On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> Bob,
>
> There is a general aromatic problem that I'm having with find SMILES
> that's easiest to explain with a specific scenario. If I load benzene
> and run "var x={*}.find('SMILES');echo @x," I get:
>
> c1=cc=cc=c1
>
> If I use model kit mode to make 1,3-cyclohexadiene, the same "var
> x={*}.find('SMILES');echo @x" produces
>
> c1=cc=ccc1
>
>
I'll look into that. Almost certainly a bug. It should only use lower case c
if the ring is totally flat and there are no sp3 centers. I'm really
surprised it's doing that. The code is only supposed to insert lower case
"c" when:
-- the ring is flat
-- the ring has no sp3 centers
Is it possible you are sending it a flat no-hydrogen ring? When I use the
model kit, I get:
C1=CCCC=C1
> I'm now stuck in lower case "c" mode on this ring no matter what I do to
> the ring. If I break a ring bond while the ring is no longer aromatic
> and reform the bond, I go back to upper case "C"
>
>
remember -- "aromatic" just means "flat and all sp2" for Jmol. We're not
going to get into multiple bonding issues. There's no "antiaromatic" here.
It doesn't matter if you have 6 carbons and all single bonds or 6 carbons
and all double bonds or 8 carbons (as in octadienyl dianion ligand). As long
as it's flat and there aren't any tetrahedrally directed substituents, Jmol
is going to use "c" instead of "C".
Bob
> There are really two issues here:
>
> 1) Jmol creates Kekule SMILES in lower case, and this does not seem to
> be standard. As long as compare is Jmol/Jmol, this is not a problem. And
> in fact, NIH Resolver which uses aromatic SMILES (c1ccccc1), recognizes
> the Jmol lower case Kekule SMILES for benzene.
>
It's definitely incorrect. You really have all the H atoms there and it's
not planar?
2) Getting stuck in lower case mode, however, is a problem and seems to
> be a bug.
>
> I have a feeling that calculate/reset aromatic may offer one solution to
> the problem, but I'm not sure it can be used in a general sense to
> "unaromatise" an aromatic ring. If this is not a bug, an alternative is
> to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
> side affects.
>
>
See if you can find out more about what exactly the NIH server is requiring,
if that's the issue. There's also a
/noaromatic/ flag in Jmol's SMILES business that turns off aromatic
checking. That might be useful.
Help me define what the context is. Where are these being used?
> Otis
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 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
------------------------------------------------------------------------------
This SF.net Dev2Dev email is sponsored by:
Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
