1. A computer method for encoding and building products of a virtual combinatorial library, the products of the virtual combinatorial library being formed in accordance with a chemical reaction and selected reagents, the computer method comprising the steps of: (1) encoding in computer readable form at least one chemical transformation for generating product connection data from reagent connection data; (2) encoding in computer readable form at least one reagent substructure pattern involved in forming the products of the virtual combinatorial library; (3) generating reagent mapping data from the at least one reagent substructure pattern and reagent connection data for a set of reagents; (4) compiling into computer instructions the encoded at least one chemical transformation; (5) generating a library object comprising the compiled computer instructions, the generated reagent mapping data, and the reagent connection data for the set of reagents; (6) storing the library object in a memory; and (7) generating product connection data, using the compiled computer instructions and reagent mapping data and reagent connection data retrieved from the stored library object, for at least one product of the virtual combinatorial library.