#!/usr/bin/perl -w

use strict;

my @unordered = qw( 
  2HB 3HB C CA CB CG CD1 
  CD2 CE1 CZ CE2 HE2 HE1
  HH HD1 HD2 N O OH
);

# weighting hashes
my %main = (
  N => '1',
  CA => '2',
  C => '3',
  O => '4', 
  S => '5',
  P => '6',
  H => '7',
);

my %greek = (
  B => '1',
  G => '2',
  D => '3',
  E => '4',
  Z => '5',
  H => '6', 
);

sub sortable {
  my $atom = shift;

  # get components
  $atom =~ /(\d)?(N|CA|C|O|S|P|H)(B|G|D|E|Z|H)?(\d)?/;
  my ($left,$main,$greek,$right) = ( $1, $2, $3, $4 );

  # get weights or use default early sorting values
  $main = $main ? $main{ $main } : '0';
  my $main_alone; # need to flag if main element is alone
  if ( $greek ) {
    $main_alone = '1';
    $greek = $greek{ $greek };
  } else {
    $main_alone = '0';
    $greek = '0';
  } 
  $left  ||= '0';
  $right ||= '0';

  # I assume that left numbers take precedence over right
  "$main_alone$main$greek$left$right";   
}

# use the string "cmp" operator - we are comparing strings,
# not numbers. We could have populated
# the weighting hashes with letters instead of numbers

my @ordered = sort { sortable( $a ) cmp sortable( $b ) } @unordered;

# if you have to get the value out of an object it would be:
# @ordered = sort { sortable( $a->AtomName ) cmp sortable( $b->AtomName ) } @unordered;

print join "\n", map { $_ ."\t". sortable( $_ ) } @ordered;


##</code><code>##

N       01000
CA      02000
C       03000
O       04000
CB      13100
CG      13200
CD1    13301
CD2    13302
CE1     13401
CE2     13402
CZ      13500
OH      14600
2HB     17120
3HB     17130
HD1     17301
HD2     17302
HE1     17401
HE2     17402
HH      17600