b_hall,

As far as reading PDB files the Chemistry::File::PDB module looks like it would be of some use to you. Failing that search Cpan. Regeards the rest of the chemistry stuff, without spending time finding out exactly what it all means its over my head. You may find the article Building a 3D engine in Perl over at Perl.com useful:

"This article is the first in a series aimed at building a full 3D engine. It could be the underlying technology for a video game, the visualization system for a scientific application, the walkthrough program for an architectural design suite, or whatever."

Hope this helps.

Martin