run the optimization concode_field_sep double gapIni concode_elem_sep int equLen concode_elem_sep double stopLenPer concode_elem_sep double gapExt concode_elem_sep int pro2Len concode_elem_sep int pro1Len concode_elem_sep boolean debug concode_elem_sep double increase concode_elem_sep int keepStep concode_elem_sep int[][] equSet concode_elem_sep Atom[] cod2 concode_elem_sep double[][] sij concode_elem_sep int maxKeepStep concode_elem_sep Atom[] cod1 concode_elem_sep int equLen0 concode_elem_sep double rmsd concode_elem_sep double stopRmsdPer concode_elem_sep double stopRmsd concode_elem_sep int maxLen concode_elem_sep double Dc concode_elem_sep double rmsdCut concode_field_sep void setParameters concode_elem_sep boolean defineEquPos concode_elem_sep void superimposeBySet concode_elem_sep void calMatrix concode_elem_sep void optimize concode_elem_sep double optimizeResult
void function ( int arg0 ) { superimposeBySet ( ) ; if ( debug ) System . err . println ( "srini_string" + rmsd ) ; maxKeepStep = 4 ; keepStep = 0 ; optimize ( arg0 ) ; }