Bob,
Thanks. Your explanation of what aromatic means is the key here. I see
now why this is happening. If I start with benzene and make
1,3-cyclohexadiene, then it ends up in flat energy minimum that
"minimize" does not change. I always get the lower case smiles. If I use
"drag" to pull it out of shape, then I get upper case. If I make
cyclohexene from benzene, "minimize" eventually get it and twists a bit.
Once it twists, I get upper case.
One thing here is that it looks like the statement "aromatic just means
flat and all sp2 for Jmol" is not quite correct. Flat seems to be a
sufficient condition.
The context here may seem strange, but we are working on student model
kit exercises, and we want the Jmol model kit to allow the same kind on
tactile playing that a ball and stick model kit allows - e.g. take a
double bond out of benzene. To be sure, I do not see the problem if I
make 1,3-cyclohexadiene from cyclohexane. That should have been a clue
that the flatness was the issue!
Re NIH, for all of the following, the Resolver returns benzene (no
explicit hydrogens in submitted SMILES):
Jmol lower case benzene
Jmol lowercase cyclohexadiene
Jmol lower case cylohexene
Jmol lower case cyclohexane, which is, of course synonymous with
"aromatic SMILES" for benzene.
Evidently, the Resolver is just ignoring "=" in this lower case context.
Otis
Otis Rothenberger
chemagic.com
On 9/2/2010 1:52 AM, Robert Hanson wrote:
On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> 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 <http://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
[email protected]
<mailto:[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
------------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
