Re: [Jmol-users] Help with ChemDoodle Web
Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.comwrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with ChemDoodle Web
...of course, this is in daily flux, and one thing I haven't implemented is the fact that you can go directly to resolver now by AJAX. I'm hoping to get that set up for RCSB as well, and then we will have full resolver/pdb loading by the UNSIGNED applet. Yeah! On Wed, Apr 18, 2012 at 9:52 AM, Robert Hanson hans...@stolaf.edu wrote: Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.comwrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with ChemDoodle Web
Hi Otis, See if you encounter the same issue with Bob's js script, if you do I will look into it. Sometimes AJAX messes with the file line delimiters which can cause this issue. I would like to know what exactly is causing this issue though. We also just added a new ChemDoodle.io.file.content() function which uses AJAX to retrieve file content from a local url. I haven't encountered any issues with it yet. More on it is now in the tutorial (in Obtain File Content via AJAX): http://web.chemdoodle.com/tutorial/loading-data Hope this helps, Kevin On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote: Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com wrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with ChemDoodle Web
Thanks Bob, That sounds like a plan if I can make it work in our AKA application. On a 3D view link in this application, I'm just trying to branch mobile devices to a non-Java option. Am I correct in assuming that in: applet.loadFile() xxx can be a call to a server side script (my server) that loads a Resolver (or PubChem/ChemSpider) SDF file? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote: Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com wrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with ChemDoodle Web
yeah, yeah. That is PRECISELY what JmolCD.js does. Automatic branching. On Wed, Apr 18, 2012 at 10:09 AM, Otis Rothenberger osrot...@chemagic.comwrote: Thanks Bob, That sounds like a plan if I can make it work in our AKA application. On a 3D view link in this application, I'm just trying to branch mobile devices to a non-Java option. Am I correct in assuming that in: applet.loadFile() xxx can be a call to a server side script (my server) that loads a Resolver (or PubChem/ChemSpider) SDF file? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote: Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.comwrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with ChemDoodle Web
On Wed, Apr 18, 2012 at 10:21 AM, Robert Hanson hans...@stolaf.edu wrote: yeah, yeah. That is PRECISELY what JmolCD.js does. Automatic branching. On Wed, Apr 18, 2012 at 10:09 AM, Otis Rothenberger osrot...@chemagic.com wrote: Thanks Bob, That sounds like a plan if I can make it work in our AKA application. On a 3D view link in this application, I'm just trying to branch mobile devices to a non-Java option. Am I correct in assuming that in: applet.loadFile() xxx can be a call to a server side script (my server) that loads a Resolver (or PubChem/ChemSpider) SDF file? For the resolver, just use: Jmol.searchQuery(applet, $tylenol); or applet.setSearchTerm($tylenol); like that. (These are equivalent) $ means NCI; = means PDB: Jmol.searchQuery(applet, =1dcc); Bob Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Apr 18, 2012, at 10:52 AM, Robert Hanson wrote: Otis, forget that. Don't go there. Period. This is just what we are setting up now, and you are going to love it. 1) Use JmolCD.js 2) Follow the lead shown in http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm. You can use JmolCD.js to create a standard ChemDoodle canvas or a Jmol applet or have Jmol choose automatically based on the browser capability. 3) There is no need to have the MOL data stuffed into a variable that way. Just load the file from your server just like for Jmol, even if it is just a ChemDoodle canvas, using: applet.loadFile() Bob On Wed, Apr 18, 2012 at 9:17 AM, Otis Rothenberger osrot...@chemagic.com wrote: All, I know this is not a ChemDoodle list, but with all the recent ChemDoodle activity on the list, I've been playing with the Web Components. Here's a big frustration, and maybe someone on the list can help me: If I literally define a JavaScript molfile variable - e.g.: lsdfStr = 'CH4\nAPtclcactv04181210043D 0 0.0 0.0\n \n 5 4 0 0 0 0 0 0 0 0999 V2000\n 0. -0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0\n 0. -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0. 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8900 -0. 0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\n 1 5 1 0 0 0 0\nM END\n\n' then I can dynamically load it into a Transformer3D Canvas - no problem. If on the other hand I define lsdfStr via AJAX to Resolver, subsequent use of the same load routine throws an obscure JS error - TypeError: h is undefined. If I directly copy the returned AJAX text and paste it into a direct definition of lsdfStr, the dynamic load works. Any thoughts would be appreciated. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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
