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
