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 | OEChem - Python Theory Manual
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| OEChem - Python Theory Manual
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In 1968, Edsger Dijkstra, one of the great pioneers of computer science, wrote a classic paper, "Go To Statement Considered Harmful", Communications of the ACM, Vol. 11, No. 3, pp. 147-148, March 1968. The first sentence of that paper contains "the observation that the quality of a programmer is a decreasing function of the density of GOTO statements in the programs they produce". This paper had such dramatic impact that 35 years later most programmers know they should avoid using "GOTO", but would have difficulty explaining why.
Dijkstra's argument was not that GOTO was evil per se, but that it
showed that the programmer probably had given the problem enough
thought to discover a cleaner, more elegant solution without its use.
This argument is equally valid for the "Smallest Set of Smallest
Rings" in chemical information processing. The use of SSSR probably
shouldn't be forbidden, but it is almost always used in algorithms for
which it is inappropriate. Both the relatively high computational
cost, 
, and the non-deterministic ambiguity in choosing SSSR
membership lead to real bugs in almost all chemoinformatics uses.
Indeed, the OEChem library itself demonstrates that it's possible to
develop state-of-the-art algorithms for cycle perception, aromaticity
perception, symmetry perception and 2D depiction, without once using
SSSR.
The fundamental problem is that Plotkin's original definition of Smallest Set of Smallest Rings is not unique. For example, the molecule cubane, has five rings in its SSSR, as determined by the Frèrejacque number (no. of rings = no. of bonds - no. of atoms + 1). This means that although all eight atoms are symmetric, four will be members of three SSSR rings and four will be members of two SSSR rings. Obviously SSSR membership can't be used as a graph theoretical invariant in symmetry perception. Indeed the choice of which rings are part of the SSSR and which aren't is arbitrary, and often dependent upon the input order of the molecule. For example, in aromaticity the non-determinism of ring membership can result the same atom being aromatic in one input ordering and aliphatic in another. Because of this many alternative definitions to SSSR have been proposed over the years, including Extended SSSR, the set of "synthetically important" rings, K-rings, etc...
We believe that it is a great service to our customers that we do not include any SSSR functionality in OEChem. This is a conscious decision. The forerunners of OEChem, babel and OELib, both contained efficient algorithms for determining SSSR, and these remain freely available on the Internet today. Furthermore, many useful ring perception routines are available in OEChem including; the ability to determine whether an atom or bond is acyclic or part of a ring, the smallest ring size that an atom or bond are in, the size of the smallest aromatic ring an atom or bond are in, and whether an atom or bond are in a ring of a particular size.
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| OEChem - Python Theory Manual
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