Well, you need some kind of embeddable viewer that you can feed with your data. I would guess that you need to find a Java molecule viewer applet that takes an URL as an argument. That URL should then point to your molecule data.

Another way of doing it would be with SWF. Then you could, possibly, use swf modules to generate the molecule viewer on the fly, probably from some template SWF file.

The hard part of this really isn't the Perl parts. The hard part is the molecule viewer itself. Find it, and the rest will fall into place...