I'm still interested in how the CDK business works. I would like Jmol to remain compatible with that. And, of course, you will be missing out on so much good stuff....

On Fri, Feb 27, 2009 at 8:08 AM, Alexander Klenner <klenner@bioinformatik.uni-frankfurt.de> wrote:
Ok, maybe i should have done this before updating to 11.7.
 I can get my picked atom now ;) Robert thanks a lot for your help!

Cheers,

Alex

Robert Hanson schrieb:
> Alex, certainly you should be able to use the older version if you
> need to. It was really just a very basic misunderstanding about
> "selection" -- so that one little change should be all you need. As
> for CDKJmolAdapter, I don't know. If you have an application and you
> can send it to me or put it on SVN, I can take a look and see what is
> going wrong there. JmolAdapter is rather complex, I admit, but I'd be
> interested in what the use of a CDK adapter would be.
>
> Bob
>
>
> On Fri, Feb 27, 2009 at 7:24 AM, Alexander Klenner
> <klenner@bioinformatik.uni-frankfurt.de
> <mailto:klenner@bioinformatik.uni-frankfurt.de>> wrote:
>
>     Hey,
>
>     thanks for the fast answering of my questions, I really didn't get the
>     difference between selection and just picking and atom... I did what
>     Robert suggested but unfortunately I encountered a different  problem
>     now. I updatet  to Jmol 11.7 and now my whole CDK-Jmol connections
>     broke
>     down :(.
>
>     I think when I started this projected some month ago (was paused
>     though)
>     I found something  like a CDKJmolAdapter.class. My connection is
>     pretty
>     much this code with some changes for atomtyping and rewriting jmol
>     molecules to cdk. First of all due to all the new abstract methods in
>     JmolAdapter in the newer Version I had to switch to smarterJmolAdapter
>     which doesn't seem to be a problem.
>
>     But the method I was using to add the molecule to the viewer is now
>     deprecated and doesn't take CDK-molecules as arguments as it did
>     before:
>
>     viewer.openClientFile(String,String,CDK-Molecule)
>
>     It asks for a AtomSetCollection
>
>     Is there a way to extract this AtomSetCollection from an CDK molecule
>     object (is it equivalent to any cdk data sctucture for example?
>     )or does
>     something like a new adapter class already exist?
>
>     Greetings,
>
>     Alex
>
>
>     Robert Hanson schrieb:
>     > Alex, the distinction you need to make is between a Jmol atom
>     > "selection" using the SELECT command and a mouse action to pick an
>     > atom, which is a callback. You are watching for the select command.
>     > What you want to do is implement org.jmol.api.JmolStatusListener.
>     > Check out how this is done in Jmol.java. The two specific
>     methods you
>     > will want to implement are:
>     >
>     >     public boolean notifyEnabled(int type)
>     >     public void notifyCallback(int type, Object[] data)
>     >
>     >
>     > You register your status listener at Jmol viewer allocation time:
>     >
>     >     viewer = JmolViewer.allocateViewer(display, modelAdapter,
>     >         null, null, null, appletContext = commandOptions,
>     >         new MyStatusListener());
>     >
>     > Where MyStatusListener() implements JmolStatusListener.
>     >
>     > Referring to Jmol 11.7 here.
>     >
>     >
>     > Bob
>     >
>     >
>     > On Thu, Feb 26, 2009 at 7:23 AM, Alexander Klenner
>     > <klenner@bioinformatik.uni-frankfurt.de
>     <mailto:klenner@bioinformatik.uni-frankfurt.de>
>     > <mailto:klenner@bioinformatik.uni-frankfurt.de
>     <mailto:klenner@bioinformatik.uni-frankfurt.de>>> wrote:
>     >
>     >     Hi all,
>     >
>     >     is there a way to add something like the 'SelectionListener'
>     to my
>     >     instance of the viewer ( I am using the viewer to visualize some
>     >     molecules that are in CDK Molecule representation)
>     >     that actually will react if I mouse-klick an atom in the viewer?
>     >
>     >     I tried the following but that won't do anything so far...
>     >
>     >      MyViewer.addSelectionListener(new JmolSelectionListener() {
>     >                 public void selectionChanged(BitSet selection) {
>     >                                   //do some nice stuff whenever
>     atom is
>     >     klicked
>     >                               }
>     >
>     >            });
>     >
>     >     I do see the system outs from the StatusManager class that
>     confirms,
>     >     that I did pick an atom.
>     >
>     >     Is there a way to do this or do I have to implement something by
>     >     myself?
>     >
>     >     Thanks for any help or suggestions,
>     >
>     >     Alex
>     >
>     >
>     >
>     >     --
>     >     Alexander Klenner, Dipl.-Bioinf.
>     >     Johann Wolfgang Goethe-University Frankfurt
>     >     Department of Biosciences
>     >     Siesmayerstrasse 70
>     >     D-60323 Frankfurt
>     >     Tel: +49 (0) 69 798 24879
>     >     Fax: +49 (0) 69 798 24880
>     >     klenner@bioinformatik.uni-frankfurt.de
>     <mailto:klenner@bioinformatik.uni-frankfurt.de>
>     >     <mailto:klenner@bioinformatik.uni-frankfurt.de
>     <mailto:klenner@bioinformatik.uni-frankfurt.de>>
>     >
>     >
>     >
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>     >
>     > --
>     > 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
>     >
>     ------------------------------------------------------------------------
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Open Source Business Conference (OSBC), March 24-25, 2009, San
>     Francisco, CA
>     > -OSBC tackles the biggest issue in open source: Open Sourcing
>     the Enterprise
>     > -Strategies to boost innovation and cut costs with open source
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>     > -Receive a $600 discount off the registration fee with the
>     source code: SFAD
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>
>     --
>     Alexander Klenner, Dipl.-Bioinf.
>     Johann Wolfgang Goethe-University Frankfurt
>     Department of Biosciences
>     Siesmayerstrasse 70
>     D-60323 Frankfurt
>     Tel: +49 (0) 69 798 24879
>     Fax: +49 (0) 69 798 24880
>     klenner@bioinformatik.uni-frankfurt.de
>     <mailto:klenner@bioinformatik.uni-frankfurt.de>
>
>
>     ------------------------------------------------------------------------------
>     Open Source Business Conference (OSBC), March 24-25, 2009, San
>     Francisco, CA
>     -OSBC tackles the biggest issue in open source: Open Sourcing the
>     Enterprise
>     -Strategies to boost innovation and cut costs with open source
>     participation
>     -Receive a $600 discount off the registration fee with the source
>     code: SFAD
>     http://p.sf.net/sfu/XcvMzF8H
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>
>
> --
> 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
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> ------------------------------------------------------------------------
>
> _______________________________________________
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>


--
Alexander Klenner, Dipl.-Bioinf.
Johann Wolfgang Goethe-University Frankfurt
Department of Biosciences
Siesmayerstrasse 70
D-60323 Frankfurt
Tel: +49 (0) 69 798 24879
Fax: +49 (0) 69 798 24880
klenner@bioinformatik.uni-frankfurt.de


------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H
_______________________________________________
Jmol-users mailing list
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--
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