in reply to confused with distances

If there are going to be many helices, I'd use a hash of hashes, where each element is an array reference: 

$atoms{HELIX1}{A} = [ ( -1.115,   8.537,   7.075)];

[download]
#!perl

use warnings;
use strict;


my %atoms;
my $key;

while(<DATA>)
{
    chomp;
    next if /^\s*$/;

    if(/^[^\s]/){
        
        s/:.*$//;

        $key = $_;

        print "\$_: $_\n","\$key: $key\n";
    }
    else{
        s/^\s*|\s*$//g;
        (my $sub, my $idx,my $x, my $y,my  $z) = split(/\s+/,$_,5);
        print "\t\$_: $_\n","\t\$sub: $sub\n\txyz",join(", ", ($x, $y,
+ $z)),"\n";
        $atoms{$key}{$sub} = [ (+$x, +$y, +$z)]; # force numerical con
+text
        }
}

__DATA__
HELIX1:                   x       y       z
           A     1      -1.115   8.537   7.075
           B     2      -2.745   5.280   7.165
           C     3      -0.777   3.267   7.329
           D     4       1.610   5.225  10.885
           E     5       0.296   5.263  10.912

HELIX2:
           K     1      -0.696  13.041  22.357
           L     2       1.152  11.081  23.082
           M     3       2.200  17.590  18.424

[download]

While the above code is, doubtless, is less elegant and otherwise inferior to what those monks more fluent in Perl than I would write, it will process a small amount of data (say a few thousand points). Now, why would your assignment be to calculate the square of the distance: R2 = ∑(xi − xj)2?

Do you really mean: R = √∑(xi − xj)2?

emc

" The most likely way for the world to be destroyed, most experts agree, is by accident. That's where we come in; we're computer professionals. We cause accidents."
—Nathaniel S. Borenstein

In Section Seekers of Perl Wisdom