Families of Variable Names

Similarly:

     71                 $chain1[$i] =~ s/X/0/g; $chain2[$i] =~ s/X/0/g;
     72                 $chain3[$i] =~ s/X/0/g; $chain4[$i] =~ s/X/0/g;
     73                 $chain5[$i] =~ s/X/0/g; $chain6[$i] =~ s/X/0/g;
     74                 $chain7[$i] =~ s/X/0/g;
     75                         print OUTFILE2 "\n(ct_si  $ct_si{tdi}
     76 $chain1[$i]$chain2[$i]$chain3[$i]$chain4[$i]$chain5[$i]$chain6[$i]$chain7[$i]
     77  )";

Becomes:

      for (@chain) { $_->[$i] =~ s/X/0/g }
      my @chars = map $_->[$i], @chain;
      print OUTFILE2 "\n(ct_si  $ct_si{tdi}\n", join("", @chars), "\n )";

8 lines become 4
This version of the program is extract2.pl