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).