Bob,
More than pretty cool!
Years ago we were using JME SMILES to auto-grade student responses on
organic quizzes. The big problem is that a JME SMILES is not unique for
structures with stereo information. Now all one has to do is include a
Jmol/JME combination on the quiz page. By processing student responses
with the Jmol SMILES match and returning the value of the function to
JavaScript, complete auto-grading of SMILES is possible. Almost 10 years
ago that was the Web quizzing Holy Grail for us!
I'm still having problems with the Jmol compare function, did you get my
off list note on this? I was on the road, and I was not sure about the
email send. I'm back home in FL now.
Otis
On 5/11/2010 9:05 AM, Robert Hanson wrote:
Well, maybe not, but this is PRETTY COOL!
/Jmol 12.0.RC11 allows unprecedented matching of non-canonical SMILES
strings independent of any 3D structure. This includes both atom and
bond stereochemistry, including cis/trans, allene, tetrahedral, square
planar, trigonal bipyramidal, and octahedral stereochemistry. Starting
with a SMILES string from some source, you can test for an equivalent
structure WITHOUT any need for "canonicalization" of the SMILES (that
is, turning it into some standard form). While canonicalization is
important for database searching just in terms of speed, with this
addition to Jmol, it is no longer necessary for pattern matching
between two SMILES strings or pattern searching of a SMILES string
using a SMARTS pattern. This feature is completely independent of any
actual Jmol model (although that, too, can be tested against a SMILES
or SMARTS string). Thus, for example, you can have a user create a 2D
structure in JME and use Jmol to test its equivalence to some
reference SMILES or SMARTS string you are expecting.
Think about it...I think this will open up all sorts of possibilities
for student input of 2D or 3D structures.
see
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
//http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
/
--
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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Otis Rothenberger
chemagic.com
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