Re: [Jmol-users] Another Resolver Thought

[Robert H. <ha...@st...>]

If you have the signed applet, there should be no need for server-side
scripting. Just use the

file()

function to load the contents of the resolver file -- which would be the
InChI string, right? Then send the proper load command to Jmol.

Bob

On Mon, Dec 13, 2010 at 2:46 PM, Otis Rothenberger <osr...@ch...>wrote:

> All,
>
> While working on a structure database for our Jmol application, I found
> myself spending a lot of time searching PubChem and the NIST Webbook. In
> all cases, I was searching a model that was already in the Jmol window.
> This falls into the category of the obvious finally hitting me: Jmol can
> hook directly to PubChem and NIST Webbook via query string request
> passed through NCI/NIH Resolver. I was doing this manually because
> neither of these databases uses a SMILES query string. With Resolver,
> however, the following is possible:
>
> Jmol SMILES ---->  Resolver InChI ----> NIST or PubChem Query
>
> The appropriate URL structure is below. I have NIST set for IR/MS:
>
> urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI=" + nihInchi +
> "&Units=SI&cIR=on&cMS=on"
>
> urlNm = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=" +
> nihInchi + "+i"
>
> This would require the signed applet and access to server side
> scripting. If a Resolver InChI query is added to Jmol, the signed applet
> should work without server side scripting.
>
> The double hit schematic above (Resolver then NIST/PubChem) leads to
> pop-up blocker problems. I get around this by writing a dynamic "Click
> for Search Results" link using the information returned from Resolver.
> An example can be found at:
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> Follow "The Model Tools" link.
>
> Otis
>
>
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
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-- 
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