10 May 2009 21:14:18 UTC
- Distribution: Chemistry-Ring
- Module version: 0.20
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- Latest versionITUB Ivan Tubert-Brohman
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 $ring->is_aromatic; # "aromatize" a molecule Chemistry::Ring::aromatize_mol($mol); # get the rings involving an atom (after aromatizing) my $rings = $mol->atoms(3)->attr('ring/rings');
This module provides some basic methods for representing a ring. A ring is a subclass of molecule, because it has atoms and bonds. Besides that, it has some useful geometric methods for finding the centroid and the ring plane, and methods for aromaticity detection.
This module does not detect the rings by itself; for that, look at Chemistry::Ring::Find.
This module is part of the PerlMol project, http://www.perlmol.org/.
- Chemistry::Ring->new(name => value, ...)
Create a new Ring object with the specified attributes. Same as
Returs a vector with the centroid, defined as the average of the coordinates of all the atoms in the ring. The vecotr is a Math::VectorReal object.
- my ($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.
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.
Nothing is exported by default, but you can export these subroutines explicitly, or all of them by using the ':all' tag.
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).
Ivan Tubert-Brohman <email@example.com>
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.
Module Install Instructions
To install Chemistry::Ring, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Chemistry::Ring
For more information on module installation, please visit the detailed CPAN module installation guide.