/ 
Chemistry-Ring-0.17
River stage one • 4 direct dependents • 7 total dependents
/ Chemistry::Ring::Find

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 containg $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).

VERSION

0.17

SEE ALSO

Chemistry::Ring, http://www.perlmol.org.

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

Copyright (c) 2004 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.