1234
 N
 CA
 C
 O
 CB
 CG
 CD1
 CD2
 CE1
 CE2
 CZ
 OH
 H
2HB
3HB
 HD1
 HD2
 HE1
 HE2
 HH
             HD1 HE1
              |   |
      1HB    CD1-CE1
 H-N   |   /        \
   CA-CB-CG          CZ-OH-HH
   C   |   \        /
   O  2HB    CD2-CE2
              |   |
             HD2 HE2


##</code><code>##

#########sort atoms into three groups#########
foreach my $a (@names){
	push @main, $self->{'all'}{$a} if $self->{'all'}{$a}->mainHeavy;
	push @heavy, $self->{'all'}{$a} if $self->{'all'}{$a}->sideHeavy;
	push @proton, $self->{'all'}{$a} if $self->{'all'}{$a}->proton;
	$names{$self->{'all'}{$a}->atomName}=$a;
    }

##########do main chains, single digits############
    foreach my $a (@main){
	if($a->atomName eq 'N'){
	    $main{1}=$a;
	}elsif($a->atomName eq 'CA'){
	    $main{2}=$a;
	}elsif($a->atomName eq 'C'){
	    $main{3}=$a;
	}elsif($a->atomName eq 'O'){
	    $main{4}=$a;
	}
    }

#########Do side chain################
    my %heavyweights = ( 'C' => 1,
			 'N' => 2,
			 'O' => 3);
    my %greekweights = ( 'A' => 1,
			 'B' => 2,
			 'G' => 3,
			 'D' => 4,
			 'E' => 5,
			 'Z' => 6,
			 'H' => 7 );
    
    foreach my $a (@heavy){
	$main{$heavyweights{$a->atomEl}.$greekweights{$a->atomRemote}} = $a;
    }

####Do protons############
#I actually used 4 digits, because of the proton quanitifier #itself
    foreach my $a (@proton){
	print $a->atomName;
	my $n = '9';
	$n .= $greekweights{$a->atomRemote} if $a->atomRemote;
	$n .= 0 unless $a->atomRemote;
	$n .= $a->atomBranch if $a->atomBranch;
	$n .= 0 unless $a->atomBranch;
	$n .= $a->hydNumber if $a->hydNumber;
	$n .= 0 unless $a->hydNumber;
	$main{$n} = $a;
    }

    foreach my $i ( sort{ $a<=>$b } keys %main ){
	print $main{$i}->atomName." $i\n";
	push @result, $main{$i};
    }
__END__

N 1
CA 2
C 3
O 4
CB 12
CG 13
CD 14
NE2 25
OE1 35
H 9000
HA 9100
HB 9202
HB 9203
HG 9302
HG 9303
HE2 9521
HE2 9522