Ok, bear with me. I have used the suggestion:

my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>$ARGV[0]
+);
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Which works (and I'm ignoring several filehandle warnings). Now, I have written a shell script:

#!/bin/bash
while read DSSPLine ; do
echo $DSSPLine
DSSP_Output.pl $DSSPLine.dssp
done
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QUESTION: In each interation, the output of DSSP_Output.pl is written to a CSV file. Is there a way such that (in perl) this output is written for all 30,000 iterations to one file only?

The very obvious answer is to use a DSSP array like you mentioned, I have tried that (in a way):

use strict; # 'use strict' requires that you use 'my' for all local va
+riables, 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...
}
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But when I do this, and run the commandline with a txt file of the DSSP filenames:

 DSSP_Output.pl DSSP_codes.txt

I get an exception!

Please let me know what you think...apologies for all the headache...

A <slowly deconfusing> InfoSeeker