#!/usr/local/bin/perl
use strict;
use warnings;
use LWP::Simple;


my $url3 = "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2j6p&template=ligands.html&l=1.1";
my $content =get ($url3);

use HTML::TreeBuilder;
my $p = HTML::TreeBuilder->new;
$p->parse_content($content);
my @href;
my $href;
my @anchors = $p->look_down(_tag => q{a});
for my $anchor (@anchors)
	{
  	my $txt = $anchor->as_text;  
  	if ($txt=~ /EPE\s/)
		{
    		print $txt, qq{\n};
    		$href = $anchor->attr(q{href});
    		print $href, qq{\n};
 		chomp ($href);
		push @href, $href;
 #now I need to go to the link where there are my EPE ligand and then parse and extract the link of the RunLigplot.pl that is the output of a program LigPlot, written in perl, is a postcript, and I need that file as a script to extract info....I need to repeat these parsing for every link,for every EPE.... 
		}
	}
$p->delete;

for my $param ( @href )
	{
	my $content = get ( "http://www.ebi.ac.uk$param" );
	process_content ($content); # << This is missing from your code !!!
	}

sub process_content
	{
	my $content = shift;
	$p = HTML::TreeBuilder->new;
	$p->parse_content($content);
	my @href0;
	my @anchors0 = $p->look_down(_tag => q{a});
	for my $anchor0 (@anchors0)
		{
		my $href0 = $anchor0->attr(q{href});
		  
		if ($href0=~ /ligplot\d\d_\d\d'/)
		{
    		print $href0, qq{\n};
    		push @href0, $href0;
		for my $param0 ( @href0 )
			{
  			$content = get ( "http://www.ebi.ac.uk$param0" );
        		my $content = shift;		
			print my $param0;
			#I need to download files from every link $param0...
my @files = (["http://www.ebi.ac.uk$param0", "$pdb.$param0.pl"],
);  
for my $duplet (@files) {
    mirror($duplet->[0], $duplet->[1]);
}			
			}
	$p->delete;

	}
}
 
 }