OK, I think we are about there. It should be very simple now to write pages
that use JME.jar and JmolSmilesApplet.jar to ask students to input simple
structures and then compare those structures to known correct or near-miss
answers. Each file is only about 40K in size, so they are very fast at
loading. I'm open to suggestions for making JmolSmilesApplet.jar even
better, but even as it is now...
...You can dispense with the need for a "canonical" SMILES string to match
in any situation. I realize there are situations where one might want a
canonical version, but for educational testing it is no longer necessary.
...You can compare two SMILES strings for constitutional (just take out the
"@" signs) or stereochemical equivalence.
...If you use JmolApplet.jar instead of JmolSmilesApplet.jar, you can also
select specific atoms from the matched set of atoms using {...} around the
atoms to select.
...You can use either a SMILES match or a SMARTS match. All of the important
aspects of SMARTS are implemented, including all the "primitives".
...If you want to adapt this, feel free. It's just a few Java files.
Probably what we should do is write a simple open-source version of JME to
provide a frame to JmolSmilesApplet. It's too bad that Peter's work is not
extensible in that regard. Peter, you sure you don't want to do this? But it
would be a nice project - either to use a streamlined version of JChemPaint
or just start from scratch. I mostly like Peter's interface, but there are
some very good ideas in JChemPaint as well. Suggestions? What we are looking
for is a very small, simple interface. Nothing fancy. If it comes from CDK
it will need to be VERY highly streamlined. Interestingly, my first version
was 120K, then I refactored Jmol and got it down to 43K, then I did a clean
build and discovered it was only 39K. Interesting process.
Bob
--
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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