From: Otis R. <osr...@ch...> - 2010-12-13 20:46:34
|
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 |
From: Robert H. <ha...@st...> - 2010-12-13 21:03:10
|
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 |
From: Otis R. <osr...@ch...> - 2010-12-13 22:26:08
|
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 Rothenberger chemagic.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... <mailto: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= > <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 <http://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... > <mailto: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 list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2010-12-13 23:18:35
|
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 |
From: Robert H. <ha...@st...> - 2010-12-14 00:26:28
|
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 |
From: Robert H. <ha...@st...> - 2010-12-14 00:56:02
|
Actually, there's a new line character in that file. You should use: nihInchi=load(" http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey ").lines[0] On Mon, Dec 13, 2010 at 5:26 PM, Robert Hanson <ha...@st...> wrote: > 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 > -- 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 |
From: Robert H. <ha...@st...> - 2010-12-14 00:57:51
|
I guess that's nihInchi=load(" http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey ").trim() On Mon, Dec 13, 2010 at 6:55 PM, Robert Hanson <ha...@st...> wrote: > Actually, there's a new line character in that file. You should use: > > nihInchi=load(" > http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey > ").lines[0] > > > > On Mon, Dec 13, 2010 at 5:26 PM, Robert Hanson <ha...@st...> wrote: > >> 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 >> > > > > -- > 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 |
From: Otis R. <osr...@ch...> - 2010-12-14 04:08:59
|
Bob, From the console, either seems to work. But to finish this thought for folks who might want to try it (i.e. hooking the InChI for a loaded Jmol model to external database like NIST) with the signed applet, the returned InChI must go into a JavaScript variable needed to write the data link. You explained this process to me a while back, so I'll post the process here for completeness: If from the location window, you enter: javascript: jmolScript("nihstuff = load('http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey').trim()") Then the following would illustrate how to get Jmol nihstuff into a JavaScript variable: javascript: var jmTojs = jmolEvaluate("@nihstuff"); alert(jmTojs ) The alert: InChIKey=IJDNQMDRQITEOD-UHFFFAOYSA-N As I mentioned earlier, I thought that I was using InChI - not InChIKey. It does not matter. Ether way, the URL has the following structure: http://webbook.nist.gov/cgi/cbook.cgi?InChI=IJDNQMDRQITEOD-UHFFFAOYSA-N&Units=SI I just strip out the InChIKey=, and construct the following: var urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI=" + jmTojs + "&Units=SI&cIR=on&cMS=on" Finally, an open.window() will produce pop-up headaches. Consequently, I write a dynamic link to make the user take the pop-up legal action. Otis Otis Rothenberger chemagic.com |
From: Robert H. <ha...@st...> - 2010-12-14 16:38:05
|
I see, so what you mean you are interested in doing is to display the WebBook page for a given structure in Jmol. Yes, that would need some JavaScript. Just change your "stdinchikey" to "stdinchi" in that first call and you will get the InChiI, not the key. Then you don't strip anything; just trim the line and insert it, since it already starts with "InChI=" Interesting! Bob On Mon, Dec 13, 2010 at 10:08 PM, Otis Rothenberger <osr...@ch...>wrote: > Bob, > > From the console, either seems to work. But to finish this thought for > folks who might want to try it (i.e. hooking the InChI for a loaded Jmol > model to external database like NIST) with the signed applet, the > returned InChI must go into a JavaScript variable needed to write the > data link. You explained this process to me a while back, so I'll post > the process here for completeness: > > If from the location window, you enter: > > javascript: jmolScript("nihstuff = > load(' > http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey').trim(<http://cactus.nci.nih.gov/chemical/structure?string=CCCC&representation=stdinchikey%27%29.trim%28> > )") > > Then the following would illustrate how to get Jmol nihstuff into a > JavaScript variable: > > javascript: var jmTojs = jmolEvaluate("@nihstuff"); alert(jmTojs ) > > The alert: InChIKey=IJDNQMDRQITEOD-UHFFFAOYSA-N > > As I mentioned earlier, I thought that I was using InChI - not InChIKey. > It does not matter. Ether way, the URL has the following structure: > > > http://webbook.nist.gov/cgi/cbook.cgi?InChI=IJDNQMDRQITEOD-UHFFFAOYSA-N&Units=SI > > I just strip out the InChIKey=, and construct the following: > > var urlNm = "http://webbook.nist.gov/cgi/cbook.cgi?InChI=" + jmTojs + > "&Units=SI&cIR=on&cMS=on" > > Finally, an open.window() will produce pop-up headaches. Consequently, I > write a dynamic link to make the user take the pop-up legal action. > > 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 |
From: Otis R. <osr...@ch...> - 2010-12-18 17:47:15
|
Bob, One last thought on this chain. As you can see, I've developed a bit of interest in connecting Jmol to outside data other than sdf data using Resolver to translate as needed. I've focused on three databases for a variety of reasons: 1) NIST WebBook IR/MS data - Uses InChI query - Limited db, but good for advanced model kit problems. 2) PubChem - Uses InChI query - Huge db, and excellent for model kit "see what you created" exercises. 3) CAS Common Chemisty Service - Uses CAS# query - Limited db, but with a focus on public outreach (a magic word for me). All of the above are easy to link to the model in the Jmol window using the methods in this chain. The latter is particularly nice for high school level. Under an ongoing cooperative effort with Wikipedia, the CAS# search return gives a direct link to the Wikipedia article that matches the CAS# if an article exists. One problem with CAS# query is the proliferation of CAS#'s. Resolver returns them all. Only one is reliable, and its location in the Resolver return appears random. A filter of the returned data for the shortest CAS# seems to work. It's also a good idea to strip SMILES stereochemistry (@) before the Resolver SMILES to CAS# translation. I'd like an item (4) above - nmr data. I can't find a source suited to our methodology, however. SDBS Compounds and Spectral Search would be nice, but there is no query access. I'll write to them, but I don't have high hopes. They use a disclaimer screen that seems to be important to their data release approach. Perhaps they would be agreeable to Jmol users arriving at the disclaimer with a CAS# good to go. As usual, an operational example is at http://chemagic.com/web_molecules/script_page_large.aspx Use Tools menu. Otis Otis Rothenberger chemagic.com On 12/14/2010 11:37 AM, Robert Hanson wrote: > I see, so what you mean you are interested in doing is to display the > WebBook page for a given structure in Jmol. Yes, that would need some > JavaScript. Just change your "stdinchikey" to "stdinchi" in that first > call and you will get the InChiI, not the key. Then you don't strip > anything; just trim the line and insert it, since it already starts > with "InChI=" > > Interesting! > > Bobinfo/jmol-users |