[Jmol-users] ChemSpider

[Otis R. <osr...@ch...>]

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