Systematic analysis of the types of chemical structures contained in a compound library and their diversity is a basic practice for the rational design and use of such libraries. Indeed, the diversity of the analysis is a major criterion to identifying bioactive compounds and it can be applied for multiple purposes, such as design, acquisition, and selection of compounds for screening (virtual and experimental), and analysis of structure-activity relationships. Diversity analysis is also incorporated into de novo design strategies to evaluate the structural novelty of chemical libraries . Furthermore, diversity analysis has applications not only in drug discovery but also in natural product research, food chemistry, organic chemistry, and material sciences, among other areas.