Abstract: In alternative embodiments the invention provides libraries of compounds, or drugs or drug candidates, manufactured and selected for having a desired property such as a biological or a chemical activity, and methods for making and using them. In one embodiment, the invention provides methods for identifying desirable compounds from very large compound sets using a compound fragment as the query. In alternative embodiments, the invention provides methods of making compounds, and libraries of compounds, using a “feasible reaction” growth scheme.