relax SVN archive

Fix for the breakage of the relax help system.

This was reported at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481.

The problem was that the TERM environmental variable was turned off to avoid the GNU readline
library on Linux systems emitting the ^[[?1034h escape code. See the message at
http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for more details. However the
Python help system obviously requires this environmental variable. Now only if the TERM variable is
set to 'xterm' will it be reset, and to 'linux' instead of the blank string ''.

Updated all of the frame order scripts for the frame_order.pdb_model and pymol.frame_order changes.

These are the scripts for the CaM frame order test data.

Redesign of the pymol.frame_order user function to match the redesign of frame_order.pdb_model.

The file names are no longer given but rather the file root. Then all PDB files matching that file
root in the given directory will be loaded into PyMOL.

Clean up of the frame_order.pdb_model user function definitions.

Some elements were no longer of use, and some descriptions have been updated.

Merged revisions 24407 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24407 | bugman | 2014-07-02 14:42:51 +0200 (Wed, 02 Jul 2014) | 6 lines

Created the new lib.structure.files module.

This currently contains the single find_pdb_files() function which will be used to find all *.pdb,
*.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
........

Created the new lib.structure.files module.

This currently contains the single find_pdb_files() function which will be used to find all *.pdb,
*.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.

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.