In our previous work [Gounaris, C.E., Floudas, C.A., Wei, J., 2006. Rational design of shape selective catalysis and separation: I. Concepts and analysis. Chemical Engineering Science, in press, doi: 10.1016/j.ces.2006.09.012], we introduced the concept of molecule projections, referred to as footprints, and briefly described rigorous criteria that define them. We also introduced the concept of strain index and showed how it can be used to identify portals that have the potential of being highly selective between two molecules. In this paper, we present in detail the mathematical formulations for the calculation of footprints and the complete mathematical model and algorithmic framework developed for the calculation of the strain index of any given molecule/portal pair. Thirty-eight molecules of interest, as well as a collection of 123 zeolite structures, involving 217 different windows, have been considered and selectivity results at ambient temperature are presented. A number of commercially interesting examples are studied in further detail, across a wide range of temperatures. It should be noted that the methodology is generic and can be applied for any pair of molecule and portal. The results indicate that there is a great potential in systems involving non-regular portals that are usually not considered in the selection process of a catalyst or molecular sieve. (c) 2006 Elsevier Ltd. All rights reserved.