Subject: RE:Ring perception algorithms

From: [email-masked] (Marvin Waldman)
Date: Wed, 29 Mar 1995 09:29:27 -0800

There are dozens (maybe hundreds) of papers in the chemical information
literature on this subject.  A recent paper on the topic with a
rather clever new algorithm for this problem is:

"Efficient Exact Solution of the Ring Perception Problem", R. Balducci
and R.S. Pearlman, J. Chem. Inf. Comput. Sci., pp. 822-831, vol. 34, (1994).

It has many references to earlier algorithms for dealing with ring
perception.  You will find that most of the effort in these algorithms
is devoted to finding what is known as the SSSR which stands for
Smallest Set of Smallest Rings.  The problem of finding whether or
not a bond is a ring bond is a much easier problem to solve which almost
all of these algorithms do as part of their approach to finding the
SSSR.  An algorithm I found reasonably straightforward to implement
and is also reasonably efficient with regard to locating all the
ring bonds in the molecule in one pass through the connectivity tree
is:

"An Algorithm for the Perception of Synthetically Important Rings",
J. Gasteiger and C. Jochum, J. Chem. Inf. Comput. Sci., pp. 43-48,
vol. 19, (1978).

Regards,

Marvin Waldman, Ph.D.
Director, Rational Drug Design
Biosym Technologies, Inc.
e-mail: [email-masked]