On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
>> For most "ordinary" molecules, the LSSR is the same as the SSSR. The LSSR
>> and
>> SSSR only differ with "cage" structures, where the rings themselves form
>> rings,
>> i.e. when there exists a set of R rings that "covers" all atoms, but R is
>> fewer
>> than the number of bonds that must be broken to make the structure acyclic.
>> And
>> in these cases, the choice of rings for the SSSR is arbitrary, whereas the
>> LSSR is not.
>
> I don't follow the part about number of bonds that must be broken to
> make the structure acyclic. Do you mean closure bonds? Regardless, we
> probably mean the same thing with LSSR.
By "rings form rings," I mean structures like cubane. For cubane you can find
four rings that together include every atom and bond, but you have to break at
least five bonds to make the structure acyclic. Any structure that can be
constructed by creating a "ring of rings" has this problem. For example, with
cubane you can imagine laying out four rectangles side by side (SSSR=4), and
then folding it into a cube. You've made a ring out of a set of existing rings.
The LSSR algorithm is simple:
for S in (3, 4, 5, 6, ...)
find all rings of size S, add to LSSR
if all cyclic atoms and bonds are included in at
least one ring in the LSSR, quit
It's nice because a breadth-first ring-finder algorithm naturally finds rings
from smallest to largest. You don't waste any time finding even one ring
larger than the largest ring in the LSSR.
The other nice thing about an LSSR is that there is only one possible set of
rings, so canonicalizing the order within the set is easy: smallest-to-largest,
and within each size, use the atom labeling that canon.c provides (you don't
even need to run the full SMILES canonicalizer, just the atom labeler).
Craig
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