while(<FH>){
   
   if($_ =~ C B A R){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
   
   if($_ =~ Q U A D){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
   
   if($_ =~ C R O D){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
   
   if($_ =~ C B E A M){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
   
   if($_ =~ C E L A S 1){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
  ... 
}

##</code><code>##

while(<FH>){
   
   if($_ =~ C B A R){
      do something
      This bit is not the same for all elements and it is average 100 lines long
   }
}