The CHMTRN/PATRAN logic considers the effect of exposed or protected functional groups and either rewards or penalizes the reaction accordingly. We therefore did not modify the BBs to computationally add or remove protecting groups. We did however generate modified products by removing protecting groups. Thus, whereas a standard reaction with reactants R1 and R2 yielding product P that does not involve any protecting group is executed to the scheme of: We used the following structures for the handling of protecting groups: