Not a Perl solution for the OP, however, I just found VMD:

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

... and it looks really interesting.

HTH,

planetscape

In reply to Re: Lightweight Molecule Viewer with SVG by planetscape
in thread Lightweight Molecule Viewer with SVG by b_hall

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