use warnings;
use strict;
use XML::LibXML;

my $xml = <<'EOT';
<root>
<REGION seq_beg="1" pdb_beg="2"  seq_end="3"  pdb_end="4"  type="1"/>
<REGION seq_beg="5" pdb_beg="6"  seq_end="7"  pdb_end="8"  type="2"/>
<REGION seq_beg="9" pdb_beg="10" seq_end="11" pdb_end="12" type="3"/>
</root>
EOT
my $topo_initial = "ABCDEFGHIJK";
my $side1 = "x";
my %opposite = ( x => "?" );

my $dom = XML::LibXML->load_xml(string => $xml);
for my $node ($dom->findnodes('//REGION')) {
	my $offset = $node->{seq_beg} - 1;
	my $length = $node->{seq_end} - $node->{seq_beg} + 1;
	if ( $node->{type}==1 ) { 
		substr($topo_initial, $offset, $length, ($side1 x $length) );
	}
	elsif ( $node->{type}==2 ) { 
		substr($topo_initial, $offset, $length, ($opposite{$side1} x $length) );
	}
	else { 
		substr($topo_initial, $offset, $length, ('U' x $length) );
	}
}

use Test::More tests=>1;
is $topo_initial, "xxxD???HUUU";