreciated.