Here, the fragmentation algorithm logic must be implemented. Well-documented example code can be found in the three classes ErtlFunctionalGroupsFinderFragmenter, SugarRemovalUtilityFragmenter, and ScaffoldGeneratorFragmenter. For high-performance processing, especially for larger molecule sets, MORTAR uses parallel computing with multiple threads. The set of input molecules is divided onto a number of parallel threads specified by the user, these subsets are fragmented in parallel, and the results are then recombined to create the coherent final set of fragments. MORTAR logs internal information and problems automatically using the Java logging API. A log file is written for every application session and can be accessed by the user.