/* Normal/DFP/BTx Lizard Intercostal Neuromuscular Junction */

INCLUDE_FILE = "nmj_parameters.mdl"
btx_factor=norm_btx_factor
ache_d_factor=norm_ache_d_factor

TIME_STEP = dt
TIME_STEP_MAX = 10000*dt
ITERATIONS = it
EFFECTOR_GRID_DENSITY = grid_density
RADIAL_SUBDIVISIONS = rad_sub
RADIAL_DIRECTIONS = rad_dir

delta=0.51*cleft
sv1=(-14*inter_fold)-delta
sv2=(-14*inter_fold)+delta
sv3=(-13*inter_fold)-delta
sv4=(-13*inter_fold)+delta
sv5=(-12*inter_fold)-delta
sv6=(-12*inter_fold)+delta
sv7=(-11*inter_fold)-delta
sv8=(-11*inter_fold)+delta
sv9=(-10*inter_fold)-delta
sv10=(-10*inter_fold)+delta
sv11=(-9*inter_fold)-delta
sv12=(-9*inter_fold)+delta
sv13=(-8*inter_fold)-delta
sv14=(-8*inter_fold)+delta
sv15=(-7*inter_fold)-delta
sv16=(-7*inter_fold)+delta
sv17=(-6*inter_fold)-delta
sv18=(-6*inter_fold)+delta
sv19=(-5*inter_fold)-delta
sv20=(-5*inter_fold)+delta
sv21=(-4*inter_fold)-delta
sv22=(-4*inter_fold)+delta
sv23=(-3*inter_fold)-delta
sv24=(-3*inter_fold)+delta 
sv25=(-2*inter_fold)-delta
sv26=(-2*inter_fold)+delta
sv27=(-1*inter_fold)-delta
sv28=(-1*inter_fold)+delta
sv29=-delta
sv30=delta
sv31=(1*inter_fold)-delta
sv32=(1*inter_fold)+delta
sv33=(2*inter_fold)-delta
sv34=(2*inter_fold)+delta
sv35=(3*inter_fold)-delta
sv36=(3*inter_fold)+delta
sv37=(4*inter_fold)-delta  
sv38=(4*inter_fold)+delta
sv39=(5*inter_fold)-delta
sv40=(5*inter_fold)+delta
sv41=(6*inter_fold)-delta 
sv42=(6*inter_fold)+delta
sv43=(7*inter_fold)-delta
sv44=(7*inter_fold)+delta
sv45=(8*inter_fold)-delta
sv46=(8*inter_fold)+delta
sv47=(9*inter_fold)-delta
sv48=(9*inter_fold)+delta
sv49=(10*inter_fold)-delta
sv50=(10*inter_fold)+delta
sv51=(11*inter_fold)-delta
sv52=(11*inter_fold)+delta
sv53=(12*inter_fold)-delta
sv54=(12*inter_fold)+delta
sv55=(13*inter_fold)-delta
sv56=(13*inter_fold)+delta
sv57=(14*inter_fold)-delta
sv58=(14*inter_fold)+delta

PARTITION_X = [sv1,sv2,sv3,sv4,sv5,sv6,sv7,sv8,sv9,sv10,
          sv11,sv12,sv13,sv14,sv15,sv16,sv17,sv18,sv19,sv20,
          sv21,sv22,sv23,sv24,sv25,sv26,sv27,sv28,sv29,sv30,
          sv31,sv32,sv33,sv34,sv35,sv36,sv37,sv38,sv39,sv40,
          sv41,sv42,sv43,sv44,sv45,sv46,sv47,sv48,sv49,sv50,
          sv51,sv52,sv53,sv54,sv55,sv56,sv57,sv58]
PARTITION_Y = [-50, 50]
PARTITION_Z = [-50, 50]

DEFINE_MOLECULES {
  ACh { DIFFUSION_CONSTANT_3D = D }
  AChR.R { DIFFUSION_CONSTANT_2D = 0 }
  AChR.ARs { DIFFUSION_CONSTANT_2D = 0 }
  AChR.ARt { DIFFUSION_CONSTANT_2D = 0 }
  AChR.A2Rc { DIFFUSION_CONSTANT_2D = 0 }
  AChR.A2Ro { DIFFUSION_CONSTANT_2D = 0 }
  BTxAChR.R { DIFFUSION_CONSTANT_2D = 0 }
  BTxAChR.AR { DIFFUSION_CONSTANT_2D = 0 }
  AChE.E { DIFFUSION_CONSTANT_2D = 0 }
  AChE.AE { DIFFUSION_CONSTANT_2D = 0 }
}

DEFINE_REACTIONS {
  ACh' + AChR.R' -> AChR.ARs' [Kp1]
  ACh' + AChR.R' -> AChR.ARt' [Kp1]

  AChR.ARs' -> ACh' + AChR.R' [Km1]
  AChR.ARt' -> ACh' + AChR.R' [Km1]

  ACh' + AChR.ARs' -> AChR.A2Rc' [Kp2]
  ACh' + AChR.ARt' -> AChR.A2Rc' [Kp2]

  AChR.A2Rc' -> ACh' + AChR.ARs' [Km2]
  AChR.A2Rc' -> ACh' + AChR.ARt' [Km2]

  AChR.A2Rc' -> AChR.A2Ro' [beta]
  AChR.A2Ro' -> AChR.A2Rc' [alpha]


  ACh' + BTxAChR.R' -> BTxAChR.AR' [Kp1]
  BTxAChR.AR' -> ACh' + BTxAChR.R' [Km1]


  ACh'' + AChE.E' -> AChE.AE' [Kpe]
  AChE.AE' -> AChE.E'         [Kme]
}


DEFINE_RELEASE_PATTERN release_pattern_1 {
  DELAY = r_delay_1
  RELEASE_INTERVAL = r_interval_1
  TRAIN_INTERVAL = t_interval_1
  TRAIN_DURATION = t_duration_1
  NUMBER_OF_TRAINS = n_trains_1
}

all_release_sites OBJECT {
  release_site_1 SPHERICAL_RELEASE_SITE {
    LOCATION = r_location_1
    MOLECULE = ACh
    NUMBER_TO_RELEASE = n_release_1
/*
    SITE_DIAMETER = r_diameter_1
*/
    SITE_DIAMETER = 0
    RELEASE_PATTERN = release_pattern_1
  }
}

DEFINE_SURFACE_CLASSES {
  absorb {
    ABSORPTIVE = ACh
  }
  basal_lamina {
    TRANSPARENT = ACh
  }
}

enclosure OBJECT {

  top_piece BOX {
    CORNERS = [-Rex,-Rex,0],[Rex,Rex,cleft]
    REMOVE_ELEMENTS  { INCLUDE_ELEMENTS = [BOTTOM]}
    DEFINE_SURFACE_REGIONS {
      boundary {
        ELEMENT_LIST = [LEFT,RIGHT,FRONT,BACK]
        SURFACE_CLASS = absorb
      }
    }
  }

  bottom_piece BOX {
    CORNERS = [-Rex,-Rex,-depth3],[Rex,Rex,0]
    REMOVE_ELEMENTS{
	INCLUDE_ELEMENTS = [TOP]
    }
  }
}

fold_template OBJECT {
  upper BOX {
    CORNERS = [-cleft/2,-Rex,-depth1],[cleft/2,Rex,0]
    REMOVE_ELEMENTS {
           INCLUDE_ELEMENTS = [FRONT,BACK,TOP,BOTTOM]
    }
    DEFINE_SURFACE_REGIONS {
      sides1 {
        ELEMENT_LIST = [LEFT,RIGHT]
        MOLECULE_DENSITY {
          AChR.R, = achr_d*btx_factor*btx_factor
          BTxAChR.R, = achr_d*2*btx_factor*(1-btx_factor)
        }
      }
    }
  }
  middle BOX {
    CORNERS = [-cleft/2,-Rex,-depth2],[cleft/2,Rex,-depth1]
    REMOVE_ELEMENTS{
	INCLUDE_ELEMENTS = [FRONT,BACK,TOP,BOTTOM]
    }
    DEFINE_SURFACE_REGIONS {
      sides2 {
        ELEMENT_LIST = [LEFT,RIGHT]
        MOLECULE_DENSITY {
          AChR.R, = achr_d_mid*btx_factor*btx_factor
          BTxAChR.R, = achr_d_mid*2*btx_factor*(1-btx_factor)
        }
      }
    }
  }
  bottom BOX {
    CORNERS = [-cleft/2,-Rex,-depth3],[cleft/2,Rex,-depth2]
    REMOVE_ELEMENTS {
	INCLUDE_ELEMENTS = [FRONT,BACK,TOP,BOTTOM]
    }
  }
  ache_fold_sheet BOX {
    CORNERS = [0,-Rex,-depth3],[cleft,Rex,cleft/2]
    REMOVE_ELEMENTS{
	INCLUDE_ELEMENTS = [FRONT,BACK,TOP,BOTTOM,RIGHT]
    }
    DEFINE_SURFACE_REGIONS {
      fold {
        ELEMENT_LIST = [LEFT]
        SURFACE_CLASS = basal_lamina
        MOLECULE_DENSITY {
          AChE.E' = ache_d_fold*ache_d_factor
        }
      }
    }
  }
}

top_of_fold BOX {
  CORNERS = [cleft/2,-Rex,0],[inter_fold-(cleft/2),Rex,cleft]
  REMOVE_ELEMENTS{
	INCLUDE_ELEMENTS = [TOP,LEFT,RIGHT,FRONT,BACK]
  }
  DEFINE_SURFACE_REGIONS {
    sides3 {
      ELEMENT_LIST = [BOTTOM]
      MOLECULE_DENSITY {
        AChR.R, = achr_d*btx_factor*btx_factor
        BTxAChR.R, = achr_d*2*btx_factor*(1-btx_factor)
      }
    }
  }
}

ache_primary_sheet BOX {
  CORNERS = [-Rex,-Rex,cleft/2],[Rex,Rex,cleft]
  REMOVE_ELEMENTS {
     INCLUDE_ELEMENTS = [FRONT,BACK,LEFT,RIGHT,TOP]
  }
  DEFINE_SURFACE_REGIONS {
    primary {
      ELEMENT_LIST = [BOTTOM]
      SURFACE_CLASS = basal_lamina
      MOLECULE_DENSITY {
        AChE.E' = ache_d*ache_d_factor
      }
    }
  }
}

fold_assembly OBJECT {
  fold_top OBJECT top_of_fold { }
  fold_bottom OBJECT fold_template { TRANSLATE = [inter_fold,0,0] }
}

right_folds OBJECT {
  fold_1 OBJECT fold_assembly { }
  fold_2 OBJECT fold_assembly { TRANSLATE = [1*inter_fold,0,0] }
  fold_3 OBJECT fold_assembly { TRANSLATE = [2*inter_fold,0,0] }
  fold_4 OBJECT fold_assembly { TRANSLATE = [3*inter_fold,0,0] }
  fold_5 OBJECT fold_assembly { TRANSLATE = [4*inter_fold,0,0] }
  fold_6 OBJECT fold_assembly { TRANSLATE = [5*inter_fold,0,0] }
  fold_7 OBJECT fold_assembly { TRANSLATE = [6*inter_fold,0,0] }
  fold_8 OBJECT fold_assembly { TRANSLATE = [7*inter_fold,0,0] }
  fold_9 OBJECT fold_assembly { TRANSLATE = [8*inter_fold,0,0] }
  fold_10 OBJECT fold_assembly { TRANSLATE = [9*inter_fold,0,0] }
  fold_11 OBJECT fold_assembly { TRANSLATE = [10*inter_fold,0,0] }
  fold_12 OBJECT fold_assembly { TRANSLATE = [11*inter_fold,0,0] }
  fold_13 OBJECT fold_assembly { TRANSLATE = [12*inter_fold,0,0] }
  fold_14 OBJECT fold_assembly { TRANSLATE = [13*inter_fold,0,0] }
}

INSTANTIATE nmj OBJECT {
  nmj_enclosure OBJECT enclosure { }
  primary_ache OBJECT ache_primary_sheet { }
  middle_fold OBJECT fold_template { }
  post_synaptic_right OBJECT right_folds { }
  post_synaptic_left OBJECT right_folds { ROTATE = [0,0,1],180 }
  nmj_release_sites OBJECT all_release_sites { }
}

VIZ_DATA_OUTPUT {
  MODE = DX
  MOLECULE_FILE_PREFIX = "./viz/nmj"
  OBJECT_FILE_PREFIXES {
    nmj = "./viz/nmj"
  }
  STATE_VALUES {
    nmj = 1
    ACh = 1
    AChR.R = 2
    AChR.ARs = 3
    AChR.ARt = 3
    AChR.A2Rc = 4
    AChR.A2Ro = 5
    AChE.E = 6
    AChE.AE = 7
  }
  ITERATION_LIST = [0,50,100,250]
}


REACTION_DATA_OUTPUT {
  STEP = freq
  { COUNT[ACh,WORLD] } => "./dat/ACh.dat"
  { COUNT[AChR.R,WORLD] } => "./dat/AChR.R.dat"
  { COUNT[AChR.ARs,WORLD] + COUNT[AChR.ARt,WORLD] } => "./dat/AChR.AR.dat"
  { COUNT[AChR.A2Rc,WORLD] } => "./dat/AChR.A2Rc.dat"
  { COUNT[AChR.A2Ro,WORLD] } => "./dat/AChR.A2Ro.dat"
  { COUNT[AChE.E,WORLD] } => "./dat/AChE.E.dat"
  { COUNT[AChE.AE,WORLD] } => "./dat/AChE.AE.dat"
}