You dont tell us what $ref is, so I'll assume that is is some primary key in a flat database. From the PDB format spec , each atom has one chainID and one resSeq, which I guess you are calling resNumber.

So I'd rejig the data strucure as 

foreach my $ref (keys %$data){
   if($data->{$ref}->type eq 'ATOM'){
      my $atom = $data->{$ref}->atom;
      $self->{$ref}{atoms} = $atom;
      $self->{$ref}{'residues'} = $atom->resNumber;
      $self->{$ref}{'chain'} = $atom->chainId;
   }
}

[download]
Using this, one can still step through chainIDs and resNumbers by extracting all $ref keys.

-Mark

In reply to Re: Optimizing PDB data structures by kvale
in thread Optimizing PDB data structures by seaver

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