document: Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries A molecular equivalence number -LRB- meqnum -RRB- classifies a molecule with respect to a class of structural features or topological shapes such as its cyclic system or its set of functional groups . Meqnums can be used to organize molecular structures into nonoverlapping , yet highly relatable classes . We illustrate the construction of some different types of meqnums and present via examples some methods of comparing diverse chemical libraries based on meqnums . In the examples we compare a library which is a random sample from the MDL Drug Data Report -LRB- MDDR -RRB- with a library which is a random sample from the Available Chemical Directory -LRB- ACD -RRB- . In our analyses , we discover some interesting features of the topological shape of a molecule and its set of functional groups that are strongly linked with compounds occurring in the MDDR but not in the ACD . We also illustrate the utility of molecular equivalence indices in delineating the structural domain over which an SAR conclusion is valid
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