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 > <[email protected] > <mailto:[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]> > > <mailto:[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]> > > <mailto:[email protected] > <mailto:[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] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[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 > > > ------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------------ > > 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] > <mailto:[email protected]> > > 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] > <mailto:[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] > <mailto:[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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > 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 > -- 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
