Thanks Craig,
Looks like that might have been fixed.. the parser will throw an error on the
dot but actually parses and matches it okay if component grouping is specified.
The component grouping isn’t actually checked but the disconnected query
matches as expected. Might take a closer look this weekend.
J
> [john~]$ echo -e 'CC\nC.C\n' > tmp
> [john~]$ obgrep 'C.C' tmp
> ==============================
> *** Open Babel Error in SMARTSError
> SMARTS Error:
> C.C
> ^
>
> [john~]$ obgrep '(C).(C)' tmp
> CC
> C.C
On Oct 21, 2014, at 8:38 PM, Craig James <cja...@emolecules.com> wrote:
> 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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