Re: [Jmol-users] How to use JmolApplet to display molecules protected by authenticated session?

[Mike M. <mi...@as...>]

Hi all,
I have tried unsuccessfully to remove myself from the forum.  Can you please 
try to do so manually as I have tried everything I can to do it myself,
Thanks,
Mike Miller,


-----Original Message-----
 From: Robert Hanson <ha...@st...>
 To: jmo...@li...
 Date: Thu, 30 Aug 2012 08:16:38 -0500
 Subject: Re: [Jmol-users] How to use JmolApplet to display molecules 
protected by authenticated session?

 You  won't be able to load binary data into Jmol using any script command. 
Sorry. This won't work with .jmol files.

So basically you have the problem that Java itself can't load the file as a 
script, and the file is binary. Right?

I can probably do something  about that. As long as the binary data is 
mappable to Java byte[]
I'll get back to you with a test tonight or tomorrow. I think it should be 
possible, but it's going to be rather tricky.

Bob


On Thu, Aug 30, 2012 at 5:38 AM, Mikko Rantalainen 
<mik...@pe... [mailto:mik...@pe...]> wrote:

2012-08-28 22:04 Europe/Helsinki: Robert Hanson:

> Main problem I see there is that you are not waiting for the applet to
 > initialize. You need to do that call from within an appletReadyCallback
 > function.OK. I fixed that. I tried both Jmol.js and Jmol-JSO libraries 
and I'm
 pretty sure my current problem is only related to data to be passed to
 applet's method loadInlineString().

 I've prepared a demo at http://peda.net/veraja/demo/mikko/testit/jmol 
[http://peda.net/veraja/demo/mikko/testit/jmol]


 What already works:

 demo-load-sdf.html:
         load SDF file via Jmol applet

 demo-load-jmol.html:
         load JMZ/JMOL file via Jmol applet

 demo-ajax-load-sdf.html:
 load SDF file via ajax in paraller with Jmol applet loading


 What does not work:

 demo-ajax-load-jmol.html:
 load JMZ/JMOL file via ajax in paraller with Jmol applet loading


 The files demo-ajax-load-sdf.html and demo-ajax-load-jmol.html are
 identical except for the file to load (ioversol.sdf vs ioversol.jmol).

 I believe that the problem is around line 96 of file
 "demo-ajax-load-jmol.html" where I have the binary data in javascript
 variable "data" and I'm trying to call Jmol.js function
 "jmolLoadInline(data)". I guess I would need to do some kind of
 conversion to get the binary data to correctly end up to the applet. (If
 I have understood correctly, Java strings are technically a bit
 different compared to JavaScript strings. I guess this causes problems
 with the binary contents in variable "data" which contains binary zeros
 among other stuff.)

 In short: I have a binary file contents (ZIP-archive / JMZ / .jmol) in a
 variable called "data". How can I get jmolLoadInline() to work with the
 full data?

 The example files have been prepared to work in a local filesystem
 (tested Firefox 14, Google Chrome 22 denies XHR access to files in local
 filesystem so that cannot be used).

--
 Mikko
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr [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