Child of Autopoietic_System_Final_Project-Nicolas_Pelaez

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;;;;;;;;;;COMPUTATIONAL AUTOPOIESIS;;;;;;;;;;;;
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turtles-own
 [ partner 
 ]
; There are 3 cehmical species in the model: A, B and M 
breed [ As A ] ; A is the catalyst of the reaction converting B into M
breed [ Bs B ] ; B is the substrate that is converted into M (see reactions below)
breed [ Ms M ] ; M is the component of the Membrane and can spontaneously be 
; degraded back into B (see reactions below)
breed [ LMs LM ] ; LMs represent the Linked Membrane components. There were separated as a 
; different breed form Ms to facilitate coding but represent the same molecular species.

to setup
   clear-all
   ;set-default-shape As to "molecule1" ; REMEMBER TO CHANGE THE SHAPES OF THE TURTLES
   ;set-default-shape Bs to "molecule2"  ; REMMBER TO CHANGE THE SHAPES OF THE TURTLES
   create-As Number_A-Catalysts
     [ setxy 0 0;random-xcor random-ycor 
       set color blue 
     ] 
   
   create-Bs Number_B-Substrates 
     [ setxy random-xcor random-ycor 
       set color red 
     ]
     tick
     ask turtles [ set partner nobody ]; this resets partnerships form previous runs. 
   create-ordered-LMs Initial_Number_LMs ; use 40 LMs as initial number!!!!!
     [ ; this is to create the initial membrane components required to start the simulation
            let i 1
            foreach sort LMs [
            ask ? [
      ;show ?
      ;show i
      create-link-with (item i sort LMs)
         ]
         set i (i + 1) mod count LMs 
         ]
         layout-circle sort LMs 5; (count LMs / 8); (count LMs / 8))
        ask links [ tie ]
        set color pink
     ] 
;      ask LMs 
;       [
;         if any? other (LMs in-radius 0.5 )
;         [ set partner one-of other turtles-here with [partner = nobody]
;            ;create-link-with parter ; 
;            ; restrict number of partners to two.....
;             create-link-with one-of other LMs 
;        ]
;       ]  
; sort is not ordered. it creates a list [ ]
;ask? refers to a dude in the lost. ? means to pick some one in the list. 
;beause i is 1 at the begining of list and. mod is like the colck arithmetic to wrapp around in  the list 
; create-links-with turltles with  [count link-neighbors = 1 ]
end 

to go
  tick
  move-turtles
   if (count As <= 0) or (count Bs <= 0) or (count Ms >= 300)
    [ stop ] 
    ask turtles
     [ 
        if (breed = As)    
           [ synthesize-M ] ; do the M synthesis reaction
        if (breed = Ms)  
           [ 
             disintegrate-Ms
             disintegrate-LMs
             link-Ms
             link-LMs
             ] ; do M spontaneous disintegration reaction         
     ]
     do-plot
end 

to move-turtles
  ask turtles
   [ 
     if breed = As [
       left random 40 right random 40
       forward 0.1
       let nearbyMembraneMs (LMs in-radius 0.5) ;with [ any? link-neighbors ] 
       if any? nearbyMembraneMs 
       [
         face one-of nearbyMembraneMs
         right 180 ; this makes the As stay away form the Ms. This property is required in   
         fd 0.1    ; order to achive impermeability of As through the membrane.
       ]
     ]
     if breed = Bs [
       left random 40 right random 40
       forward 0.1
     ]
     if breed = Ms [
       left random 40 right random 40
       forward 0.1
       let nearbyMembraneMs (other LMs in-radius 0.5) ;with [ any? link-neighbors ] 
       if any? nearbyMembraneMs 
       [
         face one-of nearbyMembraneMs
         right 180
         fd 0.1
       ]
     ]
;     if breed = LMs [  ; this is to move the circle
;        ask LMs [ rt random 1 lt random 1 fd 0.1 ]
;     ]
   ]
end 

to synthesize-M ; synthesis of M is given by the rule: if 1A + 2Bs come close enough this gives 1M an A and the Bs dissapear
  ;self is an A particle
  if synthesize-M? ; this turns on and off the synthesis reaction according to a switch
  [
    ; how do I ask only one breed. the catalysts As to do this, and not any other breed???
    if (count Bs in-radius reaction-range) >= 2; QUESTION: if I want to match 1 A with 2 Bs do I use As or A and a number?
     [ 
       let reacting-Bs n-of 2 Bs in-radius reaction-range
       ask reacting-Bs [ die ]
       hatch-Ms 1 [ set color green ] 
     ]
  ]    
end 

to disintegrate-Ms ; some few Ms once formed disintegrate spontaneously and give back 2Bs 
  if disintegrate-M? ; this turns on and off the disintegration reaction according to a switch
   [ 
     if random-float 100 <= Probability_M-disintegration ; QUESTION: check this to see if it correctly coded!
     [ hatch-Bs 2 [set color yellow ]
       die 
     ]
     
   ]
end   

to disintegrate-LMs
  if disintegrate-LM?
  [
    if random-float 1000 <= Probability_LM-disintegration; 
    [ hatch-Ms 1 [ set color green ]       
     ask one-of LMs [die] ;QUESTION: when there are no more LMs I get an error message 
                   ;because NetLogo gets an empty agent set (Nobody). how can I solve that?
    ]    
  ]
end 

to link-Ms   ; this is to link the formed Ms
;  if any? other (Ms in-radius 0.1)
;  [
;  create-link-with one-of other Ms
;  ]
end 

to link-LMs ; this links the formed Ms to prelinked MS called LMs
  ; the procedure intends to repair the membrane when it has gaps between to adjacent single linked LMs.
   ask LMs
   [
     ask LMs with [ count link-neighbors < 2 ] 
      [
       set color yellow
       let linking-targets (LMs in-radius 1 with [count link-neighbors < 2 ])
       if (any? LMs in-radius 1 with [count link-neighbors < 2 ] ) and (any? Ms in-radius 0.9) 
         [ set color orange
          ask Ms in-radius 0.9  [ die ]
          hatch-LMs 1 
;             [ 
;                ; this is to create the initial membrane components required to start the simulation
;            let i 1
;            foreach sort LMs [
;            ask ? [
;      ;show ?
;      ;show i
;      create-link-with (item i sort LMs)
;         ]
;         set i (i + 1) mod count LMs 
;         ]
;         layout-circle sort LMs 5 
;        ask links [ tie ]
;        set color pink
;     ] 
;               
               layout-circle LMs 5; (count LMs / 8) 
               ;setxy mean [xcor] of linking-targets mean [ycor] of linking-targets
               print linking-targets
               ;print self 
               set color gray ; this is not working, the color thing, and I don't know why.....
             ]
          ;hatch-LMs 1 
         ]
         
       ;if any? MLs in-radius 0.5   
      ]
   ;let unlinked-LMs LMs with [ count link-neighbors < 2 ]
     ;show unlinked-LMs
     ;ask unlinked-LMs [ set color yellow ] 
   ;if any? LMs in-radius 1 with  [count link-neighbors < 2 ]
    ;[hatch 1
    ;hatch 1 print self
    ;set breed LMs
    ;create-links-with (LMs in-radius 1)
    ;setxy mean [xcor] of link-neighbors ; or use layout circle......  or face the dud on your right and average of....
          ;mean [ycor] of link-neighbors 
         ;set heading
         ;die  
         ;; JOHSE"S IDEA: LMS own cordinates for the guys that are nearby me....
       
    ;SUGGESTIONS:  at beggining let them know how far away they are from each other....
;    is-list? 1
;    count my-links ;< 2 ;with-max [ 1 ];link-neighbors = 1  ] 
  ;ask LMs [ if in-link-neighbors = 1   
  
;     if any? linked-neighbor other (Ms in-radius 0.1)
;  create-link-with one-of other Ms
end 

to setup-plot
  set-current-plot "Molecule Concentrations"
  ;set-plot-y-range 0 Number-Molecules-APol
end  

to do-plot ; plot concentrations of of the three chemical species
  set-current-plot "Molecule Concentrations"
  set-current-plot-pen "A Catalysts"
  plot count As
  set-current-plot-pen "B Substrates"
  plot count Bs
  set-current-plot-pen "M Product"
  plot count Ms
  set-current-plot-pen "Linked Ms (LMs)"
  plot count LMs
end  

;QUESTIONS:
;-how can I represent the membrane
;-how can I restrict the movement within a bounded structure: coding options? 
;-how can I represent the links between M-M-Ms?
;SUGGESTIONS
;ADD ANOTHER RULE, M'S CAN ONLY HAVE 2 LINKS.also: 
; IF THERE IS ANY M WITHIN A GIVE NEIGHBORHOOD THEN they can CREATE A LINK.