use IO::File;
use strict;
for my $file (@ARGV) {
    warn("$file: $!"), next unless my $in = new IO::File($file, "<");

    my ($data, $var, $idx);
    $data .= $var while $in->read($var, 1024);

    new IO::File(sprintf('%s_struct%02d.txt', $file, ++$idx), ">")->write($_) for $data =~ /(RTON.*?DONE)/gs;
}