mmpdb_from_nb.ipynb

Are you aware of chembl-downloader? I made it so we could more easily write code that does these SQL statements (like in cell 5) and requires no prior setup since it uses SQLite.

import chembl_downloader

# this gets put directly in a pandas dataframe
df = chembl_downloader.query(
    """\
    select canonical_smiles, molregno, activity_id, standard_value, standard_units 
    from activities
        join assays using (assay_id)
        join compound_structures using (molregno)
    where tid = 165 
        and standard_type = 'Ki' 
        and standard_value is not null 
        and standard_relation = '='
        and canonical_smiles not like '%.%';
    """
)

This also has the benefit of automatically getting the latest version of ChEMBL for you