On Tue, Oct 8, 2013 at 10:27 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:
> On 10/08/2013 11:35 AM, Geoffrey Hutchison wrote:
>
> > I'm willing to hear suggestions as far as SMILES and InChI limits,
> > but I don't even know if a 1000-atom SMILES would be particularly useful.
> That, plus the potential for overwhelming the computer (i.e., the
> computer would "hang" while it computes the SMILES and InChI) were the
> reason for these particular limits.
>
I don't know about InChI, but there's no reason for a 1000-atom limit for
SMILES. Parsing a SMILES is an O(N) process. You just read the string and
build the molecule. That's probably true of just about every parser except
for those that have to deduce bonds from atom coordinates.
The exception to this claim is aromaticity detection. And that has little
to do with SMILES; parsing any molecule could trigger the aromaticity
algorithm.
If there needs to be a limit, it could be on the number of rings in a ring
system (a group of rings that all share at least one atom with other rings
in the group). But even that shouldn't be a problem any more. I rewrote
the aromaticity-detection algorithm a couple years ago to use a
breadth-first, fail-early strategy (rather than the original which was
essentially random trial-and-error), and it's orders of magnitude faster
for very large ring systems such as fullerenes.
Craig
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