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. I can only do that if some requests are taken seriously by the developers. I've written all this in some way or other quite recently, but I'll be happy to repeat. First of all, my thoughts on using the Jmol application rather than the applet. 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. 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. So, precisely not "all the functionality". 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.
I might actually be interested in some interface to the full application functionality, but that would perhaps be shown as a separate "CaGe viewer" and certainly a different step in my work.
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". This should be possible to request in the data, not through some external settings, I think. Hence my previous example using a molecule convention called "MathGraph", as agreed with the developers at the time (Jmol 0.6.1 was current then). * 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. (With 0.6.1, you were able to press some keys for similar things.) * 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. * inline models (molecule data passed as a parameter, not using files or scripting.)
Sebastian
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