Sorry, but your pseudo code is just a little to pseudo. Without a clear understanding of the internals of the PDB::Atom objects and it's methods, I find it impossible to understand what is going on.

One casual comment though. In general, perl's objects carry a considerable performance penalty relative to it's standard hashes and array's. Iterating large volumes of data represented as objects will be much slower than processing that same data stored in a hash or an array.

This is no surprise, nor a critisism of Perl. Just s statement of fact. The extra levels of indirection and lookup are bound to carry a penalty, but when dealing with large volumes where speed is a criteria, it is best avoided.