#!/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 @anchors = $p->look_down(_tag => q{a});
for my $anchor (@anchors){
  my $txt = $anchor->as_text;  
  if ($txt=~ /EPE\s/){
    print $txt, qq{\n};
    my $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.... 
my $i=1;
for my $href(@href) {my $url4= "http://www.ebi.ac.uk$href[$i];
$content=get($url4);
$i=$i+1;
}
}
}
$p->delete;

$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});
    my $txt4 = $href0->as_text;  
    if ($txt4=~ /ligplot\d\d_\d\d'/){
    print $txt4, qq{\n};
    
push @href0, $txt4;
 }
}
$p->delete;
};
my $u=1;
foreach $txt4(@href0){
my $url5= "http://www.ebi.ac.uk$txt4[$u]";
$u=$u+1;


#I need to download every file of EPE (as http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunLigplot.pl?pdb=2j6p&file=ligplot04_01 and http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunLigplot.pl?pdb=2j6p&file=ligplot04_02) in this case, these are my $url5
use LWP::Simple;
my @files = (["$url5", "2j6p.$u.pl"],
         ["http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetText.pl?pdb=2j6p&chain=A&seq_fasta=1?pdb=2j6p&chain=A&seq_fasta=1", "$path/$Dir/2j6p.seq.fasta"]
);  
for my $duplet (@files) {
    mirror($duplet->[0], $duplet->[1]);
}