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 <
[email protected]> 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
> > <[email protected]
> > <mailto:[email protected]>> 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
> > [email protected]
> > <mailto:[email protected]>
> >
> >
> >
> ------------------------------------------------------------------------------
> > Open Source Business Conference (OSBC), March 24-25, 2009, San
> > Francisco, CA
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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
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Jmol-users mailing list
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> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
>
>
> --
> 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
> [email protected]
>
>
>
> ------------------------------------------------------------------------------
> 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
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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
------------------------------------------------------------------------------
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-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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