Completing a thought here, Jmol does hook nicely to ChemSpider. ChemSpider
has also provided an interesting Jmol link - see end of email.
Taxol seems to be the first thing people try to test this sort of thing, so
I'll cut to the chase:
http://chemagic.com/web_molecules/script_page_large.aspx?rid=10368587
The initial Xe atom is just screen candy until Jmol get's the job done.
Please note that query string only directs numerics to ChemSpider, thus
http://chemagic.com/web_molecules/script_page_large.aspx?rid=taxol goes to
PubChem and FAILS. Actually, the coding intent of ?rid is either CSID or
InChIKey - not name. Numeric goes to ChemSpider and InChIKey goes to
PubChem.
Here's the server url that grabs to SDF from ChemSpider:
http://chemagic.com/web_molecules/pubchem.aspx?csid2sdf=10368587
Initial Observations:
1) Some files like taxol come in without H's. That's easily fixed by Jmol.
2) Metal atoms in the molecule seem to screw things up - returned as 2D.
3) Larger molecules like taxol seem to do OK. Here's one of the red tide
toxins:
http://chemagic.com/web_molecules/script_page_large.aspx?rid=9041149
Having said all of this, it turns out that ChemSpider has already used Jmol
to provide a URL that may be of interest to the Wikipedia group:
http://www.chemspider.com/ImageView.aspx?mode=3d&id=9041149
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Otis Rothenberger" <[email protected]>
Sent: Friday, June 17, 2011 2:25 AM
To: [email protected]
Subject: [Jmol-users] ChemSpider
Bob,
Resolver seems to be having a lot of down time lately. I recently noticed
that ChemSpider seems to be computing SDF's. The URL is pretty simple:
http://www.chemspider.com/FilesHandler.ashx?type=str&3d=yes&id=10368587
The id is the ChemSpider CSID. Two thoughts come to mind. First, since the
ChemSpider CSID is included in the Wikipedia page, this might provide a
back-up for Resolver in the Wikipedia/Jmol connection (Two Jmol links - one
for Resolver and one for ChemSpider)
Second, for more general Jmol use, the following becomes possible (In
theory, I haven't connected the parts yet.) in an AJAX sequence:
1) Name to CID from PubChem
Example: http://chemagic.com/web_molecules/pubchem.aspx?name2cid=taxol
2) CID to 2D SDF from PubChem - Don't panic on the 2D! Keep reading.
Example: http://chemagic.com/web_molecules/pubchem.aspx?cid2sdf2d=36314
The PubChem 2D SDF contains a wealth of information. Specifically, in the
above parsing - InChI, InChIKey, and SMILES. One hit, and you have all the
identifiers.
3) InChIKey to CSID from ChemSpider
Example:
http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key=RCINICONZNJXQF
-MZXODVADSA-N
And we're back to the SDF url at the top of the email. Convoluted, but it
all moves pretty quickly.
The weak link in all of this is item 1. Because of query result
ranking/ordering, PubChem can miss a name target. I'm still working on
improving item one. InChI input to PubChem works, and we have a smiles to
InChI conversion, but there are query string length limits. Big molecules
become a problem.
Anyway, the simple CSID to SDF url seems like a simple Resolver back-up. I
don't know much about Marvin molConverter, but it looks like the 3D SDF's
are generated by Marvin.
Finally, the following ChemSpider page contains specific information about
what's behind some of the CheMagic url's above:
http://www.chemspider.com/InChI.asmx
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
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