Re: [Jmol-developers] myJmol as variable in Jmol.script

[Angel Herráez]

Hi Klaus

Go to http://chemapps.stolaf.edu/jmol/docs/ and search for "rotationRadius"
You will see there is "set rotationRadius"
therefore you can try

show rotationRadius

and it works!

Examples of use:

show rotationRadius  // rotationRadius = 20.94923
rr = rotationRadius; print rr;  // 20.94923



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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

yes, if you check

show orientation

you will see a parameter "rotation radius"

You can set that to a new number, then disable zoom. It sets the
magnification for "100%".



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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

Klaus,

When you create an applet, it automatically creates a top-level object with
the name of your applet.

However, you can't do anything with that object until it is at least
started to be created.

Have you tried any of the html files in the jsmol/ directory? There are
plenty of examples of this. One  that comes to mind is
http://chemapps.stolaf.edu/jmol/jsmol/simple2_old.htm


I do not recommend eval(name), and I have never needed it.


On Mon, May 9, 2016 at 2:25 AM, Klaus Schaper  wrote:

> Hi everybody,
>
>
>
> Thanks to Rolf, that did the trick! I successfully converted a little bit
> of script to the new syntax and the other functions will hopefully cause no
> problems.
>
>
>
>
>
> However, one more problem remains. After converting the script to the new
> syntax using
>
>
>
> 1) Jmol.getApplet(Ziel, Info);
>
>
>
> and
>
>
>
> 2) Jmol.script(eval(name), commands);
>
>
>
> The code will run in my JSmol enviiroment, but not in the Jmol environment.
>
>
>
> My conclusion is, that
>
> either the new syntax is not compatible to the old Jmol using JAVA,
>
> or that I did not include all necessary files in my html document. Which 
> files (beside the old Jmol.js) do I have to include?
>
>
>
> Klaus
>
>
>
>
>
>
>
>
> 
>
>
>
> PD Dr. Klaus Schaper
>
>
>
> http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de
>
>
>
> e-mail: scha...@klaus-schaper.de
>
>
>
> 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
>
>
>
>
> 
>
>
>
>
>
>
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Northfield, MN
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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Angel Herráez]

Hello Klaus 

I think that it should be possible to do what you want without using eval(), 
which is usually not recommended by javascript gurus.

The variable is indeed an object and not a string, but that is what Jmol  
expects.
There may be a problem when the variable has not been defined 
beforehand; not sure if it will be your case. The trick in that case is to 
define 
it first like
  myJmol = "myJmol"

Better: 
I made a page with your functions and it is working as desired when I use it 
like this


but I get the error when I use it like this:


So the issue would be you must pass the object, not the name.

If you don't want to write the object manually, like I did, I suggest that you 
use the following instead of eval; one way to refer to objects ny their name is 
to use 
 window[objectname]

That would allow for example this to apply to all Jmol objects named A, B, C, 
D:

function setAll() {
for (i=65; i<69; i++) {
KS_AtomeHervorheben( window[String.fromCharCode(i)] )
}
}





> However, one more problem remains. After converting the script to the new 
> syntax using
> The code will run in my JSmol enviiroment, but not in the Jmol 
> environment.
> either the new syntax is not compatible to the old Jmol using JAVA,
> or that I did not include all necessary files in my html document. Which 
> files (beside the old Jmol.js) do I have to include?

It is compatible, but you must be moving to new syntax also for the Java 
mode. You must not use Jmol.js any longer, instead just change:

Info.use = 'java'

Info.use = 'html5'   // default



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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Robert Hanson]

I would put a line

alert(name)

in that function to see what that variable is. Perhaps it is not defined at
the time you are making  the call.


Also, I don't  recommend giving an applet a name like "A" or "B" -- to easy
to use a variable that is used by something else. I would suggest "jmolA"
"jmolB" or something like that. What most people do is "jmolApplet1"
"jmolApplet2" .

Bob



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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Rolf Huehne]

Am 07.05.16 um 10:22 schrieb Klaus Schaper:
> Hi everybody,
>
> I just decided as recommended to switch from jmolScript to the modern
> Jmol.script syntax.
>
> I create to applets with the following function:
>
> function KS_ErzeugeAppRechteck(Ziel)
>
> {
>
> var Info = {src: "Ethan.xyz"};
>
> Info.j2sPath
> ="http://schelm.hhu.de/home/Lehre/scheLM_Test/_INCLUDE/JSMOL/j2s;;
>
> Jmol.getApplet(Ziel, Info);
>
> }
>
> I call this function twice from my webpage:
>
>  KS_ErzeugeAppRechteck('A'); 
>
>  KS_ErzeugeAppRechteck('B'); 
>
> Thus creating to applets with the name A and B.
>
> If I run the following function I can set the color of two atoms in A to
> blue:
>
> function KS_AtomeHervorheben()
>
> {
>
> Jmol.script(A, "select hydrogen;color white;select
> atomno=3,atomno=6; color atoms blue");
>
> }
>
> __
>
> If I change myJmol to B I can change the color of two atoms in B
>
> __
>
> function KS_AtomeHervorheben()
>
> {
>
> Jmol.script(B, "select hydrogen;color white;select
> atomno=3,atomno=6; color atoms blue");
>
> }
>
> However, what I really would like to do is to pass the name of the
> applet by the function call and parse it into the jmol.script command.
>
> function KS_AtomeHervorheben(name)
>
> {
>
> Jmol.script(name, "select hydrogen;color white;select
> atomno=3,atomno=6; color atoms blue");
>
> }
>
> However, I get the following error “TypeError: a._checkDeferred is not a
> function”.
>
> Is there any way to path the name of the app by the function call to the
> Jmol.script command or is there any other way to get the job done. I
> have webpages containing 7 Jsmol apps and I do not want to write the
> same commands 7 times.
>
Klaus, I think 'A' and 'B' are objects and not just names. So you could 
try to use the 'eval' function to address the objects:

Jmol.script(eval(name), "select hydrogen;color white;select 
atomno=3,atomno=6; color atoms blue");

Regards,
Rolf

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