You wrote that:

The way my program runs, is that, while it reads in the file, for every new residue it reads in, it iterates through the list currently in memory (avoiding residues in the same chain of course) to look for new interactions

A lowly novice takes a brave step in offering advice... Not as a Perl guru (haven't been writing it long enough to qualify for that lofty title... just as someone who works with clinical data a bit, and learned Perl while doing it...

One thing that instantly popped into my mind was to consider using associative arrays, rather than having to 'iterate through a list in memory'.

Since you have a large set of potential, non-sequential items to compare, you can save a great deal of time by not having to bother searching through a list, and just index the associative array by the residue types.

Maybe set up the residue array, and just concatenate new residue interactions as you come across them, then write when you're done in one fell swoop?

I can't offer anything else off the top of my head... code sample would definately help, though.

Trek

In reply to Re: Iteration speed by TrekNoid
in thread Iteration speed 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.