Re: [Jmol-users] which jmol applet?
Hi Jeff
That shuld be in the doc... No! jmolEvaluate is not documented in
http://jmol.sourceforge.net/jslibrary/
Let me take a look at Jmol.js code...
function jmolEvaluate(molecularMath, targetSuffix)
So, you work as with jmolScript. That would be:
var Energy = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)' , 0 );
using 0 for the first applet, 1 for the second, etc., or their names if
you set them.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] loading external files in the signed applet
I am setting up a web page with the ability to load local files as
well as external files (for example, files coming from the pdb)
When I run the page locally, the applet is able to load any local
file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari):
java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms
eval ERROR: java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
line 1 command 1 of file null:
load http://www.rcsb.org/pdb/files/1gzx.pdb;
When the page is loaded from a webserver, the applet is unable to
load any local file, as well as remote files coming from elsewhere
than the webserver :
FileManager.openFile(''file:Users/paul/Desktop/
ac.pdb'') //''file:Users/paul/Desktop/ac.pdb''
FileManager opening http://ordinateur-de-judith-ciosi.local/~paul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
file ERROR: http://ordinateur-de-judith-ciosi.local/~paul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
java.io.FileNotFoundException: http://ordinateur-de-judith-
ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
openFile(''file:Users/paul/Desktop/ac.pdb''): 3 ms
eval ERROR: java.io.FileNotFoundException: http://ordinateur-de-
judith-ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
line 1 command 1 of file null:
load ''file:Users/paul/Desktop/ac.pdb''
I searched the mailing list archive for this issue and found a one
year old thread, which stated that this behavior is linked to the
inability to accept loading external files when the command is issued
by an unsigned javascript. A workaround is to reload the jmol applet
with the new file.
I would like to know if there is any other solution to make the
signed applet accept an external file ? I am also wondering at how
this problem has been dealt with in jmol protein explorer ?
Thanks in advance,
Paul
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] loading external files in the signed applet
Paul, check out this page to see how yours might be different.
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
It's using the signed applet and working just fine. Maybe has to be newer
than 11.6.RC8, but I don't think so. It should load files from the PDB using
load = and files from your hard drive using, for example:
load c:/temp/caffeine.xyz
Also, the Jmol Protein Explorer is using using the signed applet without a
hitch.
Bob
On Sat, Aug 30, 2008 at 7:32 AM, Paul Pillot
[EMAIL PROTECTED] wrote:
I am setting up a web page with the ability to load local files as
well as external files (for example, files coming from the pdb)
When I run the page locally, the applet is able to load any local
file, but sends an error message (Jmol 11.6.RC8, Mac OSX, Safari):
java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
openFile(http://www.rcsb.org/pdb/files/1gzx.pdb): 61 ms
eval ERROR: java.security.AccessControlException: access denied
(java.net.SocketPermission www.rcsb.org:80 connect,resolve)
line 1 command 1 of file null:
load http://www.rcsb.org/pdb/files/1gzx.pdb;
When the page is loaded from a webserver, the applet is unable to
load any local file, as well as remote files coming from elsewhere
than the webserver :
FileManager.openFile(''file:Users/paul/Desktop/
ac.pdb'') //''file:Users/paul/Desktop/ac.pdb''
FileManager opening
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
file ERROR:
http://ordinateur-de-judith-ciosi.local/~paul/http://ordinateur-de-judith-ciosi.local/%7Epaul/
JMolUSc/''file:Users/paul/Desktop/ac.pdb''
java.io.FileNotFoundException: http://ordinateur-de-judith-
ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
openFile(''file:Users/paul/Desktop/ac.pdb''): 3 ms
eval ERROR: java.io.FileNotFoundException: http://ordinateur-de-
judith-ciosi.local/~paul/JMolUSc/''file:Users/paul/Desktop/ac.pdb''
line 1 command 1 of file null:
load ''file:Users/paul/Desktop/ac.pdb''
I searched the mailing list archive for this issue and found a one
year old thread, which stated that this behavior is linked to the
inability to accept loading external files when the command is issued
by an unsigned javascript. A workaround is to reload the jmol applet
with the new file.
I would like to know if there is any other solution to make the
signed applet accept an external file ? I am also wondering at how
this problem has been dealt with in jmol protein explorer ?
Thanks in advance,
Paul
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Professor of Chemistry
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
I'm working with them -- they are mostly waiting for 11.6 to be stable. Then they will go to that. Bob On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez [EMAIL PROTECTED] wrote: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Assuming that they update their Jmol.js file!!! They are still using 10.2, and I think there have been requests for update already, to no avail - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
RCSB beta site is using Jmol 11.4. See for example: http://betastaging.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1O1I Current version there is 11.4.6, I think. On Sat, Aug 30, 2008 at 8:08 AM, Robert Hanson [EMAIL PROTECTED] wrote: I'm working with them -- they are mostly waiting for 11.6 to be stable. Then they will go to that. Bob On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez [EMAIL PROTECTED]wrote: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Assuming that they update their Jmol.js file!!! They are still using 10.2, and I think there have been requests for update already, to no avail - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry 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 -- Robert M. Hanson Professor of Chemistry 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] New feature inquiry
This is a preliminary inquiry about two feature requests. In my MolnIquiry site, I have imbedded line objects as bonds that can then be ?picked?; for example, students are asked to click on a peptide bond.). Creating these objects is a task, particularly if many are needed, and the lines can become visible if wireframe is turned off. Is it technically feasible that Jmol could: 1. generate a series of IDed objects between the connected atoms of an atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? where j is incrementally increased with each line? 2. set the color of an object as ?transparent? (but still pickable). Does anyone see any other applications of these features? Thanks. Steve Dept of Biology and Environmental Science Marietta College This message was sent using Marietta College WebMail. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
Quoting Robert Hanson [EMAIL PROTECTED]: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Bob, have you tried that already? If this is allowed it would be exactly what should pe prevented within Jmol.js! It should only be allowed to load a different Jmol version from the same server! Otherwise anyone could use your/our service by 'URL Spoofing' to deliver an evil Jmol applet (or even a totally different applet) to the user!!! Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
that's why I'm asking. Yes, I have tried this. We could make it only the applet from the server -- in other words not allow a new codebase -- if you think that is a major concern. How would you see the spoof working, Rolf? Bob On Sat, Aug 30, 2008 at 12:56 PM, [EMAIL PROTECTED] wrote: Quoting Robert Hanson [EMAIL PROTECTED]: One of the interesting aspects is that I could use JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar for example to go to the PDB website and use MY applet instead of theirs. Bob, have you tried that already? If this is allowed it would be exactly what should pe prevented within Jmol.js! It should only be allowed to load a different Jmol version from the same server! Otherwise anyone could use your/our service by 'URL Spoofing' to deliver an evil Jmol applet (or even a totally different applet) to the user!!! Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New feature inquiry
Steve, there's probably not much sense in creating a generic bond-equivalent object like that. But you can do what you say yourself. For example, if a student is asked to click on a peptide bond, you know what bond it is, so you can create the link yourself and, like you say, make them transparent but still clickable. That you can do right now. But I see your point about lots of these. I don't see why we can't set up bond picking if that is what you are after. Wouldn't that be better? Bob On Sat, Aug 30, 2008 at 10:41 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: This is a preliminary inquiry about two feature requests. In my MolnIquiry site, I have imbedded line objects as bonds that can then be ?picked?; for example, students are asked to click on a peptide bond.). Creating these objects is a task, particularly if many are needed, and the lines can become visible if wireframe is turned off. Is it technically feasible that Jmol could: 1. generate a series of IDed objects between the connected atoms of an atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j? where j is incrementally increased with each line? 2. set the color of an object as ?transparent? (but still pickable). Does anyone see any other applications of these features? Thanks. Steve Dept of Biology and Environmental Science Marietta College This message was sent using Marietta College WebMail. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
Quoting Robert Hanson [EMAIL PROTECTED]: that's why I'm asking. Yes, I have tried this. We could make it only the applet from the server -- in other words not allow a new codebase -- if you think that is a major concern. How would you see the spoof working, Rolf? The HTML code shown below just hides the 'JMOLJAR=...' extension within the status line. Althugh my Firefox 3 does show the real URL, even when I exceptionally allow status line changes, it still works with my Internet Eplorer 7. And this is just the most simple way. There are more sophisticated techniques possible. a href=http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1dehMODE=biological1JMOLJAR=http://www.fakejenalib.com/fakejmol.jar; onmouseout=window.status='';return true onmouseover=window.status='http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1dehMODE=biological1';return trueJenaLib Jmol Viewer/a Since it may be possible that the complete version is only shown as links here is a (modified) repeat of the Javascript portion: onmouseout=window.status='';return true onmouseover=window.status='original_URL';return true Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New feature inquiry
Jmol 11.6.RC12 now has
set atomPicking [default TRUE]
set bondPicking [default FALSE]
The report from the bond picking looks like this:
[bond,69 1 [GLY]37.C #263 -- [GLY]37.CA #262
1.5251089,21.2975,16.2235,6.473]
The First number is the bond ID. It is the number you would use to get the
bond properties:
print getProperty(BondInfo[69])
or
print getproperty(BondInfo, 69)
This number is also one more than the number you would use to specify that
bond using bond set notation (because in that case 0 is the first bond):
select [{68}]; color BOND white
The number 1 is the bond order; next are the identities of the two atoms and
the bond distance. The last three numbers are the coordinates of the center
of the bond.
That work for you, Steve?
Bob
On Sat, Aug 30, 2008 at 1:11 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Steve, there's probably not much sense in creating a generic
bond-equivalent object like that. But you can do what you say yourself. For
example, if a student is asked to click on a peptide bond, you know what
bond it is, so you can create the link yourself and, like you say, make them
transparent but still clickable. That you can do right now. But I see your
point about lots of these. I don't see why we can't set up bond picking if
that is what you are after. Wouldn't that be better?
Bob
On Sat, Aug 30, 2008 at 10:41 AM, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
This is a preliminary inquiry about two feature requests. In my
MolnIquiry site, I have imbedded line objects as bonds that can then be
?picked?; for example, students are asked to click on a peptide bond.).
Creating these objects is a task, particularly if many are needed, and the
lines can become visible if wireframe is turned off.
Is it technically feasible that Jmol could:
1. generate a series of IDed objects between the connected atoms of an
atom set e.g.: ?select (atom expression), drawConnected line, ID ?line?+j?
where j is incrementally increased with each line?
2. set the color of an object as ?transparent? (but still pickable).
Does anyone see any other applications of these features?
Thanks.
Steve
Dept of Biology and Environmental Science
Marietta College
This message was sent using Marietta College WebMail.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the
world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Professor of Chemistry
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
--
Robert M. Hanson
Professor of Chemistry
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New feature inquiry
On 30 Aug 2008 at 14:20, Robert Hanson wrote: Jmol 11.6.RC12 now has set atomPicking [default TRUE] set bondPicking [default FALSE] Nice! and quick Are those 2 independently set, or are they alternative options? And, how does that combine with the different set picking variants? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed change to Jmol.js
Quoting Robert Hanson [EMAIL PROTECTED]: ok. Shucks. That's convincing. OK if it allows same-server jar changes? Yes, I think so. If the server is compromised then I guess it won't make much difference anyhow. Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New feature inquiry
all three are independent: set atomPicking set bondPicking set drawPicking On Sat, Aug 30, 2008 at 2:49 PM, Angel Herráez [EMAIL PROTECTED] wrote: On 30 Aug 2008 at 14:20, Robert Hanson wrote: Jmol 11.6.RC12 now has set atomPicking [default TRUE] set bondPicking [default FALSE] Nice! and quick Are those 2 independently set, or are they alternative options? And, how does that combine with the different set picking variants? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] The results of your email commands
Bob, (This seemed to have been bounced -- so I'm trying again) I am trully overwelmed. This is great! It should work; I would like to pass the ID of the 'picked' bond to a javascript variable. Is the report returned to the pickCallback function as is atom picking, such that the ID can be parsed out. Or is there another way (jmolEvaluate?) to pass the report or ID to a javascript variable? I'll admit to confusion about passing getProperty info to javascript. Thanks. Steve This message was sent using Marietta College WebMail. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] The results of your email commands
Yes, this information comes back as a string in the pickCallback (second
parameter). The third parameter is an atom index:
0+ atom
-2 draw
-3 bond
Also, you can always check the most recent pick information using
var x = jmolEvaluate(_pickInfo)
or
var x = jmolEvaluate(_atomPicked)
You should be able to parse that as a JavaScript array directly:
var info = eval(jmolEvaluate(_pickInfo))
or from that second parameter, HOWEVER -- strings passed back to JavaScript
are Java strings, not JavaScript strings, so ALWAYS do
+ xxx
to turn them into JavaScript strings before you do anything with them. So in
a callback:
function myPickCallback(app, msg, atomIndex) {
var info = eval( + msg)
}
not just
function myPickCallback(app, msg, atomIndex) {
var info = eval(msg)
}
Bob
I've put sample JAR files up in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar
(transferring now - takes a few minutes)
Bob
On Sat, Aug 30, 2008 at 3:09 PM, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Bob,
(This seemed to have been bounced -- so I'm trying again)
I am trully overwelmed. This is great! It should work; I would like to
pass the ID of the 'picked' bond to a javascript variable. Is the report
returned to the pickCallback function as is atom picking, such that the ID
can be parsed out. Or is there another way (jmolEvaluate?) to pass the
report or ID to a javascript variable? I'll admit to confusion about
passing getProperty info to javascript.
Thanks.
Steve
This message was sent using Marietta College WebMail.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Professor of Chemistry
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bond picking
Bob,
Wonderful. I'll let you know how it works.
Thanks again.
Steve
Yes, this information comes back as a string in the pickCallback (second
parameter). The third parameter is an atom index:
0+ atom
-2 draw
-3 bond
Also, you can always check the most recent pick information using
var x = jmolEvaluate(_pickInfo)
or
var x = jmolEvaluate(_atomPicked)
You should be able to parse that as a JavaScript array directly:
var info = eval(jmolEvaluate(_pickInfo))
or from that second parameter, HOWEVER -- strings passed back to JavaScript
are Java strings, not JavaScript strings, so ALWAYS do
+ xxx
to turn them into JavaScript strings before you do anything with them. So in
a callback:
function myPickCallback(app, msg, atomIndex) {
var info = eval( + msg)
}
not just
function myPickCallback(app, msg, atomIndex) {
var info = eval(msg)
}
Bob
Steven Spilatro
Dept of Biology and Environmental Science
Marietta College
This message was sent using Marietta College WebMail.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bond picking -- and getProperty in general
getProperty can be a very inefficient function. The algorithm is designed to
return the entire property set, then do the selections. So, for example, if
you say:
print getProperty(atomInfo[3])
and there are 3 atoms, then first a vector containing 3 elements is
produced and only after that is one selected.
I'm reminded that I thought of that and had a solution to it but forgot. The
alternative format:
print getProperty(atomInfo, {atomIndex=3})
is far more efficient, as it only creates a single atomInfo entry -- an
array with one element.
I've checked in code now that combines these:
print getProperty(atominfo[1].sym, {atomIndex=3})
creates only one entry and then selects the information about atom symbol
from that single entry. ([0] would work as well, because that means the
last entry, and there is only one)
In checking through the code, I also noticed that bondInfo works
similarly, but both atoms of the bond must be selected. I've now changed
that so that if you specify just one atom, then bondInfo gives you what
you think it would -- the bond info for that atom:
print getProperty(bondInfo, {atomno=2})
[[ information about all bonds to atom #2 are displayed ]]
Similarly,
print getProperty(bondInfo[1], {atomno=2})
give information about just the first bond to atom #2.
In addition, getProperty(modelInfo) was not allowing an atom expression,
but it seems to me that would make sense as well:
print getProperty(modelInfo, {atomIndex=2})
or perhaps
print getProperty(modelInfo, {1.3})
So I have added that.
Finally, getProperty(auxiliaryInfo) also could allow for specifying the
model, so I have added that as well:
print getProperty(auxiliaryInfo, {1.3})
These changes should make for much more efficient extraction of information.
Bob
--
Robert M. Hanson
Professor of Chemistry
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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
