Activity for JSmol
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Bob Hanson committed [r1070] on Code
README
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JSmol project integrated into Jmol project. remaining code put in folder unused/
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JSmol project integrated into Jmol project. remaining code put in folder unused/
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adds site/JSmol_dev.htm
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house-cleaning - unused
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testing upload
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JSmol project no longer Java nature -- strictly for JavaScript aspects of Jmol
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deleting
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refactoring, cleaning
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refactoring JSmol JavaScript back to JSmol project
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update for SourceForge https protocol
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adds Jmol Point Group Explorer, fixes cyclflip2.spt, better cip.htm, new jsmol.zip
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antialiasdisplay
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adds Jmol._lastAppletID
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jsmetest3, klotho, j2sjmol for e.printStackTrace(), adds Jmol.___JmolVersion="14.32.52" // also 15.2.52p
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adding J/bspt/PointIterator
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adds symmetry sg for CALCULATE SPACEGROUP
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JSmol update for drag and drop into console
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JSmol javaScript update includes cip, simple2 updates and Jmol 14.32.1
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delete
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14.31.47 emdb
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Jmol.___JmolVersion="15.1.45" - ModelKit save state
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Jmol.___JmolVersion="15.1.44"
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Jmol 14.31.42
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Core adds JU/JSJSONParser and JU/JSONException.js
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Jmol.___JmolVersion="15.1.40"
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applet._j2sFullPath
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es6/wasm
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inchi update
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inchi addition, jars
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build adds JM/MMConstraint.js
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Jmol.___JmolVersion="14.31.16"
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update
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Jmol 14.31.4/15.1.6
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E.g. in the jmol readme https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/ I saw a comment from 2018 that all development is moving to GitHub (to the SwingJS version) but there still seems to be development on the SVN as well. What are the plans in this regard (sorry if this is already written somewhere else)? The SVN repo is still the primary repo for Jmol and JSmol. All my distribution is through that channel. https://github.com/BobHanson/Jmol-SwingJS is in sync with that but not compatible,...
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Leopold Talirz posted a comment on discussion General Discussion
Dear Bob, since we (like many others) are avid users of JSmol, we were wondering whether you'd be happy to share some thoughts on your future plans for the development of JSmol. E.g. in the jmol readme I saw a comment from 2018 that all development is moving to GitHub (to the SwingJS version) but there still seems to be development on the SVN as well. What are the plans in this regard (sorry if this is already written somewhere else)? I think also for JSmol, a move to GitHub could be a great way...
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JSpecView refactoring almost complete
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JSpecView refactoring almost complete
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JSpecView refactoring almost complete
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various fixes
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nmr_predict_HC.htm fixes
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Jmol.___JmolVersion="14.29.31"
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minor upgrades
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Yes, it's not always the case, so it is a bit surprising to me that you need that. Maybe because the body is not created yet. Also, note that you should not create jmolApplet0_infodiv. That is created already as part of the HTML you retrieve. Not sure why you are returning that. div = document.createElement('div'); div.id = "jmolApplet0_infodiv"; return document.querySelector("body").appendChild(div); On Tue, Sep 18, 2018 at 1:16 PM Leopold Talirz leoteo@users.sourceforge.net wrote: Ok, I believe...
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Ok, I believe the problem is on my side this time. I'll be looking into this now - no need for you to spend more time on this for the time being. Thanks a million for the _cover(false) suggestion - this would have taken me a long time to figure out.
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Using your suggestion I can make the applet load as well now - thanks again! I guess you were already running the bokeh server - indeed the button does not work there although it should. The problem is that in return Jmol.script(_this._graph, _this.model.info_source.x[0]); for some reason _this._graph is undefined. But I guess you have already figured this out ;-)
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Using your suggestion I can make the applet load as well now - thanks again! I guess you were already running the bokeh server - indeed the button does not work there although it should. The problem is that in return Jmol.script(_this._graph, _this.model.info_source.x[0]); for some reason _this.graph is undefined. But I guess you have already figured this out ;-)
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Thanks a lot - I'll look into it immediately checking why the button is not working.... Just very briefly to avoid wasting your time: the button should not work in the .html version (it should only work when running the bokeh server)
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By using the html code that way, you are creating a "deferred applet" -- just a cover image until sometime later. So add jmolApplet0._cover(false); at the end of JSMolView.prototype._init checking why the button is not working.... [image: image.png] On Tue, Sep 18, 2018 at 10:29 AM Leopold Talirz leoteo@users.sourceforge.net wrote: Dear Bob, bokeh can either run as a server or (as long as you don't need to call back from python into your app) produce html output. Both have the same issue - for simplicity...
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Dear Bob, bokeh can either run as a server or (as long as you don't need to call back from python into your app) produce html output. Both have the same issue - for simplicity find here the html output produced by bokeh with the JSmol extension https://www.dropbox.com/s/9f9t8pdkleahbxq/jsmol.html?dl=1 In case you would like to produce the html locally/run the bokeh server, it's very simple as well. I've just updated the installation instructions on https://github.com/ltalirz/jsmol-bokeh-extension/...
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I'd like to learn more about this. Can you send a link to an active site? On Tue, Sep 18, 2018 at 3:01 AM Leopold Talirz leoteo@users.sourceforge.net wrote: P.S. Looking in the JS console, it turns out that when using the HTML approach, no messages from JSmol are shown at all (not even "JSmol load jmolApplet0 loadClazz...") JSmol not loading with getAppletHtml(...) https://sourceforge.net/p/jsmol/discussion/general/thread/48083aa7/?limit=25#7750 Sent from sourceforge.net because you indicated interest...
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P.S. Looking in the JS console, it turns out that when using the HTML approach, no messages from JSmol are shown at all (not even "JSmol load jmolApplet0 loadClazz...")
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Dear Bob, thanks for getting back to me so rapidly and sorry for the late reply! (I didn't realize I need to subscribe to the thread to be notified - now I am) This is node? This is coffeescript (see the link to the full code). I'm very new to JS/coffeescript though. Your suggestion has the same result as my code with the first line uncommented (applet is inserted, but loader animation is shown indefinitely). The fact that both approaches yield the same result is consistent with the wiki (I was just...
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catches JavaScript strict mode for arguments.callee.caller
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This is node? The overwriting is due to using Jmol.getApplet() instead of Jmol.getAppletHtml() in that first call. So: var html = Jmol.getAppletHtml("jmolApplet0", Info) Jmol.script(jmolApplet0,"background black;load https://dev-www.materialscloud.org/cofs/api/v2/cifs/febd2d02-5690-4a07-9013-505c9a06bc5b/content/download") @el.innerHTML = html should work.
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Hi, I'm trying to create a basic bokeh extension for JSmol and I'm struggling to get bokeh and JSmol work together. The code in question can be found here #Jmol.setDocument(0) Jmol.getApplet("jmolApplet0", Info) Jmol.script(jmolApplet0,"background black;load https://dev-www.materialscloud.org/cofs/api/v2/cifs/febd2d02-5690-4a07-9013-505c9a06bc5b/content/download") @el.innerHTML = Jmol.getAppletHtml(jmolApplet0) As is, jmol loads fine (but entirely overwrites the html body, which contains bokeh components)....
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Hi, I'm trying to create a basic bokeh extension for JSmol and I'm struggling to get bokeh and JSmol work together. The code in question can be found here #Jmol.setDocument(0) Jmol.getApplet("jmolApplet0", Info) Jmol.script(jmolApplet0,"background black;load https://dev-www.materialscloud.org/cofs/api/v2/cifs/febd2d02-5690-4a07-9013-505c9a06bc5b/content/download") @el.innerHTML = Jmol.getAppletHtml(jmolApplet0) As is, jmol loads fine (but entirely overwrites the html body, which contains bokeh components)....
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fix for popup menu not actuating checkbox items. single-file replacement is dist/tmp/coremenu.z.js and dist/tmp/corejsvmenu.z.js, which both go into j2s/core
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fix for popup menu not actuating checkbox items. single-file replacement is dist/tmp/coremenu.z.js and dist/tmp/corejsvmenu.z.js, which both go into j2s/core
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fix for popup menu not actuating checkbox items. single-file replacement is dist/tmp/coremenu.z.js and dist/tmp/corejsvmenu.z.js, which both go into j2s/core
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fix for popup menu not actuating checkbox items. single-file replacement is dist/tmp/coremenu.z.js, which goes in j2s/core
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fixes for new file locations
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Yes, it certainly should work. Q: JSmol version? (from context menu) Could be: -missing class files for biomolecules -bad PDB file Check -- your browser developer console. Any JavaScript or AJAX error? -- the Jmol JavaScript console. (popup-menu... JavaScript Console) Hopefully there is a message there. ​Bob Hanson
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Kulnigg Klaus posted a comment on discussion General Discussion
Greetings to all! I try to write a chemistry-e-book for students with html5 and want visualize mol-files und pdb-files. some years before - i wrote a windows applikation with html and chime browser plugin to visualize my molecule (also mol and pdb) and it works great. now it should be a locally app (complete offline) for android and ios. so far so good - it works for mol-files, but i get no sucess for pdb files! only empty screen no error! it should be very simple - only display and rotate the molecule...
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refactored core files - untested
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security upgrade
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security upgrade
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fix to remove unused JSmol implementation in JmolAudio
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revised Jmol.playAudio
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validation.htm upgraded and simple.htm fixed for electron density; ligand.htm added
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Jmol.___JmolVersion="14.29.2"
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fix for Jmol2.js not recognizing "all" in script command extensions
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14.28.3
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If System.out is not defined, then you have not loaded the main .js file for JSmol. Best to get that figured out first. On Thu, Jan 18, 2018 at 3:14 PM, jose gomez jose-gomez-ml@users.sf.net wrote: Is there a way to disable all System.out.println calls in JSmol? One of our systems is not able to load JSmol because System.out is not defined. Is there a version of JSmol.min.js that doesnt have all that debugging? Is it needed? Thank you, Jose Disable or removing all System.out.println calls https://sourceforge.net/p/jsmol/discussion/general/thread/d03ccd24/?limit=25#ae44...
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jose gomez posted a comment on discussion General Discussion
Is there a way to disable all System.out.println calls in JSmol? One of our systems is not able to load JSmol because System.out is not defined. Is there a version of JSmol.min.js that doesnt have all that debugging? Is it needed? Thank you, Jose
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Jmol.___JmolVersion="14.28.2" // released 2018.01.17
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fixes issue with http:chemapps instead of https:chemapps (Chrome/Safari cannot post to server)
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missing org/qcschema
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