Re: [Jmol-users] Jmol and xhtml

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Ok.  I think I've tracked down the problem in Firefox to using  
createElement.  It seems that in xhtml we need to use  
createElementNS.  Unfortunately, when I substituted this code

document.createElementNS('http://www.w3.org/1999/xhtml', tagname)

in place of

document.createElement(tagname)

I still get the same error.

The following

http://simonwillison.net/2003/Jun/15/javascriptWithXML/

has a discussion of the issue and a general solution although, as I  
said above, it doesn't seem to be working for me.

***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jh...@de...
***********************************************

On May 7, 2009, at 9:25 AM, Robert Hanson wrote:

> Jeff, there should be no need to do the find and replace -- the code  
> I have there lowers the case for all attribute names as it processes  
> them.
>
> error: sure looks OK to me. Does it do the same at:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/t3.xhtml
>
> ?
>
>
> So I suppose there is no way to get MSIE reading these pages, right?
>
> Bob
>
>
> On Thu, May 7, 2009 at 8:07 AM, Jeff Hansen <jh...@de...>  
> wrote:
> Ok.  So I grabbed this new Jmol.js and saved it as JmolXHTML.js.  I  
> did a find and replace on onClick, onMouseover, onMouseout, and  
> onChange to make them all lowercase.  Using that in my page instead  
> of Jmol.js worked fine in Safari.  In Firefox 3.04 it gave the  
> following error:
>
> uncaught exception: String contains an invalid character  
> (NS_ERROR_DOM_INVALID_CHARACTER_ERR)
>
> The offending line of code was:
>
> 	var e = (tagname == closetag  || tagname == "/" ? "" :  
> document.createElement(tagname))
>
>
> I don't see a problem here.  Anyone have an idea why Firebug is  
> flagging this line as a problem?
>
>
> ***********************************************
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jh...@de...
> ***********************************************
>
>
> On May 7, 2009, at 12:01 AM, Robert Hanson wrote:
>
>> Well, you are quicker than I am. Try this:
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/t2.xhtml
>>
>> and
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js
>>
>>
>> On Wed, May 6, 2009 at 8:35 PM, Jeff Hansen <jh...@de...>  
>> wrote:
>> Bob,
>>
>> The idea is to use a multiple model file in Jmol, pull out the  
>> energies of each model, and use that data to generate an svg  
>> graph.  The svg should highlight the point corresponding to the  
>> model currently being displayed and likewise if the user clicks a  
>> point on the svg it will highlight the point and update the jmol to  
>> display the corresponding model.  In other words, the svg will be a  
>> graph of the energies of the models and the svg and applet will  
>> "talk" to each other.
>>
>> Currently I am using jmolInitialize, jmolApplet, jmolEval, and  
>> jmolGetPropertyAsArray.  Of course I would prefer to use jmol.js  
>> but if necessary can do without it.
>>
>>
>> Jeff
>>
>> ***********************************************
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jh...@de...
>> ***********************************************
>>
>>
>> On May 6, 2009, at 7:52 PM, Robert Hanson wrote:
>>
>>> Ah, that sounds familiar. Correct. There is no "document.write" in  
>>> XHTML. Sorry. That pretty much rules it out.
>>>
>>> As I recall Egon at one point wrote a DOM-specific XHTML version  
>>> of a page that worked with Jmol, though not Jmol.js.
>>>
>>> But you don't necessarily have to have Jmol.js to use Jmol. You  
>>> just have to work harder to do it without.
>>>
>>> So what is the deal with "inline SVG"?
>>>
>>> Bob
>>>
>>>
>>> 2009/5/6 Angel Herráez <ang...@ua...>
>>> It seems that the first hit is caused by document.write not being  
>>> supported
>>> by XHTML (documented in several websites)
>>>
>>> My test:
>>> XHTML 1.0 Transitional
>>>
>>> _jmol.currentDocument.write(text);
>>> at line line 834 within
>>> function _jmolDocumentWrite(text) {
>>>
>>> throws an error in Firefox 3
>>> No error in Opera, but no applet
>>>
>>> Clue:
>>> Does document.write work in XHTML?
>>> No. Because of the way XML is defined, it is not possible to do  
>>> tricks like
>>> this, where markup is generated by scripting while the parser is  
>>> still parsing
>>> the markup.
>>> You can still achieve the same effects, but you have to do it by  
>>> using the
>>> DOM to add and delete elements.
>>> (source: http://www.w3.org/MarkUp/2004/xhtml-faq#docwrite)
>>>
>>>
>>> And quoting
>>> http://jmol.sourceforge.net/docs/JmolAppletGuide.html#XHTMLSupport
>>>
>>> the standard Jmol.js Javascript library will not work under properly
>>> compliant XML browsers. An alternative, largely similar, but  
>>> entirely
>>> unsupported library is available ... insert address here ...
>>> (that JmolAppletGuide doc is old --Miguel's times? . but true  
>>> indeed)
>>>
>>>
>>> I've tested the alternative to document.write given at
>>> http://weston.ruter.net/projects/xhtml-document-write/
>>> http://shepherd-interactive.googlecode.com/svn/trunk/xhtml-document-
>>> write/xhtml-document-write.js
>>>
>>> and, althogh it does not solve the problem, is on its way:
>>>
>>> Opera displays a functional applet, but below it is the  yellow  
>>> box that says
>>> "you don't have Java" (generated by Jmol.js)
>>>
>>> Firefox displays a Java box with an error, applet class not found,  
>>> and the
>>> yellow box below it
>>>
>>> IE8 displays nothing --seems not to like xhtml at all --even with  
>>> no Jmol
>>> code in the page, it just displays a blank page and does a  
>>> download --of the
>>> page?.
>>>
>>>
>>> More to come...
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The NEW KODAK i700 Series Scanners deliver under ANY  
>>> circumstances! Your
>>> production scanning environment may not be a perfect world - but  
>>> thanks to
>>> Kodak, there's a perfect scanner to get the job done! With the NEW  
>>> KODAK i700
>>> Series Scanner you'll get full speed at 300 dpi even with all image
>>> processing features enabled. http://p.sf.net/sfu/kodak-com
>>> _______________________________________________
>>> 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
>>> ------------------------------------------------------------------------------
>>> The NEW KODAK i700 Series Scanners deliver under ANY  
>>> circumstances! Your
>>> production scanning environment may not be a perfect world - but  
>>> thanks to
>>> Kodak, there's a perfect scanner to get the job done! With the NEW  
>>> KODAK i700
>>> Series Scanner you'll get full speed at 300 dpi even with all image
>>> processing features enabled. http://p.sf.net/sfu/kodak-com_______________________________________________
>>> Jmol-users mailing list
>>> Jmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> ------------------------------------------------------------------------------
>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances!  
>> Your
>> production scanning environment may not be a perfect world - but  
>> thanks to
>> Kodak, there's a perfect scanner to get the job done! With the NEW  
>> KODAK i700
>> Series Scanner you'll get full speed at 300 dpi even with all image
>> processing features enabled. http://p.sf.net/sfu/kodak-com
>> _______________________________________________
>> 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
>> ------------------------------------------------------------------------------
>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances!  
>> Your
>> production scanning environment may not be a perfect world - but  
>> thanks to
>> Kodak, there's a perfect scanner to get the job done! With the NEW  
>> KODAK i700
>> Series Scanner you'll get full speed at 300 dpi even with all image
>> processing features enabled. http://p.sf.net/sfu/kodak-com_______________________________________________
>> Jmol-users mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> ------------------------------------------------------------------------------
> The NEW KODAK i700 Series Scanners deliver under ANY circumstances!  
> Your
> production scanning environment may not be a perfect world - but  
> thanks to
> Kodak, there's a perfect scanner to get the job done! With the NEW  
> KODAK i700
> Series Scanner you'll get full speed at 300 dpi even with all image
> processing features enabled. http://p.sf.net/sfu/kodak-com
> _______________________________________________
> 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
> ------------------------------------------------------------------------------
> The NEW KODAK i700 Series Scanners deliver under ANY circumstances!  
> Your
> production scanning environment may not be a perfect world - but  
> thanks to
> Kodak, there's a perfect scanner to get the job done! With the NEW  
> KODAK i700
> Series Scanner you'll get full speed at 300 dpi even with all image
> processing features enabled. http://p.sf.net/sfu/kodak-com_______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol and xhtml

An interactive viewer for three-dimensional chemical structures.

Re: [Jmol-users] Jmol and xhtml