A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular subset can be stored, transmitted, and processed more efficiently. The resulting efficiency makes it possible to design and run applications which require complex molecular processing, such as rational drug discovery, virtual library design, etc.