relax SVN archive

Implemented the 'pymol.cartoon()' user function.

This was modified from the 'molmol.ribbon()' user function. The molmol commands have been replaced
with commands to hide everything, show the cartoon, and colour the cartoon by secondary structure.

The 'pymol.view()' user function now works.

A number of calls to pipes located at 'self.relax.data.molmol' where changed to
'self.relax.data.pymol'. The Molmol 'InitAll' and loading functions where changed to the PyMOL
equivalents. Now PyMOL executes and opens up the PDB file.

Ported r2705 and r2706 from the 1.2 line.

The command used was:
$ svn merge -r2704:2706 svn+ssh://bugman@.../svn/relax/1.2

This fixes bug #7583 (https://gna.org/bugs/?7583) and fixes a problem with one of the comments in
'specific_fns/model_free.py'.

Fix for bug #7583 (https://gna.org/bugs/?7583).

The problem was to statements 'if len(file_data[i]) != 4:' followed by 'continue'. These tests were
to avoid lines which contain no data, however it causes failures if there are not exactly for
columns! Now the minimum number of columns, based on the given column numbers, is tested for.

Emphasised the looping over the minimisation instances and fixed an incorrect comment.

The incorrect comment stated 'Require at least as many data points as params to prevent
under-fitting'. It should say over-fitting.

Added the '-K' option to the PyMOL pipe to prevent it from terminating when the script does.

The problem of the non-persistent PyMOL pipe was discusssed at
https://mail.gna.org/public/relax-devel/2006-10/msg00168.html (Message-id:
<7f080ed10610290135p7ebce039tda7cd622b7ca30ff@...>) and
https://mail.gna.org/public/relax-devel/2006-10/msg00169.html (Message-id:
<BA58D16C-56EF-4AC3-B415-34A87A0B7FAB@...>).

The solution came from 'DeLano Scientific'. The details can be seen in my post at
http://sourceforge.net/mailarchive/message.php?msg_id=37186991 and the responses within the thread
located at http://sourceforge.net/mailarchive/forum.php?thread_id=30844748&forum_id=60.

Renamed the pymol pipe kept at 'self.relax.data' from 'molmol' to 'pymol'.

Initial support for PyMOL.

The 'prompt' and 'generic_fns' Molmol files have been copied to new PyMOL files. The classes have
been renamed and setup within the prompt interface or the main generic functions class. A number of
instances where 'molmol' was written have been replaced with 'pymol'. Much work is still left. For
example PyMOL will not execute in script mode as it terminates saying:

PyMOL: normal program termination.

once the pipe is closed (after finishing the script and relax terminating).

Removed a number of unused import statements in the Molmol prompt interface file.

Created the user function 'molmol.tensor_pdb()' for displaying the diffusion tensor in Molmol.

The function takes the pre-generated diffusion tensor PDB file, created with the user function
'pdb.create_tensor_pdb()', and displays it in Molmol over the loaded structure.