GvHD and Tregs

breed [grafts graft]
grafts-own [stuck energy]
breed [tregs treg]
breed [tcells tcell]
tcells-own [bound activated]

to setup
  clear-all
  create-tcells 200 [
    set shape "dot"
    set color red
    setxy random-xcor random-ycor
    set bound nobody
    set activated true
  ]
  if mode != "start without graft" [add-grafts]
  setup-membrane
  reset-ticks
end 

to go
  mode-go
  tcells-go
  grafts-go
  tregs-go
  tick
end 

to mode-go
  (ifelse mode = "regular dosage" [if ticks mod 1000 = 1 [add-tregs] ]
    )
end 

to revert-defaults
  set treg-death 0.0020
  set tcell-reactivation 0.003
  set treg-dosage 50
end 

to setup-membrane
  ask patches [set pcolor 134]
  ask patches with [abs pycor = max-pycor] [set pcolor 138]
end 

to add-grafts
  create-grafts 40 [
    set shape "dot"
    set size 4
    set color 19
    setxy random-xcor max-pycor
    if random 2 = 1 [set ycor min-pycor]
    set stuck true
  ]
end 

to tcells-go
  ask tcells [
    ifelse bound = nobody [
      lt 30 - random 60

      ;try not to stick to walls
      if pycor = max-pycor [set heading 180]
      if pycor = min-pycor [set heading 0]

      fd 0.5

      ifelse activated [
        let my-graft one-of grafts-here
        if my-graft != nobody[
          set bound my-graft
        ]
      ]
      [ ; if unactivated, stochastic chance to be activated
        if random-float 1 < tcell-reactivation [set activated true set color red]
      ]
    ]
    [ifelse activated [
      move-to bound
      set heading random 360
      fd random-float 0.3
      ]
      [set bound nobody]
    ]
  ]
end 

to grafts-go
  ask grafts [
    set energy count tcells-here in-radius 1 with [activated]
    set color 19 - energy
    if energy >= 4 [set stuck false]
    if energy >= 10 [die]

    if not stuck [
      lt 30 - random 60
      fd 0.25

      ifelse energy = 0 [
        if pycor = max-pycor [set ycor pycor set stuck true]
        if pycor = min-pycor [set ycor pycor set stuck true]
      ]
      [
        ;try not to stick to walls
        if pycor = max-pycor [set heading 180]
        if pycor = min-pycor [set heading 0]
      ]
    ]
  ]
end 

to add-tregs
  create-tregs treg-dosage [
    set color sky
  ]
end 

to tregs-go
  ask tregs[
    lt 30 - random 60
    fd 0.25

    ;try not to stick to walls
    if pycor = max-pycor [set heading 180]
    if pycor = min-pycor [set heading 0]

    if any? tcells in-radius 1 [
      ask tcells in-radius 1 [
        set activated false
        set color 18
      ]
    ]

    if random-float 1 < treg-death [die]
  ]
end