relax SVN archive

Modified the package __all__ list checking unit test to accept *.so C modules.

Updated the target_functions package __all__ list to include the relax_fit* modules.

Merged revisions 26746-26747,26760,26768-26771,26782,26791 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26746 | bugman | 2014-11-26 11:12:30 +0100 (Wed, 26 Nov 2014) | 8 lines

Fixes for the links at the bottom of all HTML manual pages.

This is for the automatically generated documentation at http://www.nmr-relax.com/manual/index.html,
created using latex2html. The links all require double quotes, and some a trailing '/'. The links
fixed are http://www.nmr-relax.com, http://www.nmr-relax.com/manual/ and
http://download.gna.org/relax/manual/relax.pdf.
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r26747 | bugman | 2014-11-26 11:21:53 +0100 (Wed, 26 Nov 2014) | 7 lines

Removed the repository backup file text from the relax manual.

This is for http://www.nmr-relax.com/manual/Latest_sources_the_relax_repositories.html. The gzipped
repository dump file has not been created by Gna! for many, many years. The problem was identified
by the W3C link checker (http://validator.w3.org/checklink).
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r26760 | bugman | 2014-11-26 14:22:47 +0100 (Wed, 26 Nov 2014) | 5 lines

Updated all of the http://www.nmr-relax.com/manual/ links in the lib.dispersion package.

This is for all of the individual model pages in the HTML manual.
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r26768 | bugman | 2014-11-26 18:35:06 +0100 (Wed, 26 Nov 2014) | 3 lines

Improved the description for the relax_fit.select_model user function.
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r26769 | bugman | 2014-11-26 19:29:54 +0100 (Wed, 26 Nov 2014) | 12 lines

A small code rearrangement to create the new target_functions.relax_fit_wrapper module.

This follows from the idea at https://gna.org/task/?7415#comment6. The *func_wrapper() functions of
the specific_analyses.relax_fit.optimisation module have been shifted out and converted to class
methods to create the target_functions.relax_fit_wrapper module. This will be used to abstract away
all of the C code, and will form the infrastructure to allow new exponential curves to be quickly
supported.

The modules of the specific_analyses.relax_fit and specific_analyses.relax_disp packages now import
the target_functions.relax_fit_wrapper.Relax_fit_opt target function class and use that instead.
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r26770 | bugman | 2014-11-26 19:42:20 +0100 (Wed, 26 Nov 2014) | 8 lines

Shifted the C code Jacobian functions into the new target_functions.relax_fit_wrapper module.

This shifts all of the relaxation curve-fitting C code access into the
target_functions.relax_fit_wrapper module so that the rest of relax does not need to handle the C
code. This will allow for new models to be very easily supported, as they would all be set up in
this target function module.
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r26771 | bugman | 2014-11-27 09:45:09 +0100 (Thu, 27 Nov 2014) | 3 lines

Updated the formula in the description of the relax_fit.select_model user function.
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r26782 | bugman | 2014-11-27 15:16:48 +0100 (Thu, 27 Nov 2014) | 8 lines

Modified the printouts from the structure.write_pdb user function if models are present.

Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each model, the header 'MODEL
records' is printed followed by a single '.' character for each model. For structures with many models,
this results in a huge speed up of the user function which is strongly limited by how fast the
terminal can display text.
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r26791 | bugman | 2014-11-27 19:11:38 +0100 (Thu, 27 Nov 2014) | 11 lines

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.
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Merged revisions 26791 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26791 | bugman | 2014-11-27 19:11:38 +0100 (Thu, 27 Nov 2014) | 11 lines

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.
........

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.

Added systemtest Nmrglue.xtest_plot_contour to test the functionality of contour plotting.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Fixes for the Frame_order.test_simulate_rotor_z_axis system test.

Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is
required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at
[1, 0, 0] so that the axis alpha angle of pi/2 creates an axis parallel to Z. The origin to atom
distance check has also been loosened due to the PDB truncation artifact.

Added the initial systemtest Nmrglue.test_nmrglue_read to read spectrum files via nmrglue.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added the user funcion spectrum.nmrglue_read to read spectrum files via nmrglue.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Added a class instance object for handling and storing nmrglue data.

Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html