I have taken the liberty of responding on the public list. My apologies if you
did mean this as private, but I don't think that was the case.
On Dec 17, 2009, at 3:21 AM, Abhinav Chawade wrote:
> My question is, when a SMILES is parsed, how does the parser detect atoms
> which are in the ring? Looking at SMILES, it's easy to detect start and end
> of the ring. But how to detect all the other atoms which are part of the
> ring? What algorithm can be used to detect these atoms?
In SMILES in general is is not easy to determine which atoms are the start and
end of the ring. Some rather unusual SMILES are possible, like
CC1.CCC12CC.CC2
which contains no cycles. No one writes these sort of SMILES in real life.
There are two questions here. One is identifying ring bonds for a ring closure,
as needed to generate the SMILES, can be done in O(n) time. That's done with a
depth first search and if a bond goes to an atom which has already been visited
then it is a ring bond and everything in the current stack (up to where the
ring bond connects) is in the ring.
Many of the toolkits need to find not just which atoms and bonds are in a ring
but also identify the rings themselves. Cubane, for example, has lots of
different ways to make up the rings. The goal is often to find the Smallest Set
of Smallest Rings (SSSR). The code in RDKit is in GraphMol/FindRings.cpp and
this is the reference:
/*******************************************************************************
* SUMMARY:
* this again is a modified version of the BFS algorihtm in Figueras paper
to find
* the smallest ring with a specified root atom.
* JCICS, Vol. 30, No. 5, 1996, 986-991
* The follwing are changes from the original algorithm
* - find all smallest rings around a node not just one
* - once can provided a list of node IDs that should not be include in the
discovered rings
Andrew
[email protected]
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