Hi Noel, I think you are right! I use `SetAtomicNum()`, `SetVector()` to build an OBMol atom by atom, and then call `ConnectTheDots()` to add bonds. Apparently due to valency, oxygen atoms won't have more than two bonds, hydrogen not more than one. Therefore the molecule won't ever match H3O+ or H5O2+.
How should I then approach this SMARTS matching problem? My system has regular water molecules and I have only coordinates and atomic numbers, so a priori I don't know which oxygen atoms belong to H3O+ and which hydrogen atoms are bridging hydrogen in H5O2+. I'd really appreciate your suggestions. Thanks! Best regards, Peng On 10/24/2017 3:19 PM, Noel O'Boyle wrote:
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 <mailto: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 <mailto:OpenBabel-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
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