> I am about to turn my attention back to developing our interactive > chemistry education applets and appreciate any info. you have about the > current status of your jmol and cdk development efforts. Good.
> Please remind me whether it is JMol or CDK I should be using (and the > current relationship). Jmol is the applet and application for viewing molecules. CDK (Chemistry Development Kit) is a general library for chemical computations. Jmol is basically built on top of CDK ... but it *can* be used separately. As I recall, you want to work with small molecules and render orbitals, correct? > As you may recall our requirements include: > 1) embedding jmol within another java swing applet This should be straightforward. CVS contains a small .java sample of how to embed the JmolViewer into a standalone application > 2) use of jmol for ball & stick representation of molecules No problem > 3) use of some variant of your rendering code for displaying > an arrow (vector representation of dipole and other properties) Jmol already has the ability to display arrows > 4) use of some variant of your rendering code for displaying an > isosurface. Jmol does not have the ability to display iso-surfaces. But it is on our list of things to do. This is an area where we could collaborate. > I am intrigued by use the dot surface representation by > plugging in my own computation for generating the surface A variant of this would be the right approach. You could basically "clone" the dots code and use that as a starting point. In more detail ... The rendering architecture has been changed so that it is relatively easy to plug in new types of visual shapes. We would basically create a new shape for your kind of object. Within this context your shape would have access to the data structures of the currently loaded molecular model. So you can do whatever calculations you need to do, all in world-space coordinates (angstroms). In your case, your orbital calculations (I assume). As a partner for your new shape we also create a shapeRenderer. Its job is to render your shape to the screen. It makes function calls to transform world-space coordinates into screen coordinates, and uses those screen coordinates to make calls into the Graphics3D package. You can use the Jmol code that exists today and get all this done. And what you would have would be a nice 'dots' representation. The piece that is missing today is a closed-surface rendering of those dots. But that work is completely isolated to the Graphics3D package. After implementing it in the Graphics3D package, you only need to tweak your shapeRenderer to use the 'surface' graphics method instead of (or, in addition to) the 'dot' method. > If you think all of these requirements are a good match for the code > you have developed I think is a good fit. > I would like to get some more details as to where to > look. Specifically, where can I get the latest working version of the > library. All the code is checked into cvs and is available for anonymous checkout. Go to http://jmol.sf.net > Will you send me the source code for the dot demo. There is no 'dots demo' as such. This capability is built into Jmol, so it is in the source code. During development you should plan on using the jmol application instead of the applet ... a standalone app is a much more forgiving development environment and you will get a quicker turnaround cycle. You should cvs checkout the jmol source and build it from scratch. Spend a day using the jmol application (not the applet) and learning how to use the scripting commands. Figure out how to turn on the dots. Find a molecular model file in the samples directory that has some arrows so you can see what they look like. Maybe make your own file with some arrows and then put some dots around it. Spend the next day looking at the source code. Don't be shy about posting questions to the [EMAIL PROTECTED] mailing list. And let us know what is hard to understand. Miguel > > Thanks for any help, > > Peter Carr > [EMAIL PROTECTED] > (617) 353-3833 ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
