relax SVN archive

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().

Added the missing self argument to the clear_history() method.

Converted the clear_history() function to a method of the PyMOL data object.

Converted file_root() from a class method to a module function, and updated it to the new design.

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