Molecules are passed to Scaffold Generator as instances implementing the central CDK molecular structure representation, the IAtomContainer interface . From these, molecular scaffolds can be extracted according to different scaffold definitions available. These include the Murcko framework and the scaffold definition used in most of the established approaches, like HierS or the scaffold tree. It is based on Murcko frameworks but additionally includes all atoms connected to ring or linker atoms via double-bonds . In Scaffold Generator, this has been extended to all atoms connected via non-single bonds to cyclic or linker atoms.