relax SVN archive

Bug fix for the pymol.view user function for when no PDB file exists.

The pymol.view user function would fail with an AttributeError when the currently loaded data does
not exist as a PDB file. This is now caught and the non-existent PDB is no longer displayed. A
better solution might be to dump all the current structural data into a temporary file and load
that, all within a try-finally statement to be sure to delete the temporary file. This solution may
not be what the user is interested in anyway.

Created the Frame_order.test_simulate_free_rotor_z_axis system test.

This is to check the frame_order.simulate user function for the free rotor model along the z-axis.

Fix for the Frame_order.test_pdb_model_free_rotor_xz_plane_tilt system test.

This was broken while implementing the Frame_order.test_simulate_rotor_z_axis system test. Instead
of shifting the 6 atom structure so its CoM is the pivot of the motion when creating the atoms, now
the Frame_order.test_simulate_rotor_z_axis system test sets the average domain translation vector to
the pivot to achieve the same result. This preserves the z-axis orientation of the rotor models.

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

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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.
........

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.