Practical Cheminformatics

 When working in drug design, we often need filters to identify molecules containing functional groups that may be toxic, reactive, or could interfere with an assay.  A few years ago , I collected the functional group filters available in the ChEMBL database and wrote some Python code that made applying these filters to an arbitrary set of molecules easy.  This functionality is available in the pip installable useful_rdkit_utils package that's available on PyPI and GitHub.   Applying these filters is easy.  If we have a Pandas dataframe with a SMILES column, we can do something like this.  import useful_rdkit_utils as uru reos = uru.REOS("BMS")  #optionally specify the rule set to use df[['rule_set','reos']] = df.SMILES.apply(reos.process_smiles).tolist() This adds two columns, rule_set , and reos , to the dataframe with the name of the rule_set and the name of the rule matched by each molecule.  If the molecule doesn't match any rules, both columns