refactor main

[jruhym]

There is too much happening in main like iterating over all of the atoms. There should be a protein class that does this. In any case the assembly of the protein should be abstracted such that it can be called in situations that differ from globing filenames on the command line. Say for instance some one wanted to scrape the pdb for all membrane proteins and find all of their interatomic connections without downloading all to the local file system first.