mcell/mdl/testsuite/parser/valid/complex_molecules.mdl

DEFINE_COMPLEX_MOLECULE c_s_0
{
    NUMBER_OF_SUBUNITS = [ 2, 2, 2, 2 ]
    SUBUNIT[1:2, 1:2, 1:2, 1:2] = s_g_0
    SUBUNIT[  1,   1,   1, 1:2] = s_g_1
    SUBUNIT[  2,   1, 1:2,   1] = s_g_2
    SUBUNIT[  1, 1:2,   1,   2] = s_g_3
    SUBUNIT[1:2,   2,   1,   1] = s_g_4
    SUBUNIT[  2,   2,   2,   2] = s_g_5

    SHAPE
    {
      SUBUNIT[1, 1, 1, 1] = [ -0.002, -0.002, 0]
      SUBUNIT[1, 1, 1, 2] = [ -0.001, -0.002, 0]
      SUBUNIT[1, 1, 2, 1] = [  0.000, -0.002, 0]
      SUBUNIT[1, 1, 2, 2] = [  0.001, -0.002, 0]
      SUBUNIT[1, 2, 1, 1] = [ -0.002, -0.001, 0]
      SUBUNIT[1, 2, 1, 2] = [ -0.001, -0.001, 0]
      SUBUNIT[1, 2, 2, 1] = [  0.000, -0.001, 0]
      SUBUNIT[1, 2, 2, 2] = [  0.001, -0.001, 0]
      SUBUNIT[2, 1, 1, 1] = [ -0.002,  0.000, 0]
      SUBUNIT[2, 1, 1, 2] = [ -0.001,  0.000, 0]
      SUBUNIT[2, 1, 2, 1] = [  0.000,  0.000, 0]
      SUBUNIT[2, 1, 2, 2] = [  0.001,  0.000, 0]
      SUBUNIT[2, 2, 1, 1] = [ -0.002,  0.001, 0]
      SUBUNIT[2, 2, 1, 2] = [ -0.001,  0.001, 0]
      SUBUNIT[2, 2, 2, 1] = [  0.000,  0.001, 0]
      SUBUNIT[2, 2, 2, 2] = [  0.001,  0.001, 0]
    }

    SUBUNIT_RELATIONSHIPS
    {
      r0000 = [  0,  0,  0,  0]
      r0001 = [  0,  0,  0,  1]
      r0010 = [  0,  0,  1,  0]

      r0011 = [  0,  0, -1, -1]
      r0100 = [  0, -1,  0,  0]
      r0101 = [  0, -1,  0, -1]

      r0110 = [  0,  1,  1,  0]
      r0111 = [  0,  1,  1,  1]
      r1000 = [  1,  0,  0,  0]

      r1001 = [ -1,  0,  0, -1]
      r1010 = [ -1,  0, -1,  0]
      r1011 = [ -1,  0, -1, -1]

      r1100 = [  1,  1,  0,  0]
      r1101 = [  1,  1,  0,  1]
      r1110 = [  1,  1,  1,  0]

      r1111 = [ -1,  1, -1,  1]
    }

    RATE_RULES
    {
      rr0
      {
        DEFAULT: 3e2
      }

      rr1
      {
        r0000 != s_g_0: 3e3
        DEFAULT:        3e2
      }

      rr2
      {
        r0001 == s_g_0,: 3e3
        DEFAULT:        3e2
      }

      rr3
      {
        r0010 != s_g_2; & r0011 == s_g_3: 3e3
        DEFAULT:        3e2
      }

      rr4
      {
        r0100 == s_g_4' & r0101 != s_g_4: 3e3
        DEFAULT:        3e2
      }

      rr5
      {
        r0110 == s_g_0' & r0111 == s_g_1': 3e3
        r1000 == s_g_1' & r1001 != s_g_1': 3e3
        DEFAULT:        3e2
      }

      rr6
      {
        r1100 == s_g_0: 3e3
        r1101 == s_g_1': 3e3
        r1110 == s_g_2;: 3e3
        r1111 == s_g_3,: 3e3
        DEFAULT:        3e2
      }
    }
}

DEFINE_COMPLEX_MOLECULE c_v_0
{
    NUMBER_OF_SUBUNITS = [ 2, 2, 2, 2 ]
    SUBUNIT[1:2, 1:2, 1:2, 1:2] = s_v_0
    SUBUNIT[  1,   1,   1, 1:2] = s_v_1
    SUBUNIT[  2,   1, 1:2,   1] = s_v_2
    SUBUNIT[  1, 1:2,   1,   2] = s_v_3
    SUBUNIT[1:2,   2,   1,   1] = s_v_4
    SUBUNIT[  2,   2,   2,   2] = s_v_5

    SHAPE
    {
      SUBUNIT[1, 1, 1, 1] = [ -0.002, -0.002, 0]
      SUBUNIT[1, 1, 1, 2] = [ -0.001, -0.002, 0]
      SUBUNIT[1, 1, 2, 1] = [  0.000, -0.002, 0]
      SUBUNIT[1, 1, 2, 2] = [  0.001, -0.002, 0]
      SUBUNIT[1, 2, 1, 1] = [ -0.002, -0.001, 0]
      SUBUNIT[1, 2, 1, 2] = [ -0.001, -0.001, 0]
      SUBUNIT[1, 2, 2, 1] = [  0.000, -0.001, 0]
      SUBUNIT[1, 2, 2, 2] = [  0.001, -0.001, 0]
      SUBUNIT[2, 1, 1, 1] = [ -0.002,  0.000, 0]
      SUBUNIT[2, 1, 1, 2] = [ -0.001,  0.000, 0]
      SUBUNIT[2, 1, 2, 1] = [  0.000,  0.000, 0]
      SUBUNIT[2, 1, 2, 2] = [  0.001,  0.000, 0]
      SUBUNIT[2, 2, 1, 1] = [ -0.002,  0.001, 0]
      SUBUNIT[2, 2, 1, 2] = [ -0.001,  0.001, 0]
      SUBUNIT[2, 2, 2, 1] = [  0.000,  0.001, 0]
      SUBUNIT[2, 2, 2, 2] = [  0.001,  0.001, 0]
    }

    SUBUNIT_RELATIONSHIPS
    {
      r0000 = [  0,  0,  0,  0]
      r0001 = [  0,  0,  0,  1]
      r0010 = [  0,  0,  1,  0]

      r0011 = [  0,  0, -1, -1]
      r0100 = [  0, -1,  0,  0]
      r0101 = [  0, -1,  0, -1]

      r0110 = [  0,  1,  1,  0]
      r0111 = [  0,  1,  1,  1]
      r1000 = [  1,  0,  0,  0]

      r1001 = [ -1,  0,  0, -1]
      r1010 = [ -1,  0, -1,  0]
      r1011 = [ -1,  0, -1, -1]

      r1100 = [  1,  1,  0,  0]
      r1101 = [  1,  1,  0,  1]
      r1110 = [  1,  1,  1,  0]

      r1111 = [ -1,  1, -1,  1]
    }

    RATE_RULES
    {
      rr0
      {
        DEFAULT: 3e2
      }

      rr1
      {
        r0000 != s_v_0: 3e3
        DEFAULT:        3e2
      }

      rr2
      {
        r0001 == s_v_0: 3e3
        DEFAULT:        3e2
      }

      rr3
      {
        r0010 != s_v_2 & r0011 == s_v_3: 3e3
        DEFAULT:        3e2
      }

      rr4
      {
        r0100 == s_v_4 & r0101 != s_v_4: 3e3
        DEFAULT:        3e2
      }

      rr5
      {
        r0110 == s_v_0 & r0111 == s_v_1: 3e3
        r1000 == s_v_1 & r1001 != s_v_1: 3e3
        DEFAULT:        3e2
      }

      rr6
      {
        r1100 == s_v_0: 3e3
        r1101 == s_v_1: 3e3
        r1110 == s_v_2: 3e3
        r1111 == s_v_3: 3e3
        DEFAULT:        3e2
      }
    }
}

DEFINE_COMPLEX_MOLECULE c_v_1
{
    NUMBER_OF_SUBUNITS = [1]
    SUBUNIT[1] = s_v_0
    SHAPE { SUBUNIT[1] = [0, 0, 0] }
    SUBUNIT_RELATIONSHIPS { }
    RATE_RULES { }
}