Definition of the Relative Diversity Measure used
Two diversity values are most important on the output page - the "Diversity relative to ideal diverse library (40 members; max = 100)" and the "Size-normalized diversity score relative to ideal diverse library (av. no. of heavy atoms = 23.325)". Ideally, your library contains a number of molecules which is as close as possible to 40. If the average number of heavy atoms of your library (given on the output page) is is the region of 23 you can compare the relative diversity scores directly. If your library contains structures which are either much larger or much smaller, you should rather have a look at the size-normalized diversity score, which takes the different average molecule sizes of the two libraries into account.
The relative diversity calculated on this web site is calculated as the average number of unique features (details) per molecule of the library. Thus, diversity values of libraries of different size or those containing molecules with a different number of heavy atoms should not be compared directly.
The structures used for the definition of the ideal diverse library are shown in the following figure.