That's fixed at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zipI've also made it so that c=c does not match anything ever, but I'm not 100% sure that is correct.
Q: What is the relationship between Daylight SMARTS and http://opentox.informatik.uni-freiburg.de/depict<http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]>? Is that a true implementation of Daylight SMARTS, or is it one (like Jmol) that is interpreted from the (somewhat ambiguous) description at the Daylight site? What can you tell us about that site? It looks like it is returning with an official Daylight page, but is that same SMILES/SMARTS page available at Daylight? I wasn't aware of that. Looks great, though. Bob On Mon, Sep 19, 2011 at 7:18 AM, Robert Hanson <[email protected]> wrote: > Ah! I see. Right. This is a specific problem to [#n] because those cases > are ambiguous in relation to aromaticity. I'm on to it. Thanks. > > > > On Mon, Sep 19, 2011 at 2:46 AM, Martin Guetlein < > [email protected]> wrote: > >> On Mon, Sep 19, 2011 at 3:56 AM, Robert Hanson <[email protected]> >> wrote: >> > >> > Martin, >> > >> > I'm not catching on. Why isn't 7 atoms correct? There are six C-C bonds >> in the ring and one more C-C bond, 7 atoms total. >> > >> > $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H] >> > $ select smarts("[#6]-[#6]") >> > 7 atoms selected >> > $ select smarts("[#6][#6]") >> > 7 atoms selected >> > $ select smarts("[#6]=[#6]") >> > 6 atoms selected >> > >> > Right? >> > >> > Bob >> >> I think the aromatic bonds not should be matched. This is how daylight >> matches the smarts fragments: >> >> [#6]-[#6] >> >> http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236] >> >> Best regards, >> Martin >> >> >> >> > >> > On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein < >> [email protected]> wrote: >> >> >> >> >> >> On Fri, Sep 16, 2011 at 6:55 PM, Robert Hanson <[email protected]> >> wrote: >> >>> >> >>> It's working right for me: >> >>> >> >>> load $1,3-butadiene >> >>> select smarts("[#6]-[#6]") >> >>> >> >>> 2 atoms selected >> >> >> >> >> >> Thats not what I meant, it makes too many selections: >> >> >> >> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H] >> >> $ select smarts("[#6]-[#6]") >> >> 7 atoms selected >> >> >> >> Best regards, >> >> Martin >> >> >> >>> >> >>> >> >>> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein < >> [email protected]> wrote: >> >>>> >> >>>> Hi, >> >>>> >> >>>> I would like to match the following smarts [#6]-[#6], which is two >> carbon atoms connect with single bond. >> >>>> >> >>>> The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond >> type and selects all pairs of carbons, even those who are aromatic. >> >>>> >> >>>> It is not an aromticity detection problem, as 'select smarts("C-c") >> or smarts("C-C")' works fine (it does _not_ select the aromatic pairs). >> >>>> >> >>>> (Unfortunately, I cannot just use the last-mentioned expression, my >> smarts strings are created automatically and I have to stick with the >> [#<atom-number>] notation.) >> >>>> >> >>>> Best regards, >> >>>> Martin >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> Dipl-Inf. Martin Gütlein >> >>>> Phone: >> >>>> +49 (0)761 203 7633 (office) >> >>>> +49 (0)177 623 9499 (mobile) >> >>>> Email: >> >>>> [email protected] >> >>>> >> >>>> >> ------------------------------------------------------------------------------ >> >>>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> >>>> http://p.sf.net/sfu/rim-devcon-copy2 >> >>>> _______________________________________________ >> >>>> Jmol-users mailing list >> >>>> [email protected] >> >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >>>> >> >>> >> >>> >> >>> >> >>> -- >> >>> Robert M. Hanson >> >>> Professor of Chemistry >> >>> St. Olaf College >> >>> 1520 St. Olaf Ave. >> >>> Northfield, MN 55057 >> >>> http://www.stolaf.edu/people/hansonr >> >>> phone: 507-786-3107 >> >>> >> >>> >> >>> If nature does not answer first what we want, >> >>> it is better to take what answer we get. >> >>> >> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >>> >> >>> >> ------------------------------------------------------------------------------ >> >>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> >>> http://p.sf.net/sfu/rim-devcon-copy2 >> >>> _______________________________________________ >> >>> Jmol-users mailing list >> >>> [email protected] >> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >>> >> >> >> >> >> >> >> >> -- >> >> Dipl-Inf. Martin Gütlein >> >> Phone: >> >> +49 (0)761 203 7633 (office) >> >> +49 (0)177 623 9499 (mobile) >> >> Email: >> >> [email protected] >> >> >> >> >> ------------------------------------------------------------------------------ >> >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> >> http://p.sf.net/sfu/rim-devcon-copy2 >> >> _______________________________________________ >> >> Jmol-users mailing list >> >> [email protected] >> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> > >> > >> > >> > -- >> > Robert M. Hanson >> > Professor of Chemistry >> > St. Olaf College >> > 1520 St. Olaf Ave. >> > Northfield, MN 55057 >> > http://www.stolaf.edu/people/hansonr >> > phone: 507-786-3107 >> > >> > >> > If nature does not answer first what we want, >> > it is better to take what answer we get. >> > >> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> > >> > >> ------------------------------------------------------------------------------ >> > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> > Learn about the latest advances in developing for the >> > BlackBerry® mobile platform with sessions, labs & more. >> > See new tools and technologies. Register for BlackBerry® DevCon >> today! >> > http://p.sf.net/sfu/rim-devcon-copy1 >> > _______________________________________________ >> > Jmol-users mailing list >> > [email protected] >> > https://lists.sourceforge.net/lists/listinfo/jmol-users >> > >> >> >> >> -- >> Dipl-Inf. Martin Gütlein >> Phone: >> +49 (0)761 203 7633 (office) >> +49 (0)177 623 9499 (mobile) >> Email: >> [email protected] >> >> >> ------------------------------------------------------------------------------ >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> Learn about the latest advances in developing for the >> BlackBerry® mobile platform with sessions, labs & more. >> See new tools and technologies. Register for BlackBerry® DevCon today! >> http://p.sf.net/sfu/rim-devcon-copy1 >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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