Each atom has 3 positions.
You could use an associative array (i.e. hash) of positions (e.g. (x => $x, y => $y, z => $z)), but that's probably overkill.
Each atom can easily be represented by an array of positions (e.g. ($x, $y, $z)).

Each helix is made of atoms.
If you wish to name your atoms, a helix can easily be represented by an associative array (i.e. hash) of atom (e.g. (K => $atom0, L => $atom1, M => $atom2)).
If numerical indexes are sufficient identification for atoms, each helix can easily be represented by an array of atom (e.g. ($atom0, $atom1, $atom2)).
Let's go with names, since you already have names for them. 

my %helix1 = (
   A => [ -1.115,  8.537,  7.075 ],
   B => [ -2.745,  5.280,  7.165 ],
   C => [ -0.777,  3.267,  7.329 ],
   D => [  1.610,  5.225, 10.885 ],
   E => [  0.296,  5.263, 10.912 ],
);

my %helix2 = (
   K => [ -0.696, 13.041, 22.357 ],
   L => [  1.152, 11.081, 23.082 ],
   M => [  2.200, 17.590, 18.424 ],
);

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Each distance is has two index (the 'from' atom in the first helix and the 'to' atom in the second helix), so you'll need a 2D structure. We (I) decided above to use named atoms, so your distance map will be a 2D hash (e.g. $distance{A}{K} = distance($helix1{A}, $helix2{K});).

To populate %distance, think nested foreach loops. Good luck!

In reply to Re: confused with distances by ikegami
in thread confused with distances by Anonymous Monk

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