On Mon, Mar 19, 2012 at 2:58 AM, Fredrik Wallner <fred...@wallner.nu> wrote:
> No, Geoff is right. Taken from the Daylight manual at
> http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
>
> All SMILES expressions are also valid SMARTS expressions, but the
> semantics changes because SMILES describes molecules whereas SMARTS
> describes patterns. The molecule represented by a SMILES string is usually,
> but not always, matched by the same string when used as a SMARTS
>
> On the other hand, openbabel doesn't seem to handle multi component
> SMARTS, possibly due to the fact that the dot requires some special
> handling. So if you strip salts or something similar to only search for the
> largest fragment of your input molecule it should work fine.
>
No, it's not because it requires special handling. It's just a plain old
bug. There was a serious design flaw in the original code that caused a
core dump with dot-disconnected SMARTS, and fixing it would have required a
major rewrite. Nobody has had the time to do the rewrite, so we just put
code into the SMARTS matcher that blocks dot-disconnected SMARTS.
Craig
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