relax SVN archive

Redesign of the geometric object representation part of the frame_order.pdb_model user function.

The positive and negative representations of the frame order motions have been separated out into
two PDB files rather than being two models of one PDB file. This will help the user understand that
there are two identical representations of the motions, as both will now be displayed rather than
having to understand the model concept of PyMOL. The file root is taken, for example 'frame_order',
and the files 'frame_order_pos.pdb' and 'frame_order_neg.pdb' are created. If no inverse
representation exists for the model, the file 'frame_order.pdb' will be created instead.

The Monte Carlo simulations are now also treated differently. Rather than showing multiple vectors
in the axes representation component within one molecule in the same file as the frame order
representation, these are now in their own file and each simulation is now a different model. If an
inverse representation is present, then the positive representation will go into the file
'frame_order_sim_pos.pdb', for example, and the negative representation into the file
'frame_order_sim_neg.pdb'. Otherwise the file 'frame_order_sim.pdb' will be created.

Fixes for the frame_order.pdb_model user function for the rotor and free rotor models.

Test suite fixes for the recent redesign of the frame_order.pdb_model user function.

The frame order generate_pivot() function can now return the pivots for Monte Carlo simulations.

This is the specific_analyses.frame_order.data.generate_pivot() function. The sim_index argument
has been added to the function which will allow the pivots from the Monte Carlo simulations to be
returned. If the pivot was fixed, then the original pivot will be returned instead.

Improvements to the lib.structure.represent.rotor.rotor() function for handling models.

The 'rotor', 'rotor2', or 'rotor3' molecule name determination is now also model specific.

Merged revisions 24396,24399 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24396 | bugman | 2014-07-02 09:50:36 +0200 (Wed, 02 Jul 2014) | 6 lines

Python 3 fixes for the entire codebase using the 2to3 script.

The command used was:
2to3 -j 4 -w -f xrange .
........
r24399 | bugman | 2014-07-02 11:46:40 +0200 (Wed, 02 Jul 2014) | 5 lines

The internal structural object add_molecule() and has_molecule() methods are now model specific.

This allows for finer control of structural object.
........

Merged revisions 24399 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24399 | bugman | 2014-07-02 11:46:40 +0200 (Wed, 02 Jul 2014) | 5 lines

The internal structural object add_molecule() and has_molecule() methods are now model specific.

This allows for finer control of structural object.
........

The internal structural object add_molecule() and has_molecule() methods are now model specific.

This allows for finer control of structural object.

Merged revisions 24396 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24396 | bugman | 2014-07-02 09:50:36 +0200 (Wed, 02 Jul 2014) | 6 lines

Python 3 fixes for the entire codebase using the 2to3 script.

The command used was:
2to3 -j 4 -w -f xrange .
........

Python 3 fixes using the 2to3 script.

Fatal changes to the multi.processor module were reverted.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.