1. A method for structure clustering logic elements in a programmable logic integrated circuit, comprising: generating all possible configurations by clustering a first element and a second element to form first-element-and-second-element configurations, each first-and-second-element configuration having a logic connection between the first element and the second element that maps to a dedicated physical connection on the programmable logic integrated circuit; and reducing the total number of all possible configurations according to one or more predetermined criteria, thereby generating a subset of configurations from all possible configurations, each criterion having a set of parameters that are prioritized, each parameter having a predetermined value.