Ah, I see your goal now. I have two answers to your problem.

The first is to simply ignore this possible speed optimization. If you are picking one of two chains, use 

foreach my $ref (keys %$self){
   next unless $self->{$ref}{'chain'} = 1;
   # process chain 1 atoms 
}

[download]
The cost of looping and one nested dereference is probably negligible compared with the other processing you need to do, so don't waste your time on it until you have verified that this is a bottleneck and that the slowdown matters to you.

If the bottleneck is a real problem, you will have to promote the variables you will subset on and create a more ugly data structure: 

foreach my $ref (keys %$data){
   next unless $data->{$ref}->type eq 'ATOM';
   my $atom = $data->{$ref}->atom;
   $self->{$atom->chainId}{$ref}{atoms} = $atom;
   $self->{$atom->chainId}{$ref}{'residues'} = $atom->resNumber;
}
# ...
foreach my $ref (keys %{$self->{1}}) {
   # process chain 1 atoms
}

[download]
With an extra dereference per atom, I am not convinced that this will be noticably faster.

-Mark

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

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.