On Mon, Sep 19, 2011 at 5:16 PM, Robert Hanson <[email protected]> wrote: > That's fixed at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > I've also made it so that c=c does not match anything ever, but I'm not 100% > sure that is correct.
Thanks a lot, I will test it soon. > > Q: What is the relationship between Daylight SMARTS and > http://opentox.informatik.uni-freiburg.de/depict ? > > 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 Its just very simple webservice that wraps the depict match service (This one: http://www.daylight.com/daycgi_tutorials/depictmatch.cgi ). The only purpose I built it for, is that I can encode a smiles-smarts-matching-query to daylight in one URI (and can send it to a mailing list, for instance). Best regards, Martin > > > > 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 > > ------------------------------------------------------------------------------ > 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
