/**************************************************************************** * Volume complex used in tests ****************************************************************************/ DEFINE_COMPLEX_MOLECULE Complex { NUMBER_OF_SUBUNITS = [5, 5, 5] SUBUNIT[1:5, 1:5, 1:5] = V_c_su0 SHAPE { SUBUNIT[1, 1, 1] = [-.04, -.04, -.04] SUBUNIT[1, 1, 2] = [-.04, -.04, -.02] SUBUNIT[1, 1, 3] = [-.04, -.04, .00] SUBUNIT[1, 1, 4] = [-.04, -.04, .02] SUBUNIT[1, 1, 5] = [-.04, -.04, .04] SUBUNIT[1, 2, 1] = [-.04, -.02, -.04] SUBUNIT[1, 2, 2] = [-.04, -.02, -.02] SUBUNIT[1, 2, 3] = [-.04, -.02, .00] SUBUNIT[1, 2, 4] = [-.04, -.02, .02] SUBUNIT[1, 2, 5] = [-.04, -.02, .04] SUBUNIT[1, 3, 1] = [-.04, .00, -.04] SUBUNIT[1, 3, 2] = [-.04, .00, -.02] SUBUNIT[1, 3, 3] = [-.04, .00, .00] SUBUNIT[1, 3, 4] = [-.04, .00, .02] SUBUNIT[1, 3, 5] = [-.04, .00, .04] SUBUNIT[1, 4, 1] = [-.04, .02, -.04] SUBUNIT[1, 4, 2] = [-.04, .02, -.02] SUBUNIT[1, 4, 3] = [-.04, .02, .00] SUBUNIT[1, 4, 4] = [-.04, .02, .02] SUBUNIT[1, 4, 5] = [-.04, .02, .04] SUBUNIT[1, 5, 1] = [-.04, .04, -.04] SUBUNIT[1, 5, 2] = [-.04, .04, -.02] SUBUNIT[1, 5, 3] = [-.04, .04, .00] SUBUNIT[1, 5, 4] = [-.04, .04, .02] SUBUNIT[1, 5, 5] = [-.04, .04, .04] SUBUNIT[2, 1, 1] = [-.02, -.04, -.04] SUBUNIT[2, 1, 2] = [-.02, -.04, -.02] SUBUNIT[2, 1, 3] = [-.02, -.04, .00] SUBUNIT[2, 1, 4] = [-.02, -.04, .02] SUBUNIT[2, 1, 5] = [-.02, -.04, .04] SUBUNIT[2, 2, 1] = [-.02, -.02, -.04] SUBUNIT[2, 2, 2] = [-.02, -.02, -.02] SUBUNIT[2, 2, 3] = [-.02, -.02, .00] SUBUNIT[2, 2, 4] = [-.02, -.02, .02] SUBUNIT[2, 2, 5] = [-.02, -.02, .04] SUBUNIT[2, 3, 1] = [-.02, .00, -.04] SUBUNIT[2, 3, 2] = [-.02, .00, -.02] SUBUNIT[2, 3, 3] = [-.02, .00, .00] SUBUNIT[2, 3, 4] = [-.02, .00, .02] SUBUNIT[2, 3, 5] = [-.02, .00, .04] SUBUNIT[2, 4, 1] = [-.02, .02, -.04] SUBUNIT[2, 4, 2] = [-.02, .02, -.02] SUBUNIT[2, 4, 3] = [-.02, .02, .00] SUBUNIT[2, 4, 4] = [-.02, .02, .02] SUBUNIT[2, 4, 5] = [-.02, .02, .04] SUBUNIT[2, 5, 1] = [-.02, .04, -.04] SUBUNIT[2, 5, 2] = [-.02, .04, -.02] SUBUNIT[2, 5, 3] = [-.02, .04, .00] SUBUNIT[2, 5, 4] = [-.02, .04, .02] SUBUNIT[2, 5, 5] = [-.02, .04, .04] SUBUNIT[3, 1, 1] = [ .00, -.04, -.04] SUBUNIT[3, 1, 2] = [ .00, -.04, -.02] SUBUNIT[3, 1, 3] = [ .00, -.04, .00] SUBUNIT[3, 1, 4] = [ .00, -.04, .02] SUBUNIT[3, 1, 5] = [ .00, -.04, .04] SUBUNIT[3, 2, 1] = [ .00, -.02, -.04] SUBUNIT[3, 2, 2] = [ .00, -.02, -.02] SUBUNIT[3, 2, 3] = [ .00, -.02, .00] SUBUNIT[3, 2, 4] = [ .00, -.02, .02] SUBUNIT[3, 2, 5] = [ .00, -.02, .04] SUBUNIT[3, 3, 1] = [ .00, .00, -.04] SUBUNIT[3, 3, 2] = [ .00, .00, -.02] SUBUNIT[3, 3, 3] = [ .00, .00, .00] SUBUNIT[3, 3, 4] = [ .00, .00, .02] SUBUNIT[3, 3, 5] = [ .00, .00, .04] SUBUNIT[3, 4, 1] = [ .00, .02, -.04] SUBUNIT[3, 4, 2] = [ .00, .02, -.02] SUBUNIT[3, 4, 3] = [ .00, .02, .00] SUBUNIT[3, 4, 4] = [ .00, .02, .02] SUBUNIT[3, 4, 5] = [ .00, .02, .04] SUBUNIT[3, 5, 1] = [ .00, .04, -.04] SUBUNIT[3, 5, 2] = [ .00, .04, -.02] SUBUNIT[3, 5, 3] = [ .00, .04, .00] SUBUNIT[3, 5, 4] = [ .00, .04, .02] SUBUNIT[3, 5, 5] = [ .00, .04, .04] SUBUNIT[4, 1, 1] = [ .02, -.04, -.04] SUBUNIT[4, 1, 2] = [ .02, -.04, -.02] SUBUNIT[4, 1, 3] = [ .02, -.04, .00] SUBUNIT[4, 1, 4] = [ .02, -.04, .02] SUBUNIT[4, 1, 5] = [ .02, -.04, .04] SUBUNIT[4, 2, 1] = [ .02, -.02, -.04] SUBUNIT[4, 2, 2] = [ .02, -.02, -.02] SUBUNIT[4, 2, 3] = [ .02, -.02, .00] SUBUNIT[4, 2, 4] = [ .02, -.02, .02] SUBUNIT[4, 2, 5] = [ .02, -.02, .04] SUBUNIT[4, 3, 1] = [ .02, .00, -.04] SUBUNIT[4, 3, 2] = [ .02, .00, -.02] SUBUNIT[4, 3, 3] = [ .02, .00, .00] SUBUNIT[4, 3, 4] = [ .02, .00, .02] SUBUNIT[4, 3, 5] = [ .02, .00, .04] SUBUNIT[4, 4, 1] = [ .02, .02, -.04] SUBUNIT[4, 4, 2] = [ .02, .02, -.02] SUBUNIT[4, 4, 3] = [ .02, .02, .00] SUBUNIT[4, 4, 4] = [ .02, .02, .02] SUBUNIT[4, 4, 5] = [ .02, .02, .04] SUBUNIT[4, 5, 1] = [ .02, .04, -.04] SUBUNIT[4, 5, 2] = [ .02, .04, -.02] SUBUNIT[4, 5, 3] = [ .02, .04, .00] SUBUNIT[4, 5, 4] = [ .02, .04, .02] SUBUNIT[4, 5, 5] = [ .02, .04, .04] SUBUNIT[5, 1, 1] = [ .04, -.04, -.04] SUBUNIT[5, 1, 2] = [ .04, -.04, -.02] SUBUNIT[5, 1, 3] = [ .04, -.04, .00] SUBUNIT[5, 1, 4] = [ .04, -.04, .02] SUBUNIT[5, 1, 5] = [ .04, -.04, .04] SUBUNIT[5, 2, 1] = [ .04, -.02, -.04] SUBUNIT[5, 2, 2] = [ .04, -.02, -.02] SUBUNIT[5, 2, 3] = [ .04, -.02, .00] SUBUNIT[5, 2, 4] = [ .04, -.02, .02] SUBUNIT[5, 2, 5] = [ .04, -.02, .04] SUBUNIT[5, 3, 1] = [ .04, .00, -.04] SUBUNIT[5, 3, 2] = [ .04, .00, -.02] SUBUNIT[5, 3, 3] = [ .04, .00, .00] SUBUNIT[5, 3, 4] = [ .04, .00, .02] SUBUNIT[5, 3, 5] = [ .04, .00, .04] SUBUNIT[5, 4, 1] = [ .04, .02, -.04] SUBUNIT[5, 4, 2] = [ .04, .02, -.02] SUBUNIT[5, 4, 3] = [ .04, .02, .00] SUBUNIT[5, 4, 4] = [ .04, .02, .02] SUBUNIT[5, 4, 5] = [ .04, .02, .04] SUBUNIT[5, 5, 1] = [ .04, .04, -.04] SUBUNIT[5, 5, 2] = [ .04, .04, -.02] SUBUNIT[5, 5, 3] = [ .04, .04, .00] SUBUNIT[5, 5, 4] = [ .04, .04, .02] SUBUNIT[5, 5, 5] = [ .04, .04, .04] } SUBUNIT_RELATIONSHIPS { xp = [+1, 0, 0] xn = [-1, 0, 0] yp = [ 0, +1, 0] yn = [ 0, -1, 0] zp = [ 0, 0, +1] zn = [ 0, 0, -1] } RATE_RULES { binding { xp == V_c_su1 & xn != V_c_su1 & yp == V_c_su1 & yn == V_c_su0 & zp == V_c_su1 & zn != V_c_su1 : cx_max_rate yp == V_c_su1 & yn == V_c_su0 & zp == V_c_su1 & zn != V_c_su1 : cx_rate_1 xp == V_c_su1 & xn != V_c_su1 & zp == V_c_su1 & zn != V_c_su1 : cx_rate_1 xp == V_c_su1 & xn != V_c_su1 & yp == V_c_su1 & yn == V_c_su0 : cx_rate_1 zp == V_c_su1 & zn != V_c_su1 : cx_rate_2 yp == V_c_su1 & yn == V_c_su0 : cx_rate_2 xp == V_c_su1 & xn != V_c_su1 : cx_rate_2 DEFAULT : cx_normal_rate } } } DEFINE_REACTIONS { (V_c_su0) + V_i -> (V_c_su1) [COMPLEX_RATE Complex binding] }