METHOD AND SYSTEM FOR DETERMINING A CONFORMATION OF A MOLECULE USING HIGH-PERFORMANCE BINARY OPTIMIZER

A method is disclosed for determining a conformation of a molecule on at least one degree of freedom to optimize according to at least one molecular objective function, the method comprising generating using at least one corresponding degree of freedom to optimize a connected rigid bodies representation for the molecule by identifying a plurality of groups of atoms, generating a data structure representative of the connected rigid bodies representation generating at least one neighborhood for each generated neighborhood of the at least one generated neighborhoods, generating a corresponding binary optimization problem using the data structure, providing the generated corresponding binary optimization problem to a high-performance binary optimizer, obtaining a solution from the high-performance binary optimizer; and providing at least one corresponding solution.