Sorting functions are not that hard - don't be afraid, read the docs, try a simple one or two.

However the logic on something like this can get involved. I often like to transform the original value into a string that will sort easily using a very simple sort function.

In this case, I transform all atoms into a string that will sort ascabetically. A regex matches the different components of the name. Then we look up the sort values from a couple of handy hashes. Fill in default values (no value for a component means sort early).

Caveat: I know nothing about atoms, so I'm working purely from your description. I've two weighting hashes in the script. The one called 'main' doesn't correspond exactly to the 'main chain' bits described, but rather corresponds to the bit that isn't a greek or number part.

Well, the explanatory paragraph may not make sense, but hopefully the code will be clearer: 

#!/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->AtomNam
+e ) } @unordered;

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

[download]

Which gives: 

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

[download]

In reply to Re: sorting according to greek alphabet in roman letters by qq
in thread sorting according to greek alphabet in roman letters by seaver

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