AI state codon reassignment

Codon reassignments via AI state

/*created@2007Nov18*/
/*Codon reassignment via AI state*/

#include 
#include 
#include 

/*walking system*/
#define LENGTH 70 //tRNAの長さ
#define W 0.0    //アンチコドン変異(ＣＤ化推進部位)でのpの変化量
#define Z 0.0      //アンチコドン変異(ＣＤ化推進部位)でのlの変化量
#define AI_P 2.0   //ＡＩ化の推進部位変異での変化量
#define AI_L  0.5  //ＡＩ化の推進部位変異での変化量
#define D 60.0     //領域[D,LENGTH]が中立部位になる

/*animo acid availability*/
#define A1 0.6
#define A2 0.1
#define GETA 10 //コドン再配置が生じるためにＡＩ状態いるべき最低時間
#define BETA 100

/*codon system's paramters*/
#define BASEPOINT     1000.0
#define GAP           10.0
#define CODON1_WIDTH  50.0
#define CODON2_WIDTH  50.0

/*trna system*/
//l:trna range of recognition, p:center of range
//dl:change of range , dp:walking length
//So far, trna2 is fixed.
double l1,p1;
double l2,p2;
double dp,dl;

/*amino acid quantity*/
int limit_time;

/*変異回数 (walk()の呼び出し回数)*/
int t;

/*setting of codons' range */
double cdn1_min,cdn1_max;
double cdn2_min,cdn2_max;

/*AI state flag*/
//1:AI state, 0:NOT AI state
int cdn2_ai_flg = 0;

/*functions*/
init();
init_aa();
aa_comp();
walk();
int is_ai();



main(){
  init();
  init_aa();

  while(1){
    walk();
    t++;
    printf("aaa\n");
//    is_ai();
    while( is_ai() == 1 ){
      printf("is_ai()=true\n");
      aa_comp();
      printf("limit_time = %5d \n",limit_time);
      walk();
      t++;
    }
    //if reassignment failed, initialize the x1,x2
    init_aa();
   
  }
 
}



init(){

  cdn2_min = BASEPOINT;
  cdn2_max = cdn2_min + CODON2_WIDTH;
  cdn1_min = cdn2_max + GAP;
  cdn1_max = cdn1_min + CODON1_WIDTH;

  p1 = cdn1_min + CODON1_WIDTH / 2.0;
  l1 = CODON1_WIDTH / 2.0;
 
  p2 = cdn2_min + CODON2_WIDTH / 2.0;
  l2 = CODON2_WIDTH / 2.0;

  t = 0;
}


init_aa(){  //アミノ酸に対するtrna初期濃度
  limit_time = (int) BETA / ( A1 - A2 ) + GETA;
}

 
aa_comp(){
  limit_time--;

  if( limit_time <= 0 ){
    printf("codon reassigned.\n");
    printf("mutation time is %5d \n",t);
    exit(EXIT_SUCCESS);
  }
}


walk(){
  double rnd;
  double dp = 0.0;
  double dl = 0.0;
 
  rnd = drand48() * LENGTH;

  if( rnd >= 0.0 && rnd < 3.0 ){
    //hit trna in the anticodon
    printf("Mutation in anticodon.\n");
    dp = W;
    dl = Z;
  }else if( rnd >= 3.0 && rnd < D ){
    //hit trna in the non-anticodon, but effective
    dp = AI_P;
    dl = AI_L;
  }else if( rnd >= D && rnd <= LENGTH){
    //hit trna in the non-anticodon, ineffective
    dp = 0.0;
    dl = 0.0;
  }

  rnd = drand48();
  if( rnd > 0.5 ) dp = -1*dp;
 
  rnd = drand48();
  if( rnd > 0.5 ) dl = -1*dl;

  l1 = l1 + dl;
  p1 = p1 + dp;
 
}


int is_ai(){
  if(  ( p1 - l1 ) <= cdn2_max ){
    cdn2_ai_flg = 1;
  }else{
    cdn2_ai_flg = 0;
  }
  return cdn2_ai_flg;
 
}