mcell/mdl/testsuite/macromols/04-macro_surface_init.mdl

/****************************************************************************
 * Test 04: Surface macromolecule init by density/number.
 *
 *    This test is to ensure that init_effectors properly handles surface
 *    macromolecules.  Most of the information is conveyed by the time 0 viz
 *    output, but the forward reaction rate has been cranked up enough to see
 *    from the reaction data also whether the molecules were placed.  The
 *    complexes are at the center of each face, the middle of each edge, and on
 *    each corner of the box.  The subunits should conform to the corners of
 *    the box as appropriate.
 *
 *    Note, in particular, that if the complexes (or resultant subunits) were
 *    placed with incorrect orientation, we expect that close to 66% of the
 *    dimer pairs will be in the doubly-bound state, 16% will be in the
 *    singly-bound state, and 16% should perpetually be in the unbound state (1
 *    of the dimer pairs from each ring is intentionally placed with the wrong
 *    orientation to react).
 *
 * Author: Jed Wing <[email protected]>
 * Date:   2008-04-04
 ****************************************************************************/

basename = "04-macro_surface_init"
countdir = "dat/" & basename & "/"
vizdir   = "./viz_dat/" & basename & "/"
sprintf(seed, "%04g", SEED)
dt = 1e-6
iterations=1

INCLUDE_FILE="parameters.mdl"

TIME_STEP = dt
ITERATIONS = iterations
EFFECTOR_GRID_DENSITY = 15000
ACCURATE_3D_REACTIONS = FALSE

PARTITION_X = [[-0.5001 TO 0.50001 STEP 0.02]]
PARTITION_Y = [[-0.5001 TO 0.50001 STEP 0.02]]
PARTITION_Z = [[-0.5001 TO 0.50001 STEP 0.02]]

DEFINE_MOLECULES {
  camkii_subunit  { DIFFUSION_CONSTANT_2D = 0 }
  camkii_subunitB { DIFFUSION_CONSTANT_2D = 0 }
  cam             { DIFFUSION_CONSTANT_3D = cam_diffusion }
}

DEFINE_COMPLEX_MOLECULE camkii {
  NUMBER_OF_SUBUNITS = [2, 6]
  SUBUNIT[1  , 1  ] = camkii_subunit'
  SUBUNIT[2  , 1  ] = camkii_subunit,
  SUBUNIT[1:2, 2  ] = camkii_subunit,
  SUBUNIT[1:2, 3:6] = camkii_subunit'
  SHAPE {
    SUBUNIT[1, 1] = [-.11,  .0000, 0]
    SUBUNIT[1, 2] = [-.06,  .0866, 0]
    SUBUNIT[1, 3] = [ .06,  .0866, 0]
    SUBUNIT[1, 4] = [ .11,  .0000, 0]
    SUBUNIT[1, 5] = [ .06, -.0866, 0]
    SUBUNIT[1, 6] = [-.06, -.0866, 0]

    SUBUNIT[2, 1] = [-.09,  .0000, 0]
    SUBUNIT[2, 2] = [-.04,  .0866, 0]
    SUBUNIT[2, 3] = [ .04,  .0866, 0]
    SUBUNIT[2, 4] = [ .09,  .0000, 0]
    SUBUNIT[2, 5] = [ .04, -.0866, 0]
    SUBUNIT[2, 6] = [-.04, -.0866, 0]
  }
  SUBUNIT_RELATIONSHIPS {
    dimer_partner = [+1,  0]
  }
  RATE_RULES {
  }
}

DEFINE_SURFACE_CLASSES {
  class1 { MOLECULE_NUMBER { camkii' = 20 } }               // Presently broken
  class2 { MOLECULE_DENSITY { camkii' = 200.0 } }           // Presently broken
  class3 { MOLECULE_NUMBER { camkii; = 25 } }               // Presently broken
}

mainbox OBJECT {
  b BOX {
    CORNERS = [ -0.5, -0.5, -0.5 ], [ 0.5, 0.5, 0.5 ]
    DEFINE_SURFACE_REGIONS {
      /* NOTE: TEMPORARILY COMMENTED class1, class2, and class3 below
         until a code will be fixed to allow complex molecules
         placement through SURFACE CLASSES */
      top    { ELEMENT_LIST = [TOP]   /* SURFACE_CLASS = class1 */ }
      left   { ELEMENT_LIST = [LEFT]   /* SURFACE_CLASS = class2 */ }
      front  { ELEMENT_LIST = [FRONT]  /* SURFACE_CLASS = class3 */ }
 
      bottom { ELEMENT_LIST = [BOTTOM] MOLECULE_NUMBER { camkii, = 20 } }
      right  { ELEMENT_LIST = [RIGHT]  MOLECULE_NUMBER  { camkii, = 200.0 } }
      back   { ELEMENT_LIST = [BACK]   MOLECULE_DENSITY { camkii; = 200.0 } }
    }
  }
}

INSTANTIATE world OBJECT
{
  mainbox OBJECT mainbox {
  }

  rs2 RELEASE_SITE {
    SHAPE = world.mainbox.b[ALL]
    MOLECULE = cam
    NUMBER_TO_RELEASE = num_cam
  }
}

REACTION_DATA_OUTPUT
{
    OUTPUT_BUFFER_SIZE = 1000
    ITERATION_LIST=[0]
    HEADER = "# "
    {
      COUNT[camkii, WORLD]                                                               : "complexes",
      COUNT[camkii_subunit, WORLD]                                                       : "subunits",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, WORLD] : "00",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, WORLD] : "01",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, WORLD] : "11",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[top]]    : "00t",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[top]]    : "01t",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[top]]    : "11t",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[bottom]] : "00b",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[bottom]] : "01b",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[bottom]] : "11b",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[left]]   : "00l",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[left]]   : "01l",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[left]]   : "11l",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[right]]  : "00r",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[right]]  : "01r",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[right]]  : "11r",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[front]]  : "00F",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[front]]  : "01F",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[front]]  : "11F",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit']}, world.mainbox.b[back]]   : "00B",
      COUNT[SUBUNIT{camkii : camkii_subunit' [dimer_partner == camkii_subunit,]}, world.mainbox.b[back]]   : "01B",
      COUNT[SUBUNIT{camkii : camkii_subunit, [dimer_partner == camkii_subunit,]}, world.mainbox.b[back]]   : "11B"
    } => "counts.txt"
}