Scaffold Generator can be packaged in a JAR file and used as a command-line application. It requires an SD file as input parameter and creates a performance snapshot of the main functionalities of Scaffold Generator with the given data set. First, all molecules are imported and stored in memory. From these, all structures having more than ten rings are discarded. This is done because they occur rather rarely but would influence the overall processing time disproportionally. No further filtering or preprocessing, e.g. removal of counter-ions or elimination of duplicates, is done for the purpose of this performance snapshot and the following exemplary analyses. For an initial performance snapshot, all remaining molecules are processed according to the enumerative generation of parent scaffolds and the parent scaffold generation according to the scaffold tree prioritisation rules. Afterwards, the dataset is subdivided into equally large portions. The total number of fractions has to be specified in the second command-line parameter. In each following step, a growing number of created molecule subsets is combined and all included structures used to build a scaffold network and a scaffold forest, i.e. a set of scaffold trees. The number of molecules and the needed processing time is logged in every step. In the final step, all scaffolds in the network and the trees, respectively, and their frequencies determined based on their numbers of origin molecules are exported to an output file. The scaffold structures are exported as SMILES strings.