package Chemistry::Ring;

our $VERSION = '0.21'; # VERSION
# $Id$

=head1 NAME

Chemistry::Ring - Represent a ring as a substructure of a molecule


    use Chemistry::Ring;
    # already have a molecule in $mol...
    # create a ring with the first six atoms in $mol
    my $ring = Chemistry::Ring->new;
    $ring->add_atom($_) for $mol->atoms(1 .. 6);

    # find the centroid
    my $vector = $ring->centroid;

    # find the plane that fits the ring
    my ($normal, $distance) = $ring->plane;

    # is the ring aromatic?
    print "is aromatic!\n" if $ring->is_aromatic;

    # "aromatize" a molecule

    # get the rings involving an atom (after aromatizing)
    my $rings = $mol->atoms(3)->attr('ring/rings');


This module provides some basic methods for representing a ring. A ring is
a subclass of molecule, because it has atoms and bonds. Besides that, it
has some useful geometric methods for finding the centroid and the ring plane,
and methods for aromaticity detection.

This module does not detect the rings by itself; for that, look at 

This module is part of the PerlMol project, L<>.


use strict;
use warnings;
use Math::VectorReal qw(:axis vector);
use Statistics::Regression;
use Chemistry::Mol;
use base 'Chemistry::Mol', 'Exporter';
use Scalar::Util 'weaken';

our @EXPORT_OK = qw(aromatize_mol);
our %EXPORT_TAGS = ( all => \@EXPORT_OK ); 

our $N = 0;
our $DEBUG = 0;

=head1 METHODS

=over 4

=item Chemistry::Ring->new(name => value, ...)

Create a new Ring object with the specified attributes. Same as
C<< Chemistry::Mol->new >>.


sub nextID {

# make sure we don't become parent of the atoms added to us
sub add_atom { shift->SUPER::add_atom_np(@_) }
sub add_bond { shift->SUPER::add_bond_np(@_) }

sub print {
    my $self = shift;
    return <<EOF;
        id: $self->{id}
        atoms: @{$self->{atoms}}
        bonds: @{$self->{bonds}}

=item $ring->centroid

Returns a vector with the centroid, defined as the average of the coordinates
of all the atoms in the ring. The vecotr is a L<Math::VectorReal> object.


sub centroid {
    my $self = shift;
    my $c = O; # origin
    my $n = 0;
    for my $a ($self->atoms) {
	$c += $a->coords;
    $c = $c / $n; 

=item my ($norm, $d) = $ring->plane

Returns the normal and distance to the origin that define the plane that best
fits the atoms in the ring, by using multivariate regression. The normal 
vector is a L<Math::VectorReal> object.


sub plane {
    my $self = shift;
    my $reg;
    if( $Statistics::Regression::VERSION < 0.52 ) {
        $reg = Statistics::Regression->new(3, "plane for $self", [qw(b mx my)]);
    } else {
        $reg = Statistics::Regression->new("plane for $self", [qw(b mx my)]);
    for my $atom ($self->atoms) {
        my ($x, $y, $z) = $atom->coords->array;
        $reg->include($z, [1.0, $x, $y]);
    $reg->print if $DEBUG;

    # convert the theta vector (z = a + bx + cy) to a normal vector and
    # distance to the origin
    my @coef = (@{$reg->theta}, -1.0);   # -1 is d in a + bx + cx + dz = 0
    my $d = shift @coef;                 # distance (not normalized)
    my $sum_sq = 0;                      # normalization constant
    $sum_sq += $_*$_ for @coef;   
    $sum_sq ||= 1;
    ($d, @coef) = map { $_ / $sum_sq } ($d, @coef); # normalize
    return (vector(@coef)->norm, $d);

=item $ring->is_aromatic

Naively guess whether ring is aromatic from the molecular graph, with a method
based on Huckel's rule. This method is not very accurate, but works for simple
molecules. Returns true or false.


sub is_aromatic {
    my ($self) = @_;
    my $n_pi = 0;

    for my $atom ($self->atoms) {
        no warnings 'uninitialized';
        return 0 if ($atom->bonds + $atom->hydrogens > 3);        

        # build bond order histogram
        my @order_freq = (0,0,0,0);
        for my $bond ($atom->bonds) {
        return 0 if ($order_freq[3] or $order_freq[2] > 1);
        if ($order_freq[2] == 1) {
            $n_pi += 1;
        } elsif ($atom->symbol =~ /^[NOS]$/) {
            $n_pi += 2;
    #print "n_pi = $n_pi\n";
    return ($n_pi % 4 == 2) ? 1 : 0;




Nothing is exported by default, but you can export these subroutines
explicitly, or all of them by using the ':all' tag.


=item aromatize_mol($mol)

Finds all the aromatic rings in the molecule and marks all the atoms and bonds
in those rings as aromatic. 

It also adds the 'ring/rings' attribute to the molecule and to all ring atoms
and bonds; this attribute is an array reference containing the list of rings
that involve that atom or bond (or all the rings in the case of the molecule).
NOTE (the ring/rings attribute is experimental and might change in future


sub aromatize_mol {
    my ($mol) = @_;

    require Chemistry::Ring::Find;

    $_->aromatic(0) for ($mol->atoms, $mol->bonds);

    my @rings = Chemistry::Ring::Find::find_rings($mol);
    $mol->attr("ring/rings", \@rings);
    $_->attr("ring/rings", []) for ($mol->atoms, $mol->bonds);

    for my $ring (@rings) {
        if ($ring->is_aromatic) {
            $_->aromatic(1) for ($ring->atoms, $ring->bonds);
        for ($ring->atoms, $ring->bonds) {
            my $ringlist = $_->attr("ring/rings") || [];
            push @$ringlist, $ring;
            $_->attr("ring/rings", $ringlist);





=head1 SEE ALSO

L<Chemistry::Mol>, L<Chemistry::Atom>, L<Chemistry::Ring::Find>, 

=head1 AUTHOR

Ivan Tubert-Brohman <>


Copyright (c) 2009 Ivan Tubert-Brohman. All rights reserved. This program is
free software; you can redistribute it and/or modify it under the same terms as
Perl itself.