Sebastian, > My question or problem is this: Jmol has seen phantastic > improvements since the version I incorporated into CaGe, > and I'd like to be able to use the new version. Great. Please do so.
> I can > only do that if some requests are taken seriously by the > developers. Your requests have been taken seriously. > I've written all this in some way or other > quite recently, but I'll be happy to repeat. Good. While your english is quite good, apparently we still have a communication problem. > I like using an applet because of this seems > the simpler approach (you've seen the core of the > integration framework in those lines of code), and I > also do like the restrictions an applet has. Fine, then use the applet in the framework that you have set up. You showed me the code and it looked straightforward. If you think that the applet will meet your needs then by all means use it. > I don't > necessarily want users to be able to see and do all the > things offered by the application, e.g. I want a mode > of operating Jmol that does not involve a menu bar or > any mouse/keyboard actions for measuring, exporting, or > whatever else the full application may offer. I never recommended that you use the application. If you are looking for an alternative to the applet then, once again, I *strongly* recommend that you look at examples/Integration.java It shows you how to put up the JmolViewer in your own window. This is essentially the core of the applet, without the applet wrapper classes. I honestly believe that this is what you want. But *you* have to look at it and decide whether or not it meets your needs. > If that is possible e.g. by > accessing and using only some display area inside the > application window, maybe that is indeed what I want, > but the applet also is just what I want. see examples/Integration.java > Apart from that, here is what I want from Jmol to able > to integrate it: > * Some way of expressing a request that Jmol should not > apply any "intelligence" (i.e. calculations) to the > bonds and atom positions, stick to the data even if > it is "unchemical". Done ... Jmol meets your needs *today*. Atom positions have *never* been moved. If bonds are specified then they are applied, regardless of distance/length. .mol files have always supported bond connectivity. CONECT records are now supported in .pdb files. This is an item that *you* askied for. For something that is 'unchemical', open up samples/jmol.mol There is *no* checking that takes place ... if you want you can bond a hydrogen atom 50 times ... and the bonds can be 100 angstroms long. > * Two methods to get and retrieve an object holding > any display settings. I would not expect to manipulate > it or know anything about its type, only store it to > hand to another applet instance. With the current > version of the applet, display settings would be what > you adjust with the context menu. Jmol will not provide this functionality within the forseeable future. There is no such thing as 'display settings' in Jmol any more. There are 'default settings', but they are only default values. Each atom and each bond has its own 'settings' for color, size, etc. If you select a subset of the atoms and then make changes, then those atoms/bonds will have different properties. It may be the case that you *think* that they are 'display settings' because you are always working with the entire set of atoms selected. Therefore, there is not an easy way for me to implement this. I would have to give you a large data structure that contained the state of every item in the system. That would be a pain to build and a maintenance nightmare. It is not going to happen. I recommend that you implement your own buttons within your application and record the state that you think is important. > (With 0.6.1, you were > able to press some keys for similar things.) There is not one line of code in Jmol that remaining from the 0.6.1 days. > * Applet parameters for some initial display settings > such as zoom factor, drawing style, background colour, > atom size ... Just in case I don't like the defaults. Done ... Jmol meets your needs *today* One way to do this is: zoom 200; background blue; spacefill 25%; wireframe 0.1 > * inline models (molecule data passed as a parameter, > not using files or scripting.) Done ... Jmol meets your needs *today* I don't understand where we miscommunicated on this. I explained to you that it did not work in a browser context because browsers strip out newline characters. You then explained to me that you were not running it in the context of a browser and that you could provide the parameter string with the inline model. You did such a good job of explaining it to me that I assumed that it was clear to you ... it works. Just set the applet parameter loadInline="your-favorite-molecular-model" and it will work. Sebastian, you think that I am not listening to you ... and I think I know how you feel ... because I feel like you are not listening to me. Clearly we have a communication issue. You *have* asked me about several of these items before ... and I *have* answered them before. *You* think you asked good questions ... and *I* think I gave good answers. At this point I want to make my position very clear. With the exception of 'display settings', I believe that everything you want is implemented and easily available to you. Using the JmolApplet or using the JmolViewer in your own window. The *only* outstanding item on your list is the current set of object properties ... 'display settings'. Given the structure and architecture of Jmol, I will not be implementing this. Therefore, you will need to figure out what state you need to save and do this work on your own. - I believe that this will be very straightforward for you to do. - If you have specific questions about this problem then I will be glad to help you with it. - If you do not understand my explanation as to why I cannot implement this then ask again and I will try to explain again. Respectfully submitted, Miguel ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
