Here, NP structures were first deglycosylated, and (ring) substituents were recursively extracted. To set up a similar pipeline in MORTAR, the first step has to be a Sugar Removal Utility processing configured to only return aglycones of input structures. The second step would be a Scaffold Generator fragmentation that only returns side chains. A recursive fragmentation of the side chains is currently not included in MORTAR but for demonstration purposes, an Ertl algorithm processing can be chosen to extract functional groups from them. This pipeline is shown in Figure and described in more detail in the MORTAR tutorial that can be found on GitHub . Figure depicts the five most frequent functional groups resulting when this pipeline is applied to the natural product structures taken from COCONUT. The most frequent functional group identified in ring side chains is an ether or a hydroxy group (both belong to the same group because the bonds to ring atoms are cut without preserving any information). Following is a hydroxy group connected to an aliphatic carbon atom. In the depicted Sample Parent structure in row 2, this group results from the ether group that connects the side chain with the ring. When it is cleaved and saturated with hydrogen, a hydroxy group results. The third functional group is a carboxylic acid functionality. The alkene functionality is identified as the fourth-frequent substituent, followed by the ester functionality.