relax SVN archive

Redesign of the average domain position part of the frame_order.pdb_model user function.

The Monte Carlo simulations are now represented. If the file root is set to the default of
'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a compressed version. Each
simulation is in a different model, matching the geometric representation '*_sim.pdb' files. The
original structure is copied for each model, and then rotated to the MC simulation average position.

Merged revisions 24428 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24428 | bugman | 2014-07-03 14:22:30 +0200 (Thu, 03 Jul 2014) | 6 lines

Removed the Freecode section from the release checklist as Freecode has been permanently shut down.

The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead
(http://freecode.com/about).
........

Merged revisions 24425,24428 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24425 | bugman | 2014-07-03 13:25:59 +0200 (Thu, 03 Jul 2014) | 10 lines

Updated the Mac OS X framework setting up instruction document.

New sections have been added for the nose and matplotlib Python packages, as nose is needed for the
numpy and scipy testing frameworks and matplotlib might be a useful optional dependency in the
future.

The mpy4py section has been updated to avoid the non-framework fink version of mpicc which cannot
produce universal binaries. A few other parts also have small edits.
........
r24428 | bugman | 2014-07-03 14:22:30 +0200 (Thu, 03 Jul 2014) | 6 lines

Removed the Freecode section from the release checklist as Freecode has been permanently shut down.

The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead
(http://freecode.com/about).
........

Merged revisions 24407,24412,24418-24419,24421-24422,24425 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.
........
r24412 | bugman | 2014-07-02 15:38:13 +0200 (Wed, 02 Jul 2014) | 11 lines

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 ''.
........
r24418 | bugman | 2014-07-02 16:48:30 +0200 (Wed, 02 Jul 2014) | 6 lines

Backported the relax 3.2.3 CHANGES file changes to trunk.

The command used was:
svn merge -r24416:24417 svn+ssh://bugman@.../svn/relax/tags/3.2.3 .
........
r24419 | bugman | 2014-07-02 17:45:14 +0200 (Wed, 02 Jul 2014) | 6 lines

MS Windows fixes to allow relax to run again.

The code for eliminating the GNU readline ^[[?1034h escape code emission on Linux systems fails on
Windows as the 'TERM' environmental variable does not exist in os.environ.
........
r24421 | bugman | 2014-07-03 08:54:26 +0200 (Thu, 03 Jul 2014) | 8 lines

Better tab completion support in the prompt UI for Mac OS X users.

For some Python versions, the Mac supplied libedit library is used rather than GNU readline. But
this library uses a completely different language and hence tab completion was non-functional on
these systems. The library difference is now detected and the correct language sent into libedit to
activate tab completion.
........
r24422 | bugman | 2014-07-03 11:35:50 +0200 (Thu, 03 Jul 2014) | 13 lines

Improved model handling for the internal structural object.

The set_model() method has been added to allow either a model number to be set to the first
unnumbered model (in preparation for adding new models) or to allow models to be renumbered.
The logic of the add_model() has also been changed. Rather than looping over all atoms of the first
model and copying them, which does not work due to the model validity checks, the entire MolList
(molecule list) data structure is copied using copy.deepcopy() to make a perfect copy of the
structural data.

The ModelList.add_item() method has also been modified to return the newly added or numbered model.
This is used by the add_model() structural object method to obtain the model object.
........
r24425 | bugman | 2014-07-03 13:25:59 +0200 (Thu, 03 Jul 2014) | 10 lines

Updated the Mac OS X framework setting up instruction document.

New sections have been added for the nose and matplotlib Python packages, as nose is needed for the
numpy and scipy testing frameworks and matplotlib might be a useful optional dependency in the
future.

The mpy4py section has been updated to avoid the non-framework fink version of mpicc which cannot
produce universal binaries. A few other parts also have small edits.
........

Updated the relax version number to 3.2.3 on the http://www.nmr-relax.com/api/index.html webpage.

Removed the Freecode section from the release checklist as Freecode has been permanently shut down.

The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead
(http://freecode.com/about).

Updated the relax API documentation at http://www.nmr-relax.com/api/3.2/ to version 3.2.3.

Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to version 3.2.3.

Updated the Mac OS X framework setting up instruction document.

New sections have been added for the nose and matplotlib Python packages, as nose is needed for the
numpy and scipy testing frameworks and matplotlib might be a useful optional dependency in the
future.

The mpy4py section has been updated to avoid the non-framework fink version of mpicc which cannot
produce universal binaries. A few other parts also have small edits.

Updated the http://www.nmr-relax.com/download.html webpage for relax 3.2.3.