Bug: The following do anything (useful):

$res =~/\S/g;
$domchain =~/\S/g;
$pdbchain =~/\S/g;
[download]

You want:

$res =~ s/\s//g;
$domchain =~ s/\s//g;
$pdbchain =~ s/\s//g;
[download]

Also, all over you have "$var" which needlessly makes a copy of $var. Drop the quotes. You want just $var. For example,

if("$domchain" eq "$pdbchain")
should be
if($domchain eq $pdbchain)