public void runOptimization ( int maxi ) throws StructureException { superimposeBySet ( ) ; if ( debug ) System . err . println ( " initial rmsd " + rmsd ) ; // if (showAlig) // showCurrentAlignment(equLen, equSet, "after initial superimposeBySet Len:" +equLen + " rmsd:" +rmsd); maxKeepStep = 4 ; keepStep = 0 ; optimize ( maxi ) ; }
run the optimization