Chemistry::Ring::Find - Find the rings (cycles) in a molecule
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);
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/>.
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.)
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).
<
https://github.com/perlmol/Chemistry-Ring>
Chemistry::Ring
Ivan Tubert-Brohman <
[email protected]>
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.