Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
Dear List,
I've spent more time with the excellent online help, and I think I've got
the atom selection figured out for my purposes.
Chagrined,
Matt
On 7/5/12 12:36 PM, "Kubasik, Matt" wrote:
>Dear list,
>
>I am seeking guidance on getproperty (and possibly correct atom
>expressions) within JmolData.jar. Will
>x=getproperty(³atominfo[nnn].xxx²} work in JmolData.jar?
>
>I would like to use JmolData.jar to process Gaussian output files
>containing vibrational vectors of atoms in different vibrational modes.
>
>The following sequence works fine in Jmol.jar (invoked via terminal¹s
>command-line, e.g." java -jar $Jmol -on $freqfile -s $script"), but it
>prints an empty string in JmolData.jar:
>
>framenumber=258
>frame @framenumber
>c_index=16
>cvibvector=getproperty("atomInfo["+c_index+"].vibVector")
>show cvibvector
>
>Is it that ³frame² does not work in JmolData.jar? Do I need a rigorous
>atom expression (for the 16th atom of the 258th frame) for JmolData.jar?
>
>As a work-around, the following syntax for getproperty places the
>vibvector for EVERY 16th atom of EVERY frame in an array in JmolData.jar:
>
>c_index=16
>allcvibes=getproperty("atominfo.vibVector",{atomno=c_index})
>
>Is there a better way to specify a particular atom of a particular
>frame/model in JmolData.jar?
>
>Matt Kubasik
>Department of Chemistry and Biochemistry
>Fairfield University
>
>PS Getproperty "modelinfo" seems to work equally well in either Jmol.jar
>or JmolData.jar. E.g., the following works the same in both:
>freq=getproperty("modelinfo.models["+framenum+"].modelProperties.Frequency
>");
>
>
>Details:
>Jmol Version: 12.3.31 2012-06-16 00:04
>java.vendor: Apple Inc.
>java.version: 1.6.0_31
>os.name: Mac OS X
>Access: ALL
>memory: 11.3/85.0
>
>
>--
>
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>___
>Jmol-users mailing list
>Jmol-users@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Addressing specific commands to one of two applets
3rd try
Another way, without changing the newAppletWindow() function in new.js
The popup page cannot read variables from the opener page but can
execute functins there (as proved by the call to jmolGetPropertyAsString() )
So:
1. set a ***javascript function*** in the mother page that returns a value
depending on your choice ("left" or "right" in your example).
function whichJmolCalled() {
var whichJmol = 'A';
if (document.getElementById('optB').checked) { whichJmol = 'B'; }
return whichJmol;
}
which you should adapt to your case --how you specify which applet (this I
did with two radio buttons A and B)
2. modify the JmolPopup.htm source like
function getState(){
if (theScript) {
return theScript
}
if (!opener) {
alert("The page that opened this pop-up window is not available.")
return ""
}
if (typeof opener.whichJmolCalled == "undefined") { var t = "0"; }
else { var t = opener.whichJmolCalled(); }
return opener.jmolGetPropertyAsString("stateInfo","", t)
}
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Addressing specific commands to one of two applets
2nd try
It seems that the popup page cannot read variables from the opener page
(at least in my Firefox Win), so I've changed the procedure:
1. set a javascript variable in the mother page which value is set depending
on
your choice ("left" or "right" in your example). Let's say that variable is
called
whichJmol
2. change the newAppletWindow() function in new.js to read and use that
variable in the link, like
var newwin=open("JmolPopup.htm?whichJmol=" + whichJmol,"jmol_"+sm,
woptions2)
Note I am using the same word for the variable name and the URL
parameter; they could be different.
3. modify the JmolPopup.htm source like
function getState(){
if (theScript) {
return theScript
}
if (!opener) {
alert("The page that opened this pop-up window is not available.")
return ""
}
var t = location.search.split('whichJmol=')[1]; //this is crude, may be done
safer
return opener.jmolGetPropertyAsString("stateInfo","", t ? t : "0")
}
Ah, everything is fine here.
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
those aren't actual links -- that is just Jmol script that is being messed
with by your browser.
On Thu, Jul 5, 2012 at 11:38 AM, Angel Herráez wrote:
> I tried to test Bob's script, and it seems that the space after 80&
> must be removed
>
> x = "http://webbook.nist.gov/cgi/cbook.cgi?Mask=80&"; + script("show
> chemical inchi")
>
>
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Addressing specific commands to one of two applets
Nick,
For the record, this is achieved trivially using JmolApi.js instead of
Jmol.js.
1) There are no defaults -- you specify which applet in all calls.
2) The first parameter of all calls is the applet id -- the full name, not
the "extension" There are no extensions, just whatever you call the applet.
The way you set up an applet using JmolApi.js is with three commands
(recommended -- could all be one):
jmolLeft = "jmolLeft"
// looks odd, but it allows adding buttons and script calls
// prior to the introduction of the applet on the page.
Info = {} // all the parameters here -- see JmolApi.js
jmolLeft = Jmol.getApplet(jmolLeft, Info) // creates the applet
Then all the calls look like this:
Jmol.x(jmolLeft,)
Note that before the getApplet call, this variable "jmolLeft" is a string;
after it is a Jmol._JmolApplet object.
If you have more than one applet, you just define more variables:
jmolRight = "jmolRight"
etc. You can reuse Info or make separate ones. Info can be deleted after
the Jmol.getApplet() call if you want.
Along with JmolApi.js, you need two other files minimum:
JmolCore.js (first)
JmolApplet.js
JmolApi.js
That gets you the full capability of Jmol.js, plus some. All the functions
you will ever call, though, are in JmolApi.js
JmolPopup2.htm is designed for JmolApi.js. You can either define
Jmol._lastAppletID
or you can add that to the URL with "?ID=" to specify which applet is
the originator.
That's at http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolPopup2.htm
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Addressing specific commands to one of two applets
Ok, some suggestions for the popup:
The relevant code is in JmolPopup.htm within function getState()
It says
opener.jmolGetPropertyAsString("stateInfo")
jmolGetPropertyAsString() takes a target applet ID as its 3rd parameter,
http://jmol.sourceforge.net/jslibrary/index.en.html#jmolGetPropertyAsString
so I would
1. set a javascript variable in the mother page which value is set depending
on your choice ("left" or "right" in your example). Let's say that variable is
called whichJmol
2. modify the JmolPopup.htm source like
function getState(){
if (theScript) {
return theScript
}
if (!opener) {
alert("The page that opened this pop-up window is not available.")
return ""
}
var t = opener.whichJmol ? opener.whichJmol : "0";
return opener.jmolGetPropertyAsString("stateInfo","", t)
}
I think that should do it.
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Addressing specific commands to one of two applets
Hi Nick
While jmolSetTarget() applies to UI controls, jmolScript() specifies its target
directly, as the 2nd parameter
http://jmol.sourceforge.net/jslibrary/#jmolScript
So you would use
javascript:jmolScript('load
model/miscellaneous/ene_reaction/1-pentene_decomposition.xyz', 'right')"
> I also use the JmolPopup.htm method to generate a new window with the
> contents of the the
> current Jmol applet in place e.g.
> http://138.253.125.70/~eleanorvail/externalslim/Main%20Page.html click the
> More Controls
> button. Would it be possible to make this work with one of two applets at
> will?
It sure will, but I'm not familiar with the source code of JmolPopup.htm. I
will
try and have a look.
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
I tried to test Bob's script, and it seems that the space after 80&
must be removed
x = "http://webbook.nist.gov/cgi/cbook.cgi?Mask=80&"; + script("show chemical
inchi")
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
Dear list,
I am seeking guidance on getproperty (and possibly correct atom expressions)
within JmolData.jar. Will x=getproperty(“atominfo[nnn].xxx”} work in
JmolData.jar?
I would like to use JmolData.jar to process Gaussian output files containing
vibrational vectors of atoms in different vibrational modes.
The following sequence works fine in Jmol.jar (invoked via terminal’s
command-line, e.g." java -jar $Jmol -on $freqfile -s $script"), but it
prints an empty string in JmolData.jar:
framenumber=258
frame @framenumber
c_index=16
cvibvector=getproperty("atomInfo["+c_index+"].vibVector")
show cvibvector
Is it that “frame” does not work in JmolData.jar? Do I need a rigorous atom
expression (for the 16th atom of the 258th frame) for JmolData.jar?
As a work-around, the following syntax for getproperty places the vibvector for
EVERY 16th atom of EVERY frame in an array in JmolData.jar:
c_index=16
allcvibes=getproperty("atominfo.vibVector",{atomno=c_index})
Is there a better way to specify a particular atom of a particular frame/model
in JmolData.jar?
Matt Kubasik
Department of Chemistry and Biochemistry
Fairfield University
PS Getproperty "modelinfo" seems to work equally well in either Jmol.jar or
JmolData.jar. E.g., the following works the same in both:
freq=getproperty("modelinfo.models["+framenum+"].modelProperties.Frequency");
Details:
Jmol Version: 12.3.31 2012-06-16 00:04
java.vendor: Apple Inc.
java.version: 1.6.0_31
os.name: Mac OS X
Access: ALL
memory: 11.3/85.0
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
got blocked because of the image. It's an interesting script. Best with
"background white" but also kind of cool with "background black"
On Wed, Jul 4, 2012 at 7:26 PM, Robert Hanson wrote:
> I must be missing something here...
>
>
> load $caffeine
> x = "http://webbook.nist.gov/cgi/cbook.cgi?Mask=80&"; + script("show
> chemical inchi")
> y = "http://webbook.nist.gov/cgi/cbook.cgi?Spec="; +
> load(x).split("Spec=")[2].split('"')[1].replace("amp;","")
> background image @y
>
> At this point y =
> http://webbook.nist.gov/cgi/cbook.cgi?Spec=C58082&Index=0&Type=IR
>
> Right?
>
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: Reminder: IIT System Downtime Friday afternoon, July 6
>From St. Olaf IT... This includes chemapps.stolaf.edu, I believe. -- Forwarded message -- Greetings, This is a reminder that many IIT systems will be unavailable from Friday, July 6, 12:00 noon to Friday, July 6, 6:00 PM while we perform maintenance and upgrades on our servers. During this downtime, - We will have a minimal web presence online -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
I must be missing something here...
load $caffeine
x = "http://webbook.nist.gov/cgi/cbook.cgi?Mask=80&"; + script("show
chemical inchi")
y = "http://webbook.nist.gov/cgi/cbook.cgi?Spec="; +
load(x).split("Spec=")[2].split('"')[1].replace("amp;","")
background image @y
At this point y =
http://webbook.nist.gov/cgi/cbook.cgi?Spec=C58082&Index=0&Type=IR
Right?
<>--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
