As I understand , you only want unique chains , you can do this with minimum effort:
1 #!/usr/local/bin/perl
2 use strict;
3 use warnings;
4 use LWP::Simple;
5 use HTML::TreeBuilder::XPath;
6 use Data::Dumper;
7 use feature 'say';
8 my $url="http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsu
+m/GetPage.pl?pdbcode=1r9t&template=main.html";
9
10 my $p = HTML::TreeBuilder::XPath->new_from_content(get($url));
11
12 my @chain_tags = $p->findnodes("//td//a[contains(\@href,'chain=')]
+");
13 my $uniq_chains = { map { $_->attr('href') =~ /chain=(\w)/; ($1,1)
+; } @chain_tags };
14 say " Number of chains : " . scalar keys %$uniq_chains;
15 say keys %$uniq_chains;