NAME

       Chemistry::Ring::Find - Find the rings (cycles) in a molecule

SYNOPSIS

           use Chemistry::Ring::Find ':all';

           # find the smallest ring containing $atom
           my $ring = find_ring($atom);

           # find all the rings containing $bond
           my @rings = find_ring($bond, all => 1);

           # see below for more options

           # find the six 4-atom rings in cubane
           @rings = find_rings($cubane);

           # find a cubane SSSR with five rings
           @rings = find_rings($cubane, sssr => 1);

DESCRIPTION

       The Chemistry::Ring::Find module implements a breadth-first ring finding algorithm, and it
       can find all rings that contain a given atom or bond, the Smallest Set of Smallest Rings
       (SSSR), or the "almost SSSR", which is an unambiguous set of rings for cases such as
       cubane.The algorithms are  based on ideas from:

       1) Leach, A. R.; Dolata, D. P.; Prout, P. Automated Conformational Analysis and Structure
       Generation: Algorithms for Molecular Perception J. Chem. Inf. Comput.  Sci. 1990, 30,
       316-324

       2) Figueras, J. Ring perception using breadth-first search. J. Chem. Inf.  Comput.  Sci.
       1996, 36, 986-991.

       Ref. 2 is only used for find_ring, not for find_rings, because it has been shown that the
       overall SSSR method in ref 2 has bugs. Ref 1 inspired find_rings, which depends on
       find_ring.

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

FUNCTIONS

       These functions may be exported explicitly, or all by using the :all tag, but nothing is
       exported by default.

       find_ring($origin, %opts)
           Find the smallest ring containing $origin, which may be either an atom or a bond.
           Returns a Chemistry::Ring object. Options:

           all If true, find all the rings containing $origin. If false, return the first ring
               found. Defaults to false. "All" is supposed to include only "simple" rings, that
               is, rings that are not a combination of smaller rings.

           min Only find rings with a the given minimum size. Defaults to zero.

           max Only find rings up to the given maximium size. Defaults to unlimited size.

           size
               Only find rings with this size. Same as setting min and max to the same size.
               Default: unspecified.

           exclude
               An array reference containing a list of atoms that must NOT be present in the
               ring. Defaults to the empty list.

           mirror
               If true, find each ring twice (forwards and backwards). Defaults to false.

       @rings = find_rings($mol, %options)
           Find "all" the rings in the molecule. In general it return the Smallest Set of
           Smallest Rings (SSSR). However, since it is well known that the SSSR is not unique for
           molecules such as cubane (where the SSSR consists of five unspecified four-member
           rings, even if the symmetry of the molecule would suggest that the six faces of the
           cube are equivalent), in such cases find_rings will return a non-ambiguous "non-
           smallest" set of smallest rings, unless the "sssr" option is given. For example,

               @rings = find_rings($cubane);
               # returns SIX four-member rings

               @rings = find_rings($cubane, sssr => 1);
               # returns FIVE four-member rings (an unspecified subset of
               # the six rings above.)

BUGS

       The "all" option in find_ring doesn't quite work as expected. It finds all simple rings
       and some bridged rings. It never finds fused rings (which is good).

SOURCE CODE REPOSITORY

       <https://github.com/perlmol/Chemistry-Ring>

SEE ALSO

       Chemistry::Ring

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.