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From: Jonathan G. <gu...@uw...> - 2021-03-07 23:31:44
|
I see no problem with dropping the signing of the application, unless some versions of the JavaVM will not run unsigned jars. Jonathan Dr. Jonathan Gutow Chemistry Department UW Oshkosh web: https://uwosh.edu/facstaff/gutow e-mail: gu...@uw... Ph: 920-424-1326 ________________________________ From: Robert Hanson via Jmol-developers <jmo...@li...> Sent: Sunday, March 7, 2021 3:16 PM To: Jmol Developers <jmo...@li...> Cc: Robert Hanson <ha...@st...> Subject: [Jmol-developers] signing jar files CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. I have not been signing the Jmol.jar file for some time now. No one has complained. How do others feel about my continuing to do that? I know it was important for the applet, but we are not distributing the Java applet anymore. So can we be done with signing? This has been an expense of about $250 for me each year for the past many years. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place. |
From: Robert H. <ha...@st...> - 2021-03-07 21:16:59
|
I have not been signing the Jmol.jar file for some time now. No one has complained. How do others feel about my continuing to do that? I know it was important for the applet, but we are not distributing the Java applet anymore. So can we be done with signing? This has been an expense of about $250 for me each year for the past many years. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Robert H. <ha...@st...> - 2021-01-05 18:11:22
|
I've cleaned this up. Thanks Angel. Happy New Year! |
From: <ang...@ua...> - 2021-01-05 12:18:52
|
Dear Bob, I updated the image ( (c)2021 ) for the splash screen in org / openscience / jmol / app / images / Now I notice that the Help > About entry in the application's top menu bar uses a separate file for the same image (about.jpg, stuck at the 2016 version), located at org / openscience / jmol / app / jmolpanel / The relevant code is in AboutDialog.java Would it be easy to change this java file to point to the other location of the splash image? Otherwise, I will have to remember to upload any new version of the image to both places. |
From: PD D. K. S. <sc...@hh...> - 2020-12-30 07:04:41
|
Hi everybody, I am enjoying my Christmas holidays while developing some new e-teaching content. Now I have the following problem. Once I display a MO (calculated with gaussian) I get the orbital (that is OK), as well as some information regarding the orbital (File name; Model and MO number; Energy; Symmetry; Occupancy), which I do not want to display. For an example see: http://test.schelm.hhu.de/scheLM_3D/Methyl_MO/start.html just scroll to the jmol_Apps of the Methylanion and Methylcation and select any MO (select-box below the apps) and wait for a couple of seconds. Is there any way to control the output. I did not find any hint on: https://chemapps.stolaf.edu/jmol/docs/ Thanks for your help and the best wishes for 2021, Klaus **************************************************************************** ******** PD Dr. Klaus Schaper http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de <http://www.klaus-schaper.de/> e-mail: sc...@kl... <mailto:sc...@kl...> Arbeitsgruppe für Organische Photochemie Institut für Organische Chemie und Makromolekulare Chemie I Raum 26.43.00.27 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 D-40225 Düsseldorf Deutschland Telefon: +49 211 81 12571 FAX: +49 211 81 14324 **************************************************************************** ******** |
From: Robert H. <ha...@st...> - 2020-12-15 15:53:31
|
I will check this before my next update, later today. On Mon, Dec 14, 2020 at 7:04 PM Mark Perri <pe...@so...> wrote: > Hi Bob, > I've got inchi working with the latest Jmol from github if I run it by > clicking Debug at the top of eclipse. But when I build the project some of > the inchi dependencies aren't loading right. This affects build/Jmol.jar > and build/JmolData.jar > > java -Djava.awt.headless=true -Xmx512m -jar > '/home/mark/winhome/Jmol-SwingJS/build/JmolData.jar' -j 'set forceAutobond > ON;load $caffeine;print {1.1}.find("inchi")' > vwr handling error condition: java.lang.NoClassDefFoundError: > net/sf/jniinchi/JniInchiException > java.lang.NoClassDefFoundError: net/sf/jniinchi/JniInchiException > > How do I build JmolData.jar to include those dependencies? > > Thanks, > Mark > > > > On Tue, Dec 8, 2020 at 2:20 PM Robert Hanson <ha...@st...> wrote: > >> if you refresh your project, after Eclipse does its automatic building >> there should be a /site/ directory. It's the file there. >> >> On Tue, Dec 8, 2020 at 3:59 PM Mark Perri <pe...@so...> wrote: >> >>> Thanks! I'll look into the tests / data. >>> >>> One more thing, is site-resources/__JmolApplet_applet.html the correct >>> way to test out the new JSmol? It looks like I'm building .js files, but I >>> get an error when running the .html file: RangeError: Maximum call stack >>> exceeded loading JSUtil.js (and others). >>> >>> Is there a swingjs example page hosted somewhere I can look at? >>> >>> Here's my .html file: >>> Thanks, >>> Mark >>> >>> >>> >>> >>> <!DOCTYPE html> >>> <html><title>SwingJS test JmolApplet</title> >>> <head><meta charset="utf-8" /> >>> <script src= >>> "file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/swingjs2.js"></script >>> > >>> <script> >>> if (!self.SwingJS)alert( >>> 'swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' >>> + document.location.href) >>> Info = { >>> code: "_.JmolApplet", >>> main: null, >>> core: "NONE", >>> width: 600, >>> height: 400, >>> serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', >>> j2sPath: 'file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/j2s', >>> console:'sysoutdiv', >>> allowjavascript: true >>> } >>> </script> >>> </head> >>> <body> >>> <script> >>> SwingJS.getApplet('testApplet', Info) >>> getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz. >>> ClassFilesLoaded.sort().join('\n'))} >>> </script> >>> <div style=" >>> position:absolute;left:900px;top:30px;width:600px;height:300px;"> >>> <div id=sysoutdiv style=" >>> border:1px solid green;width:100%;height:95%;overflow:auto"></div> >>> This is System.out. <a href="javascript:testApplet._clearConsole()"> >>> clear it</a> <br> >>> Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files >>> <br><a href="javascript:getClassList()">get _j2sClassList.txt</a> >>> </div> >>> </body> >>> </html> >>> >>> >>> On Tue, Dec 8, 2020 at 3:48 AM Robert Hanson <ha...@st...> wrote: >>> >>>> That might only be set up on SourceForge. You will need the data >>>> directory. I am so glad you are doing this! >>>> >>>> See if this works for you. >>>> >>>> https://github.com/BobHanson/Jmol-datafiles >>>> >>>> I see that one of the G98 files fails. How about if I make you a >>>> contributor to Jmol-SwingJS? >>>> >>>> >>>> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> 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 >> >> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We >> honor with gratitude the people who have stewarded the land throughout the >> generations and their ongoing contributions to this region. We acknowledge >> the ongoing injustices that we have committed against the Dakota Nation, >> and we wish to interrupt this legacy, beginning with acts of healing and >> honest storytelling about this place.* >> > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Mark P. <pe...@so...> - 2020-12-15 01:04:58
|
Hi Bob, I've got inchi working with the latest Jmol from github if I run it by clicking Debug at the top of eclipse. But when I build the project some of the inchi dependencies aren't loading right. This affects build/Jmol.jar and build/JmolData.jar java -Djava.awt.headless=true -Xmx512m -jar '/home/mark/winhome/Jmol-SwingJS/build/JmolData.jar' -j 'set forceAutobond ON;load $caffeine;print {1.1}.find("inchi")' vwr handling error condition: java.lang.NoClassDefFoundError: net/sf/jniinchi/JniInchiException java.lang.NoClassDefFoundError: net/sf/jniinchi/JniInchiException How do I build JmolData.jar to include those dependencies? Thanks, Mark On Tue, Dec 8, 2020 at 2:20 PM Robert Hanson <ha...@st...> wrote: > if you refresh your project, after Eclipse does its automatic building > there should be a /site/ directory. It's the file there. > > On Tue, Dec 8, 2020 at 3:59 PM Mark Perri <pe...@so...> wrote: > >> Thanks! I'll look into the tests / data. >> >> One more thing, is site-resources/__JmolApplet_applet.html the correct >> way to test out the new JSmol? It looks like I'm building .js files, but I >> get an error when running the .html file: RangeError: Maximum call stack >> exceeded loading JSUtil.js (and others). >> >> Is there a swingjs example page hosted somewhere I can look at? >> >> Here's my .html file: >> Thanks, >> Mark >> >> >> >> >> <!DOCTYPE html> >> <html><title>SwingJS test JmolApplet</title> >> <head><meta charset="utf-8" /> >> <script src= >> "file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/swingjs2.js"></script> >> <script> >> if (!self.SwingJS)alert( >> 'swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' >> + document.location.href) >> Info = { >> code: "_.JmolApplet", >> main: null, >> core: "NONE", >> width: 600, >> height: 400, >> serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', >> j2sPath: 'file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/j2s', >> console:'sysoutdiv', >> allowjavascript: true >> } >> </script> >> </head> >> <body> >> <script> >> SwingJS.getApplet('testApplet', Info) >> getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz. >> ClassFilesLoaded.sort().join('\n'))} >> </script> >> <div style=" >> position:absolute;left:900px;top:30px;width:600px;height:300px;"> >> <div id=sysoutdiv style=" >> border:1px solid green;width:100%;height:95%;overflow:auto"></div> >> This is System.out. <a href="javascript:testApplet._clearConsole()"> >> clear it</a> <br> >> Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files >> <br><a href="javascript:getClassList()">get _j2sClassList.txt</a> >> </div> >> </body> >> </html> >> >> >> On Tue, Dec 8, 2020 at 3:48 AM Robert Hanson <ha...@st...> wrote: >> >>> That might only be set up on SourceForge. You will need the data >>> directory. I am so glad you are doing this! >>> >>> See if this works for you. >>> >>> https://github.com/BobHanson/Jmol-datafiles >>> >>> I see that one of the G98 files fails. How about if I make you a >>> contributor to Jmol-SwingJS? >>> >>> >>> > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > 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 > > *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We > honor with gratitude the people who have stewarded the land throughout the > generations and their ongoing contributions to this region. We acknowledge > the ongoing injustices that we have committed against the Dakota Nation, > and we wish to interrupt this legacy, beginning with acts of healing and > honest storytelling about this place.* > |
From: Robert H. <ha...@st...> - 2020-12-10 04:27:23
|
Mark, I checked in build-core.xml. If you run that, it will condense 623 files into site/swingjs/j2s/core/core_jmol.z.js (6.6 MB/1.5 MB transferred by server-side GZip). Then run build-site.xml, and __JmolApplet_applet_core.html will be transferred into /site/ from /site-resources. The only difference between these two is the line for Info.core: * core: "_jmol",* This loaded for me from https://chemapps.stolaf.edu/jmol/swingjs/site/__JmolApplet_applet_core.html in 1.4 sec (Firefox)/1.6 sec (Chrome) with the cache disabled, or 0.73/0.36 cached. I think this is about as good as we can expect. [image: image.png] On Wed, Dec 9, 2020 at 9:27 PM Robert Hanson <ha...@st...> wrote: > > > On Wed, Dec 9, 2020 at 6:25 PM Mark Perri <pe...@so...> wrote: > >> Hi Bob, >> >> I've been experimenting with bundling the Jmol-SwingJS and JSmol files to >> speed up loading. Jmol-SwingJS took 33 seconds to load because it loads >> each function dynamically, and using the menu took another 10 seconds to >> load. >> >> > Oh, right. Don't be too concerned about compression. This is all just > development-only. Other huge projects load in around 2-3 seconds once we > build the core files. > > >> After getting a list of all the swingjs files that it dynamically loads >> (681) I concatenated them into one big swingjs.js file (4.9M minimized). I >> couldn't load this in a script tag, I had to wait until I initialized the >> applet. The easiest way to time it correctly was to replace >> swingjs/j2s/javax/swing/Japplet.js with this file. Using this bundle hack >> it only took 2.1 seconds to load the applet and the menus are ready to go >> when you right click. (it also loads the molecular orbital packages). >> > > That's not actually how it is done. Let me do one for you so you can see > how it works. > > You can see the result here: >> https://beta.chemcompute.org/site/__JmolApplet_applet.html >> >> I did the same with JSmol (only 40 files) and replaced >> j2s/core/corejmol.z.js with a 2.3 M file. It loads in about half the time >> (3 seconds instead of 6) and preloads a couple of functions I use. >> >> Are there any downsides to preloading everything like this? I tried >> looking in the swingjs code and couldn't figure out where it could be >> automated (I haven't looked in the JSmol transpiler at all). >> >> > *Bob* > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Robert H. <ha...@st...> - 2020-12-10 03:28:16
|
On Wed, Dec 9, 2020 at 6:25 PM Mark Perri <pe...@so...> wrote: > Hi Bob, > > I've been experimenting with bundling the Jmol-SwingJS and JSmol files to > speed up loading. Jmol-SwingJS took 33 seconds to load because it loads > each function dynamically, and using the menu took another 10 seconds to > load. > > Oh, right. Don't be too concerned about compression. This is all just development-only. Other huge projects load in around 2-3 seconds once we build the core files. > After getting a list of all the swingjs files that it dynamically loads > (681) I concatenated them into one big swingjs.js file (4.9M minimized). I > couldn't load this in a script tag, I had to wait until I initialized the > applet. The easiest way to time it correctly was to replace > swingjs/j2s/javax/swing/Japplet.js with this file. Using this bundle hack > it only took 2.1 seconds to load the applet and the menus are ready to go > when you right click. (it also loads the molecular orbital packages). > That's not actually how it is done. Let me do one for you so you can see how it works. You can see the result here: > https://beta.chemcompute.org/site/__JmolApplet_applet.html > > I did the same with JSmol (only 40 files) and replaced > j2s/core/corejmol.z.js with a 2.3 M file. It loads in about half the time > (3 seconds instead of 6) and preloads a couple of functions I use. > > Are there any downsides to preloading everything like this? I tried > looking in the swingjs code and couldn't figure out where it could be > automated (I haven't looked in the JSmol transpiler at all). > > *Bob* |
From: Mark P. <pe...@so...> - 2020-12-10 00:25:41
|
Hi Bob, I've been experimenting with bundling the Jmol-SwingJS and JSmol files to speed up loading. Jmol-SwingJS took 33 seconds to load because it loads each function dynamically, and using the menu took another 10 seconds to load. After getting a list of all the swingjs files that it dynamically loads (681) I concatenated them into one big swingjs.js file (4.9M minimized). I couldn't load this in a script tag, I had to wait until I initialized the applet. The easiest way to time it correctly was to replace swingjs/j2s/javax/swing/Japplet.js with this file. Using this bundle hack it only took 2.1 seconds to load the applet and the menus are ready to go when you right click. (it also loads the molecular orbital packages). You can see the result here: https://beta.chemcompute.org/site/__JmolApplet_applet.html I did the same with JSmol (only 40 files) and replaced j2s/core/corejmol.z.js with a 2.3 M file. It loads in about half the time (3 seconds instead of 6) and preloads a couple of functions I use. Are there any downsides to preloading everything like this? I tried looking in the swingjs code and couldn't figure out where it could be automated (I haven't looked in the JSmol transpiler at all). Thanks, Mark |
From: Robert H. <ha...@st...> - 2020-12-08 22:20:34
|
if you refresh your project, after Eclipse does its automatic building there should be a /site/ directory. It's the file there. On Tue, Dec 8, 2020 at 3:59 PM Mark Perri <pe...@so...> wrote: > Thanks! I'll look into the tests / data. > > One more thing, is site-resources/__JmolApplet_applet.html the correct way > to test out the new JSmol? It looks like I'm building .js files, but I get > an error when running the .html file: RangeError: Maximum call stack > exceeded loading JSUtil.js (and others). > > Is there a swingjs example page hosted somewhere I can look at? > > Here's my .html file: > Thanks, > Mark > > > > > <!DOCTYPE html> > <html><title>SwingJS test JmolApplet</title> > <head><meta charset="utf-8" /> > <script src= > "file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/swingjs2.js"></script> > <script> > if (!self.SwingJS)alert( > 'swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' > + document.location.href) > Info = { > code: "_.JmolApplet", > main: null, > core: "NONE", > width: 600, > height: 400, > serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', > j2sPath: 'file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/j2s', > console:'sysoutdiv', > allowjavascript: true > } > </script> > </head> > <body> > <script> > SwingJS.getApplet('testApplet', Info) > getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz. > ClassFilesLoaded.sort().join('\n'))} > </script> > <div style=" > position:absolute;left:900px;top:30px;width:600px;height:300px;"> > <div id=sysoutdiv style=" > border:1px solid green;width:100%;height:95%;overflow:auto"></div> > This is System.out. <a href="javascript:testApplet._clearConsole()"> > clear it</a> <br> > Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files > <br><a href="javascript:getClassList()">get _j2sClassList.txt</a> > </div> > </body> > </html> > > > On Tue, Dec 8, 2020 at 3:48 AM Robert Hanson <ha...@st...> wrote: > >> That might only be set up on SourceForge. You will need the data >> directory. I am so glad you are doing this! >> >> See if this works for you. >> >> https://github.com/BobHanson/Jmol-datafiles >> >> I see that one of the G98 files fails. How about if I make you a >> contributor to Jmol-SwingJS? >> >> >> -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Mark P. <pe...@so...> - 2020-12-08 21:59:48
|
Thanks! I'll look into the tests / data. One more thing, is site-resources/__JmolApplet_applet.html the correct way to test out the new JSmol? It looks like I'm building .js files, but I get an error when running the .html file: RangeError: Maximum call stack exceeded loading JSUtil.js (and others). Is there a swingjs example page hosted somewhere I can look at? Here's my .html file: Thanks, Mark <!DOCTYPE html> <html><title>SwingJS test JmolApplet</title> <head><meta charset="utf-8" /> <script src="file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/swingjs2.js" ></script> <script> if (!self.SwingJS)alert( 'swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href) Info = { code: "_.JmolApplet", main: null, core: "NONE", width: 600, height: 400, serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', j2sPath: 'file:///C:/Users/perrim/Jmol-SwingJS/site/swingjs/j2s', console:'sysoutdiv', allowjavascript: true } </script> </head> <body> <script> SwingJS.getApplet('testApplet', Info) getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz. ClassFilesLoaded.sort().join('\n'))} </script> <div style="position:absolute;left:900px;top:30px;width:600px;height:300px;" > <div id=sysoutdiv style=" border:1px solid green;width:100%;height:95%;overflow:auto"></div> This is System.out. <a href="javascript:testApplet._clearConsole()">clear it </a> <br> Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a> </div> </body> </html> On Tue, Dec 8, 2020 at 3:48 AM Robert Hanson <ha...@st...> wrote: > That might only be set up on SourceForge. You will need the data > directory. I am so glad you are doing this! > > See if this works for you. > > https://github.com/BobHanson/Jmol-datafiles > > I see that one of the G98 files fails. How about if I make you a > contributor to Jmol-SwingJS? > > > |
From: Robert H. <ha...@st...> - 2020-12-08 12:32:40
|
I pushed one-line fixes to GaussianReader and Resolver. On Tue, Dec 8, 2020 at 5:47 AM Robert Hanson <ha...@st...> wrote: > That might only be set up on SourceForge. You will need the data > directory. I am so glad you are doing this! > > See if this works for you. > > https://github.com/BobHanson/Jmol-datafiles > > I see that one of the G98 files fails. How about if I make you a > contributor to Jmol-SwingJS? > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
From: Robert H. <ha...@st...> - 2020-12-08 11:48:15
|
That might only be set up on SourceForge. You will need the data directory. I am so glad you are doing this! See if this works for you. https://github.com/BobHanson/Jmol-datafiles I see that one of the G98 files fails. How about if I make you a contributor to Jmol-SwingJS? |
From: Mark P. <pe...@so...> - 2020-12-08 05:05:41
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I can't get InChI to work, but that's not critical right now. I added those changes to GAMESS Energy we discussed earlier and made a PR. But I'm not sure how to run the test suite. Thanks, Mark On Mon, Dec 7, 2020 at 3:48 AM Robert Hanson via Jmol-developers < jmo...@li...> wrote: > DEFINITELY on the right track, Mark. > > 1) I'm sure I have forgotten to get the JNI class files into the Jar. > > I had only added the InChI jar classes to the signed 14.31 application at > SourceForge, not GitHub 15.1.Pull and run build-app-only again. Should be > 9.4 MB, not 5 MB, with the added InChI classes. Mine is working: > $ load $caffeine > C8H10N4O2 > > $ print {*}.find("inchi") > InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 > BTW, in case you don't know, a JAR file is just a ZIP file. You can open > it with 7zip or just > copy it to "t.zip" and click on that to check for classes. > > 2) Generally in Eclipse you don't build the Jar to test; you just use the > run or debug icon on the toolbar > or right-click on the Java application or applet (in this case > org.openscience.jmol.app.Jmoland select Debug As... (or Run As..., but then > you skip all breakpoints). > > > [image: image.png] > > Bob > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |
From: Robert H. <ha...@st...> - 2020-12-07 11:48:03
|
DEFINITELY on the right track, Mark. 1) I'm sure I have forgotten to get the JNI class files into the Jar. I had only added the InChI jar classes to the signed 14.31 application at SourceForge, not GitHub 15.1.Pull and run build-app-only again. Should be 9.4 MB, not 5 MB, with the added InChI classes. Mine is working: $ load $caffeine C8H10N4O2 $ print {*}.find("inchi") InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 BTW, in case you don't know, a JAR file is just a ZIP file. You can open it with 7zip or just copy it to "t.zip" and click on that to check for classes. 2) Generally in Eclipse you don't build the Jar to test; you just use the run or debug icon on the toolbar or right-click on the Java application or applet (in this case org.openscience.jmol.app.Jmoland select Debug As... (or Run As..., but then you skip all breakpoints). [image: image.png] Bob |
From: Mark P. <pe...@so...> - 2020-12-07 07:07:24
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Hi Bob, I think I may have Jmol mostly built. I cloned the github repo (a70e09). I installed JRE 1.8_251 and added netscape.jar from Jmol-SwingJS/jars to the java build path. I had to edit build.xml to use JRE 1.8_251 and edit all the version 1.6 to 1.8 in that file. It looks like it built Jmol.jar in /build When I run Jmol.jar it reports "15.1.19 2018-01-29". I tried to check InChI capability, but I get this: $ load files ":caffeine" "$caffeine" 2 models $ print {1.1}.find("inchi") script ERROR: java.lang.NoClassDefFoundError: net/sf/jniinchi/JniInchiException Am I on the right track? Thanks, Mark |
From: Robert H. <ha...@st...> - 2020-08-11 16:42:19
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I see I forgot to answer this. Nothing like almost a year later.... Before I forget the answer as well.... *class Whatever {* * static String getSomething() { return "odd";}* * public static String main(String[] args) {* * Whatever a = null;* * System.out.println("this is " + a.getSomething());* * }* *}* > this is odd Because static methods can be called (seemingly) from objects, but the Java compiler can infer that it only needs the class, not the object, so the reference becomes the class, rather than the object, and there is no problem. On Sat, Nov 2, 2019 at 8:40 PM Mark Perri <pe...@so...> wrote: > Here's what I get: > > function getValue() {return 5} > getValue() > 5 > a=null > null > a.getValue() > Uncaught TypeError: Cannot read property 'getvalue' of null > String x = a.getValue() > Uncaught SyntaxError: Unexpected identifier > > On Wed, Oct 30, 2019 at 7:03 PM Robert Hanson via Jmol-developers < > jmo...@li...> wrote: > >> >> * Whatever a = null;* >> >> *String x = a.getSomething();* >> >> Just like that. No intervening statements. Just those two lines. >> >> No exception thrown. x gets a non-null String value (or whatever >> getSomething() returns). >> >> Q: How is that possible?? >> >> Bob >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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...> - 2020-01-20 13:09:04
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This is the developers list. I think you want the user list. Sorry for the delay due to that. You could assign a variable to the name you have the the protein and then just show that: var protein1 = {model=1.1} etc. then select protein1 On Fri, Jan 10, 2020 at 9:31 AM Mavridakis, Konstantinos < kon...@h-...> wrote: > Hello. > > > I am trying to work out a script for a web-page so that I can display > several proteins at once. Although I have read other posts where the > relative commands for use in the console of jsmol, are mentioned, I haven't > found anything on how to implement such details from code. > > > To be more precise, the goal is to have a series of buttons ( at this > point I have added jmolCheckbox options) so that, when a user click's the > protein will show up. If he checks another one, then both proteins are > shown. I use " load append" for this and so far, for displaying all the > proteins, I use "model 0" . The proteins are loaded by their names. > > > But, what I would like is this. For each button clicked, the corresponding > proteins are shown, but only the last one get's selected, so that the user > could modify the styles on each protein. Furthermore, if the user un- > checks one of the previously chosen proteins, that protein should be > hidden, but the settings implemented shouldn't be lost. > > > My problem is that these select options seem to work by calling the > proteins with numbers, like " select model 1.1 " and so on, and I can't > figure out how to have such information in the script, since I am loading > the proteins by name ; should there be a way that a function could get such > information from the jsmol? > > > My code for this part is : > > > > <script type="text/javascript"> > > jmolApplet0 = Jmol.getApplet("jmolApplet0", Info) > function jmolCheckbox(script1, script0,text,ischecked) > {Jmol.jmolCheckbox(jmolApplet0,script1, script0, text, ischecked)} > function jmolButton(script, text) {Jmol.jmolButton(jmolApplet0, > script,text)} > function jmolHtml(s) { document.write(s) }; > function jmolBr() { jmolHtml("<br>") } > function jmolMenu(a) {Jmol.jmolMenu(jmolApplet0, a)} > > > > const printproteinbuttons=LocalModels.filter(function(element){ > // return console.log(element) > return jmolCheckbox("pqrOn=true;load append '" + element + "'; > models 0; center {0 0 0 } ; reset;" ,"pqrOn=false; display not > '"+element+"'",element ,false) > > }) > > > </script> > > > > > and some other details not relevant. I could upload more code if needed. > > > Thanks for your time and any help is much appreciated. > > > K.B. > > > > > > > > > > > > > > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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: Mavridakis, K. <kon...@h-...> - 2020-01-10 15:31:00
|
Hello. I am trying to work out a script for a web-page so that I can display several proteins at once. Although I have read other posts where the relative commands for use in the console of jsmol, are mentioned, I haven't found anything on how to implement such details from code. To be more precise, the goal is to have a series of buttons ( at this point I have added jmolCheckbox options) so that, when a user click's the protein will show up. If he checks another one, then both proteins are shown. I use " load append" for this and so far, for displaying all the proteins, I use "model 0" . The proteins are loaded by their names. But, what I would like is this. For each button clicked, the corresponding proteins are shown, but only the last one get's selected, so that the user could modify the styles on each protein. Furthermore, if the user un- checks one of the previously chosen proteins, that protein should be hidden, but the settings implemented shouldn't be lost. My problem is that these select options seem to work by calling the proteins with numbers, like " select model 1.1 " and so on, and I can't figure out how to have such information in the script, since I am loading the proteins by name ; should there be a way that a function could get such information from the jsmol? My code for this part is : <script type="text/javascript"> jmolApplet0 = Jmol.getApplet("jmolApplet0", Info) function jmolCheckbox(script1, script0,text,ischecked) {Jmol.jmolCheckbox(jmolApplet0,script1, script0, text, ischecked)} function jmolButton(script, text) {Jmol.jmolButton(jmolApplet0, script,text)} function jmolHtml(s) { document.write(s) }; function jmolBr() { jmolHtml("<br>") } function jmolMenu(a) {Jmol.jmolMenu(jmolApplet0, a)} const printproteinbuttons=LocalModels.filter(function(element){ // return console.log(element) return jmolCheckbox("pqrOn=true;load append '" + element + "'; models 0; center {0 0 0 } ; reset;" ,"pqrOn=false; display not '"+element+"'",element ,false) }) </script> and some other details not relevant. I could upload more code if needed. Thanks for your time and any help is much appreciated. K.B. |
From: Angel H. <ang...@ua...> - 2019-12-20 17:18:04
|
Yes, that is what I magined. See my other reply sent to jmol-users On 20 Dec 2019 at 17:28, Klaus Schaper wrote: > > Hi Angel, > > I need JSmol to have finished execution before JS reads the canvas. After I read the canvas I > want JSmol to execute and finish again, before once again JS reads the changed canvas. > > Klaus > > > ****************************************************************************** > ****** > > PD Dr. Klaus Schaper > > http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de > > e-mail: sc...@kl... > > Arbeitsgruppe für Organische Photochemie > Institut für Organische Chemie und Makromolekulare Chemie I > Raum 26.43.00.27 > > Heinrich-Heine-Universität Düsseldorf > Universitätsstr. 1 > D-40225 Düsseldorf > Deutschland > > Telefon: +49 211 81 12571 > FAX: +49 211 81 14324 > > ****************************************************************************** > ****** > > |
From: Klaus S. <sc...@hh...> - 2019-12-20 16:28:35
|
Hi Angel, I need JSmol to have finished execution before JS reads the canvas. After I read the canvas I want JSmol to execute and finish again, before once again JS reads the changed canvas. Klaus **************************************************************************** ******** PD Dr. Klaus Schaper http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de <http://www.klaus-schaper.de/> e-mail: sc...@kl... Arbeitsgruppe für Organische Photochemie Institut für Organische Chemie und Makromolekulare Chemie I Raum 26.43.00.27 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 D-40225 Düsseldorf Deutschland Telefon: +49 211 81 12571 FAX: +49 211 81 14324 **************************************************************************** ******** |
From: Angel H. <ang...@ua...> - 2019-12-20 15:39:54
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There is another problem: in your curent setup, "JS read the canvas" might start before JSmol has finshed with "do something" Pease make clear which what you require to run in order and NOT to run in parallel |
From: Angel H. <ang...@ua...> - 2019-12-20 14:56:43
|
Hello Klaus In Javascript, alert() stops the flow and nothing wil be done until the alert is closed. It is true that Jmol scripts will run without waiting for javascript, and vice versa, but since your second Jmol.script is fired with a Javascript call, this will not execute until atfer the alert is closed. I guess you need the "do something else" to be started only after the JS "read the canvas" has finished - is that the case? |
From: Klaus S. <sc...@hh...> - 2019-12-20 14:45:50
|
Hi everybody, I have a piece of code, like the one shown below. I want to execute a Jmol.script, then read the graphic information from the canvas and then do something else. However, the do something is only executed after alert(2), which seems strange to me. My impression is, that communication with Jmol starts only after the execution of the function has finished. Is this the case? Do I have to move the Jmol.script command line in external function or is there another way. Klaus function xxx() { Jmol.script(JSmol_App_A, do something); some JS-cod, reading the content of the Jmol-canvas alert(1); Jmol.script(JSmol_App_A, do something else); alert(2); further JS-code } **************************************************************************** ******** PD Dr. Klaus Schaper http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de <http://www.klaus-schaper.de/> e-mail: sc...@kl... Arbeitsgruppe für Organische Photochemie Institut für Organische Chemie und Makromolekulare Chemie I Raum 26.43.00.27 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 D-40225 Düsseldorf Deutschland Telefon: +49 211 81 12571 FAX: +49 211 81 14324 **************************************************************************** ******** |