This is not perfect, but it's pretty good. It's a follow up to Bob's
PubChem SDF partial charge reader:
If you go to our model kit application:
http://chemagic.com/web_molecules/script_page_large.aspx
and put a model in the Jmol window (JME draw it, modelkit constructed it,
whatever...), then you can load the PubChem SDF for this model by the
following sequence:
1) Go to the Tools menu and click the PubChem link. Two new links will
appear
Open Search Results Page AND Get PubChem SDF File
2) Click the Get PubChem SDF File link. If the SDF data is found, a new
link appears
Load PubChem SDF File
Click this link to load the PubChem SDF. The value of this is that many
PubChem SDF's have partial charge data. On the above Tools menu, the MEP
links should verify this.
The convolution of two clicks to get this job done is required by the fact
that the direct load of an SDF from PubChem requires a PubChem CID. Since
the NIH/NCI Resolver does not yet resolve PubChem CID's, I have to make
PubChem do this for me. This is done by passing the Resolver accessible
InchiKey of a Jmol model (via SMILES) to PubChem. Subsequently, an entire
Web page has to be parsed, and this is a mess! For anyone interested in
trying this, I offer the following "Resolver" on the ISU Chemistry
Department server:
http://chemistry.illinoisstate.edu/osrothen/web_molecules/nih.aspx?cid=LFQSC
WFLJHTTHZ-UHFFFAOYSA-N
The query string is simply the InchiKey for the model. The return is either
the PubChem CID text string or the string "Translation" if there is an
error.
I have rigged this "Resolver" so that an SDF false (the string
"Translation" ) comes back if there is NOT a unique PubChem hit. PubChem
will return a list of possible related structures if it can't exactly match
an InchiKey. Since the correct SDF may or may not be in this list, I return
the false.
If you have not played with the Real Resolver's InchiKey for SMILES
translation, then here is the URL for ethanol:
http://cactus.nci.nih.gov/chemical/structure?string=CCO&representation=stdin
chikey
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
