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
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