my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>$ARGV[0]);

##</code><code>##

#!/bin/bash
while read DSSPLine ; do
echo $DSSPLine
DSSP_Output.pl $DSSPLine.dssp
done

##</code><code>##

use strict; # 'use strict' requires that you use 'my' for all local variables, or explicitely qualify all globals.
use warnings;
use Bio::Structure::SecStr::DSSP::Res;

my @dssp_objs =();
foreach my $file (@ARGV)
{
push @dssp_objs, Bio::Structure::SecStr::DSSP::Res->new('-file'=>$file);
}

foreach my $dssp_obj(@dssp_objs)
{
#Get PDB ID and Compound representation for each file
my $pdb_id = $dssp_obj->pdbID();
print "Analysis of PDB:: ". $pdb_id. "\n";
my $cmpd = $dssp_obj->pdbCompound();
print "Representing:: ". $cmpd. "\n";
etc...
}