#!/usr/bin/perl
use strict;
use warnings;

my @helix;
while ( <DATA> ) {
    chomp;
    next if /^\s*$/;
    if (/^([^:]+):/) {               # Start of new HELIX definition
        push @helix, { name => $1 }; # Anonymous hash with 1 element (name)
        next;
    }

     # Atom definition
    if (/^\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s*/) {
        push @{$helix[-1]{atom}}, {name => $1, id => $2, x => $3, y => $4, z => $5 };
    }
}

# Go through @helix in order
for my $i (0 .. $#helix - 1) {
    print "Comparing helix $helix[$i]{name}\n";
    my @atom_1 = sort { $a->{id} <=> $b->{id} } @{$helix[$i]{atom}};

    for my $j ($i + 1 .. $#helix) {
        print "\tAgainst helix $helix[$j]{name}\n";
        my @atom_2 = sort { $a->{id} <=> $b->{id} } @{$helix[$j]{atom}};
        for my $a1 (@atom_1) {
            for my $a2 (@atom_2) {
                my $distance = distance($a1, $a2);
                print "\t\tDistance between $a1->{name} and $a2->{name} is $distance\n";
            }
        }
    }
    print "\n\n";
}

sub distance {
    my ($a1, $a2) = @_;
    my $delta_x = ($a1->{x} - $a2->{x}) ** 2;
    my $delta_y = ($a1->{y} - $a2->{y}) ** 2;
    my $delta_z = ($a1->{z} - $a2->{z}) ** 2;
    return sqrt($delta_x + $delta_y + $delta_z);
}

__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