Ivan Tubert-Brohman

NAME

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

SYNOPSIS

    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
    Chemistry::Ring::aromatize_mol($mol);

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

DESCRIPTION

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 Chemistry::Ring::Find.

This module is part of the PerlMol project, http://www.perlmol.org/.

METHODS

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

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

$ring->centroid

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

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 Math::VectorReal object.

$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.

EXPORTABLE SUBROUTINES

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

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 versions).

VERSION

0.20

SEE ALSO

Chemistry::Mol, Chemistry::Atom, Chemistry::Ring::Find, Math::VectorReal.

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

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.




Hosting generously
sponsored by Bytemark