This code has more than a few problems. It's important to "keep your eye on the ball", so to speak, when programming. I use that term to stand in for the process of knowing where your data is, what it looks like, what variables hold what at each point while progressing through the code. The code above sort of takes guesses at what might be happening. For one thing, what do you think "$AA(@AA)" contains (you can print it to find out, and it will surprise you).

Here's one way to do it that will work for inputs that have a combination of upper case and lower case amino acids.

#!/usr/bin/env perl

use strict;
use warnings;

my %MWs;

#create the hash MWs with the amino acids and their molecular weight.

%MWs = (
    "A" => 71.1,    "D" => 115.0,    "F" => 146.1,    "H" => 137.1,
    "K" => 128.1,   "M" => 131.1,    "P" => 97.1,     "R" => 156.1,
    "T" => 101.1,   "W" => 186.2,    "C" => 103.1,    "E" => 129.1,
    "G" => 57.1,    "I" => 113.1,    "L" => 113.1,    "N" => 114.1,
    "Q" => 128.1,   "S" => 87.1,     "V" => 99.1,     "Y" => 163.1,
);

my $sum = 0.0;

print "Type amino acids. Hit [ctrl]-D when done.\n";

while ( my $line = <STDIN> ){
    chomp $line;
    next unless length $line;
    $sum += $MWs{$_} foreach
        grep {exists $MWs{$_}}
        map  {uc}
        split //, $line;
}

print "Molecular weight of this peptide is: $sum \n"

[download]

Dave

In reply to Re: MOLECULAR WEIGHT SUM by davido
in thread MOLECULAR WEIGHT SUM by mbgbioinfo

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.