If you write out your molecules as SMILES strings, what do they look like?
It's possible you are missing some bonds.
On 24 October 2017 at 17:41, <peng...@yandex.com> wrote:
> Hi,
>
> I'm wondering how I can match hydronium ions (H3O+) and H5O2+ using SMARTS
> with
> OpenBabel. I created the OBMol object with only atomic number and
> coordinates
> information, and I tried using "[#8](~[#1])(~[#1])~[#1]",
> "[#8+](~[#1])(~[#1])~[#1]", and "[OH3+]" but none of them produced any
> matches.
> If I set atomic number for oxygen atoms to 6 (pretending they are carbon)
> when
> creating OBMol, and use "[#6](~[#1])(~[#1])~[#1]", then it does match
> successfully. Is there anything I'm doing wrong here?
>
> Thanks very much!
>
> Peng
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
