relax SVN archive

Converted the open_pdb() method to the new relax design.

Converted the open_pdb() function into a class method.

Bug fix for the pipe_open() method.

The current data pipe should have been accessed, not the relax data store!

Bug fix for the cartoon() function.

The file_name object is a str, not a fn.

Fixed the references to the PyMOL command history.

Updated the pipe_open() method to the new relax design.

Updated the view() function to the new relax design.

Placed the PyMOL pipe into the PyMOL data object.

It is no longer stored in the relax data store. This will have the obvious effect of having a
single instance of PyMOL running, and not a seperate instance per data pipe.

Converted pipe_open(), pipe_open_test(), and pipe_write() to methods of the pymol data object.

Fixed the call to relax_io.file_root in vector_dist().