From: Robert H. <ha...@st...> - 2010-12-14 00:26:28
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Looks like what you do then is: nihInchi=load(" http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey ") htmlPage = load("http://webbook.nist.gov/cgi/cbook.cgi?" + nihInchI + "&Units=SI&cIR=on&cMS=on") Then htmlPage is the NIST page for butane Bob On Mon, Dec 13, 2010 at 5:18 PM, Robert Hanson <ha...@st...> wrote: > sorry - it's load() > > in Jmol: > > x = load(" > http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchi > ") > print x > > > InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3 > > > Bob > > > On Mon, Dec 13, 2010 at 4:25 PM, Otis Rothenberger <osr...@ch...>wrote: > >> Bob, >> >> I'm just after data (spectra, iupac names, etc). I never thought about >> loading the sdf files. I'll look into that. But... >> >> Will file() load data from a remote URL? Here's the appropriate info: >> >> >> http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey >> >> Recall that Markus added this standard approach to the Resolver query >> string, so the above will return the InChI for butane. Actually, it's >> returning the InChIKey. I thought I changed that to InChI, but whatever. Can >> the signed applet read this directly? The idea here is to use this InChI to >> load the NIST spectral data for the model in the window by creating a >> dynamic link via JavaScript: >> >> >> urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI=" + nihInchi + >> "&Units=SI&cIR=on&cMS=on" >> >> urlNm becomes the href for the dynamic link, and the user can thus load >> NIST spectral data directly for the model in the window. >> >> >> Otis >> >> >> Otis Rothenbergerchemagic.com >> >> >> On 12/13/2010 4:03 PM, Robert Hanson wrote: >> >> 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 >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Lotusphere 2011 >>> Register now for Lotusphere 2011 and learn how >>> to connect the dots, take your collaborative environment >>> to the next level, and enter the era of Social Business. >>> http://p.sf.net/sfu/lotusphere-d2d >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> >> >> >> -- >> 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 >> >> >> ------------------------------------------------------------------------------ >> Lotusphere 2011 >> Register now for Lotusphere 2011 and learn how >> to connect the dots, take your collaborative environment >> to the next level, and enter the era of Social Business.http://p.sf.net/sfu/lotusphere-d2d >> >> >> _______________________________________________ >> Jmol-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> ------------------------------------------------------------------------------ >> Lotusphere 2011 >> Register now for Lotusphere 2011 and learn how >> to connect the dots, take your collaborative environment >> to the next level, and enter the era of Social Business. >> http://p.sf.net/sfu/lotusphere-d2d >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > 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 > -- 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 |