genetic code

globals [ n  ;RNA PXCOR POSITION
          p1 ;PEPTISE PXCORPOSITION
          RNA ;RNA string
          first-base ; item position of 1st base in RNA
          codon ;codon variable
          s-base  ;starting base item position of a codon
          f-base  ;final base item position of a codon
          amino-acid ; translated amino acid
          amino-acid-result ; report the types of amino acids
          protein-length  ;peptide length
          base-candidates  ;nucleotides input from users
          aa1 ; amino acid 1
          aa-num ; assign a number for shuffle AAs
          aa-num-list
          filtered-list ;  find % of input nucleotides
  a-%
  c-%
  g-%
  u-%

  check-index  ;record the position of the nucleotide under check
      ]

Patches-own [base]

breed [nucleotides nucleotide]
breed [units unit]
breed [peptides peptide]
breed [primes prime]

to setup

 ca

  set base-candidates STEP-1-Input-Nucleotides ;user-input "Nucleotides (Capital A C U or G only.No space)"

  ifelse length base-candidates = 0 [user-message "no nucleotide is tested" stop][capitalize-bases]

  find-percentages

  set RNA "5'-"                                    ;create 5' end
  set-default-shape nucleotides "x"               ;set default shape as X in case having an invalid base
  set n 7                                         ;set the first base position in the world
  set first-base 3

  set s-base 3
  set f-base 6
  set p1 10
  set protein-length 0
  set amino-acid-result ""
  set aa-num-list 0
  set aa1 0

  ask patches [set pcolor 9.5 + random-float 0.4 ]
  ask patches with [pycor <= min-pycor + 2 ] [set pcolor 2]

 repeat 18
  [ set RNA word RNA item random (length base-candidates) base-candidates]      ;synthesize the RNA



  set RNA word RNA "-3'"                       ;attach 3' end


 repeat 18
    [ ask patches with [pxcor = n and pycor = 4]               ;assign base to patches
      [set base item first-base RNA]
      set n n + 1
      set first-base first-base + 1]

 ask patches with [base != 0]                                  ;let assigned patches produce bases
 [sprout-nucleotides 1
      [ if base = "A"  [set shape "nn-a"]
        if base = "C"  [set shape "nn-c"]
        if base = "G"  [set shape "nn-g"]
        if base = "U"  [set shape "nn-u"]
    ]]

  create-primes 1               ;MAKE 5' END
  [set shape "5'"
    set size 1.5
    set color 0
    setxy 6.3 4.5]



   create-primes 1               ;MAKE 3' END
  [set shape "3'"
    set size 1.5
    set color 0
    setxy 24.7 4.5]


  if any? nucleotides with [shape = "x"] [user-message "Please input correct nucleotide(s) (A, U, C, G)" stop]

ribosome

reset-ticks
end 

to translate

  if f-base > 21 [user-message "Translation has been completed" stop]

   repeat 6 [
    ask units                           ;move ribosome one codon
      [set heading 90
        forward 4
        wait 0.3]


   set codon substring RNA s-base f-base                            ;detetmine the range (the codon)
   if codon = "AUG" [set amino-acid "Met" set aa-num 1]                         ;translate
   if codon = "UUU" or codon = "UUC" [set amino-acid "Phe" set aa-num 2]
   if codon = "UUA" or codon = "UUG" or codon = "CUU" or codon = "CUC" or codon = "CUA" or codon = "CUG"[set amino-acid "Leu" set aa-num 3]
   if codon = "AUU" or codon = "AUC" or codon = "AUA" [set amino-acid "Ile" set aa-num 4]
   if codon = "GUU" or codon = "GUC" or codon = "GUA" or codon = "GUG" [set amino-acid "Val" set aa-num 5]
   if codon = "UCU" or codon = "UCC" or codon = "UCA" or codon = "UCG" or codon = "AGU" or codon = "AGC" [set amino-acid "Ser" set aa-num 6]
   if codon = "CCU" or codon = "CCC" or codon = "CCA" or codon = "CCG" [set amino-acid "Pro" set aa-num 7]
   if codon = "ACU" or codon = "ACC" or codon = "ACA" or codon = "ACG" [set amino-acid "Thr" set aa-num 8]
   if codon = "GCU" or codon = "GCC" or codon = "GCA" or codon = "GCG" [set amino-acid "Ala" set aa-num 9]
   if codon = "UAU" or codon = "UAC"  [set amino-acid "Tyr" set aa-num 10]
   if codon = "CAU" or codon = "CAC"  [set amino-acid "His" set aa-num 11]
   if codon = "CAA" or codon = "CAG"  [set amino-acid "Gln" set aa-num 12]
   if codon = "AAU" or codon = "AAC"  [set amino-acid "Asn" set aa-num 13]
   if codon = "AAA" or codon = "AAG"  [set amino-acid "Lys" set aa-num 14]
   if codon = "GAU" or codon = "GAC"  [set amino-acid "Asp" set aa-num 15]
   if codon = "GAA" or codon = "GAG"  [set amino-acid "Glu" set aa-num 16]
   if codon = "UGU" or codon = "UGC"  [set amino-acid "Cys" set aa-num 17]
   if codon = "UGG" [set amino-acid "Trp" set aa-num 18]
   if codon = "CGU" or codon = "CGC" or codon = "CGA" or codon = "CGG" or codon = "AGA" or codon = "AGG" [set amino-acid "Arg" set aa-num 19]
   if codon = "GGU" or codon = "GGC" or codon = "GGA" or codon = "GGG" [set amino-acid "Gly" set aa-num 20 ]
    if codon = "UAA" or codon = "UAG" or codon = "UGA" [set amino-acid "" user-message "Translation is terminated" ask units [die]]

   set aa-num-list sentence aa-num-list aa-num    ;assign number to aa for removing duplication and shuffle
   set aa-num-list remove-duplicates aa-num-list


       ifelse amino-acid != ""                           ;if not encounter a stop codon,
        [
         create-peptides 1                            ; make amino acid
           [set size 2
            set shape "protein-unit"
            setxy p1  min-pycor + 1
            set color white]

         set p1 p1 + 2          ;set amino acids position

         set s-base s-base + 3    set f-base f-base + 3]

     [set aa-num-list remove 0 aa-num-list
      set aa-num-list shuffle aa-num-list
      show-aa
      stop]


  ]

  set aa-num-list remove 0 aa-num-list
  set aa-num-list shuffle aa-num-list

  show-aa
end 

to ribosome

 create-units 1
   [
    set shape "l-unit"
    set size 7
    set color 27
    setxy 3.5 3]
end 

to show-aa

  repeat length aa-num-list
   [set aa-num item aa1 aa-num-list
      num-to-aa
      set amino-acid-result word amino-acid-result " "
      set amino-acid-result word amino-acid-result amino-acid
      set aa1 aa1 + 1]
end 

to num-to-aa

  if aa-num = 1 [set amino-acid "Met"]
  if aa-num = 2 [set amino-acid "Phe"]
  if aa-num = 3 [set amino-acid "Leu"]
  if aa-num = 4 [set amino-acid "Ile"]
  if aa-num = 5 [set amino-acid "Val"]
  if aa-num = 6 [set amino-acid "Ser"]
  if aa-num = 7 [set amino-acid "Pro"]
  if aa-num = 8 [set amino-acid "Thr"]
  if aa-num = 9 [set amino-acid "Ala"]
  if aa-num = 10 [set amino-acid "Tyr"]
  if aa-num = 11 [set amino-acid "His"]
  if aa-num = 12 [set amino-acid "Gln"]
  if aa-num = 13 [set amino-acid "Asn"]
  if aa-num = 14 [set amino-acid "Lys"]
  if aa-num = 15 [set amino-acid "Asp"]
  if aa-num = 16 [set amino-acid "Glu"]
  if aa-num = 17 [set amino-acid "Cys"]
  if aa-num = 18 [set amino-acid "Trp"]
  if aa-num = 19 [set amino-acid "Arg"]
  if aa-num = 20 [set amino-acid "Gly"]
end 

to find-percentages

 ifelse member? "A" base-candidates
   [set filtered-list remove "A" base-candidates
      set a-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set a-% 0]

  ifelse member? "C" base-candidates
   [set filtered-list remove "C" base-candidates
      set c-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set c-% 0]

 ifelse member? "G" base-candidates
   [set filtered-list remove "G" base-candidates
      set g-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set g-% 0]

  ifelse member? "U" base-candidates
   [set filtered-list remove "U" base-candidates
      set u-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set u-% 0]
end 

to capitalize-bases
  set check-index 0
  Repeat length base-candidates
  [
  (ifelse
    item check-index base-candidates = "a" [set base-candidates (replace-item check-index base-candidates "A")]
    item check-index base-candidates = "g" [set base-candidates (replace-item check-index base-candidates "G")]
    item check-index base-candidates = "c" [set base-candidates (replace-item check-index base-candidates "C")]
    item check-index base-candidates = "u" [set base-candidates (replace-item check-index base-candidates "U")])

    set check-index check-index + 1]
end