On Tue, Oct 21, 2014 at 6:12 AM, John May <john.wilkinson...@gmail.com>
wrote:
> > That's all I know about that key definition.
>
> Likewise - I’ve seen in a few places but not aware if it’s truly correct.
>
> Extending OB SMARTS to handle component level grouping shouldn’t be too
> much work. The parser just needs to label the components of the pattern.
> The matcher can then check this post match (same as stereochem is
> implemented) by labelling the connected components.
There is a design flaw way down deep in the SMARTS parser that makes it
segfault when you give it a dot-disconnected SMARTS of any sort. My
recollection is that when I discovered this bug, it was so fundamental to
the matching algorithm that fixing it required a pretty major rewrite. So
we decided to just reject SMARTS with dots in them until someone had lots
of time to rewrite the SMARTS matching algorithm.
As a crude and very dissatisfying work-around, I recently wrote a wrapper
that breaks a SMARTS apart, does individual matches, then uses bit vectors
to find non-overlapping results. It works but is very slow.
Craig
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