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 <
klen...@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
> > <klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@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
> > > <klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@bioinformatik.uni-frankfurt.de>
> > > <mailto:klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@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
> > > klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@bioinformatik.uni-frankfurt.de>
> > > <mailto:klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@bioinformatik.uni-frankfurt.de>>
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------------
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> > > 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
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> > >
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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
> > klen...@bioinformatik.uni-frankfurt.de
> > <mailto:klen...@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
> > Jmol-users@lists.sourceforge.net
> > <mailto:Jmol-users@lists.sourceforge.net>
> > 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
> > ------------------------------------------------------------------------
> >
> >
> ------------------------------------------------------------------------------
> > 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
> > Jmol-users@lists.sourceforge.net
> > 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
> klen...@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
> Jmol-users@lists.sourceforge.net
> 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
------------------------------------------------------------------------------
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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