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#######################
#
# FIND BETA-STRANDS
#
#######################

# Go over all AAs
beta_nucleation_window=5;
beta_nucleation_threshold=3;
j=0;

while (j<i-beta_nucleation_window) {

# Find Nucleation region
    beta_found=0;
    alpha_score=0;
    beta_score=0;
    for (k=0; k<beta_nucleation_window; k++) {   
      if (beta[a[j+k]]>100) {beta_found++}
      alpha_score+=alpha[a[j+k]];
      beta_score+=beta[a[j+k]]
    }

    if (beta_found>=beta_nucleation_threshold) {

    # Extend left
      extend=j-1;
      stop=0;
      while (extend >=0 && stop==0) {
       beta_av=0;
       for (l=0; l<4; l++) {
          beta_av+=beta[a[extend-l]]*0.25;
       }
       if (beta_av<100 && extend>=3) {stop=1}
       else {
          alpha_score+=alpha[a[extend]];
          beta_score+=beta[a[extend]];
          extend--
       }
      }
      left=extend+1;...

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