EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit

Functional groups are widely used in organic chemistry, because they provide a rationale to analyze physicochemical and reactivity properties. In medicinal chemistry, they are the basis for analyzing ligand-biomacromolecule interactions. Ertl's algorithm is an approach to extract functional groups in arbitrary organic molecules that does not depend on predefined libraries of functional groups. However, there is a lack of a complete and accurate implementation of Ertl's algorithm in the widely used RDKit cheminformatic toolkit. In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. For a RDKit molecule, it provides (i) a PNG binary string with an image of the molecule with color-highlighted functional groups; (ii) a list of sets of atom indices (idx), each set corresponding to a functional group; (iii) a list of pseudo-SMILES canonicalized strings for the full functional groups; and (iv) a list of RDKit labeled mol objects, one for each full functional group. The code is freely available in https://github.com/bbu-imdea/efgs and is part of the RDKit Contrib directory (https://github.com/rdkit/rdkit/tree/master/Contrib/efgs).