Bob,
I put a Google Standard InChI search link on my IL State Fair ACS kiosk toy
suggestion:
http://chemagic.com/web_molecules/acs.aspx
Users can play with it to see what they think about the Google search
approach. I hope the toy instructions are fairly intuitive. Here's my point
of view and some specific notes relate the Google search:
My View:
I'm interested in developing more high school teacher interest in Jmol. To
this end, I'm hoping to do some local section ACS speaking in the near
future. I think any useful student utility that helps break an
understandable mind set that Jmol is simply a "see the pretty molecule
spin" application is a useful addition. I say understandable because "Jmol
2011" is really not that well known outside a small circle of users.
Notes:
1) Google has obviously put some specific thought into chemical searching
via InChI - some specifics below.
2) For some reason, Resolver has some problems with the cyclooctatetraene
InChI. I suspect this is related to flat (aromatic) vs tub (not aromatic)
confusion in the SMILES. Without putting up a "did you mean" warning,
Google appends the search URL InCHI to improve the search.
3) Taxol seems to be big test compound with this toy, so I'll make a
special Taxol note here. Resolver has some issues with % in some SMILES. I
have not been able to work this all out, but I suspect it's a query string
issue with the percent sign location in certain SMILES. I've tried escaping
the % sign itself with little success. I dodge this issue by trapping Jmol
SMILES that have a %. I then have JME read the Jmol molfile, and I use the
JME SMILES for this molfile. This, of course, produces the non-isomeric
SMILES. I'd trap only problem SMILES if I could figure out the specific
nature of this % sign problem. Back to Google: The search works. Google has
obviously done a thorough job of indexing InChI's.
4) For very common compounds, what I will call "leach sites" evidently have
learned to use InChI's as bait (attraction pheromone?) - incredible.
5) Item 4 is not a big problem, and a real caveat to this Google search
approach is a quick Boolean AND (Google default) appended to the search
result. The "leach sites" really don't know very much chemistry.
One final note on the toy: I added a dedicated PubChem load:
a) The entry "acetone" loads via Resolver.
b) The entry "pub:acetone" loads via PubChem.
Just to test pushing Jmol Script's ability to make these loading queries, I
added a feature that will select PubChem's 2D sdf file if the 3D sdf is not
available. Taxol is just such a model. Google does not care, and the
resulting Google query works just fine. This is really just another example
of item 3 above.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <[email protected]>
Sent: Wednesday, April 13, 2011 6:22 AM
To: [email protected], [email protected]
Subject: Re: [Jmol-users] An Old Paper and Jmol/Resolver
Otis, are you suggesting we add a "Google" menu item in Jmol?
ruary 5, 1900
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