10 May 2009 21:14:18 UTC
- Distribution: Chemistry-Ring
- Module version: 0.2
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- Latest versionITUB Ivan Tubert-Brohman
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 containg $origin, which may be either an atom or a bond. Returns a Chemistry::Ring object. Options:
If true, find all the rings containing $origin. If false, return the first ring found. Defaults to false. "All" is supposed to include only "simple" rings, that is, rings that are not a combination of smaller rings.
Only find rings with a the given minimum size. Defaults to zero.
Only find rings up to the given maximium size. Defaults to unlimited size.
Only find rings with this size. Same as setting min and max to the same size. Default: unspecified.
An array reference containing a list of atoms that must NOT be present in the ring. Defaults to the empty list.
If true, find each ring twice (forwards and backwards). Defaults to false.
- @rings = find_rings($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).
Ivan Tubert-Brohman <firstname.lastname@example.org>
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.