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<p>Describing your problem in terms that only another biochemist will understand means that most of us here will only be able to guess at what your program needs to do.
<ul><li>What do <i>co-ordinates for mulit-chain proteins</i> look like?
</li><li>What does an <i>interaction between each of the residues</i> look like and how do you <i>calculate</i> it?
</li></ul>
<p>The best way to speed up iteration is to avoid iterating. Lookups are fast.
<p>If your dataset is too large to fit in memory forcing you to re-read files, then the first pass I would make is to avoid having to re-parse the files each time. A pre-processing step that parses your files into convenient data structures and then writes these to disk in [pack]ed or [cpan://Storable] binary format would probably speed up the loading considerably.
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<div>Examine what is said, not who speaks.</div>
"Efficiency is intelligent laziness." -David Dunham<br />
"Think for yourself!" - [Abigail-II|Abigail] <br />
"Memory, processor, disk in that order on the hardware side. Algorithm, algoritm, algorithm on the code side." - [tachyon]<br />
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