Miguel wrote: [Praise for JMol's bonding algorithm, and a request for molecules not rendered properly]
It is a while ago, and I am no longer working on that project, but you might remember me asking something similar in 2000. Out of sentimentality, I'm still lurking. I used an old version of the JMol Applet in a Java application I developed, and tried to make you aware of the fact that sometimes people calculate their own structures, complete with "final" bond and atom position information, and don't want a viewer program trying to be smart and decide where atoms and bonds should be.
Did I ever report back when I finished my project? You can see the results at "http://www.mathematik.uni-bielefeld.de/~CaGe/";. On the website, we praise JMol because the version we have does exactly what we want, but I don't know if that would still be true in the current version.
My point is, I didn't get all I wanted from a standard version of the JMol Applet, so I ended up changing bits of the source code myself, using CML data with a new "Convention" of "MathGraph". I sent messages about my changes, but these seemed to get lost in the activies of JMol development. It would be good if a position such as mine wasn't completely forgotten. From that perspective, Miguel's response is not to the point.
My specific requirements were: * Exact representation of input data in terms of atom positions and bonds (Sometimes our bonds even were "impossible" from a chemistry point of view, but I still wanted JMol to faithfully show what it was given to show.) I also needed this to be possible in CML, since that was the only format one could hand to the applet in a parameter. There was no scripting back then. * getter and setter methods for display settings (things like the drawing modes that existed back then)
I dreamed of being able to always take the newest version and "plug it in" to my application, and I'd wonder if that could be made possible.
Sebastian Lisken
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