relax SVN archive

Created the TSMFK01 model target function for 2-site very-slow exchange model, range of microsecond to second time scale.

Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001)
Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

The function is probably not correct, since there is some problems with using the end_index
to handle the unpacking of the parameters.

Signed-off-by: Edward d'Auvergne <edward@...>

Added the TSMFK01 model to the user_functions/relax_disp.py select_model user function frontend.

Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001)
Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>

lib/dispersion/lm63.py is copied to tsmfk01.py as part of the implementation of the TSMFK01 model equation.

Progress sr #3071: https://gna.org/support/index.php?3071 -
Implementation of Tollinger/Kay dispersion model (2001)
Following the guide at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Added the new 'TSMFK01' model to the specific_analyses\relax_disp\variables.py module.

This is the Tollinger/Kay model for the 2-site very-slow exchange model for CPMG-type experiments, which cover the range of microsecond to second time scale.
Paper by M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and L.E. Kay (2001).

Progress sr #3071: https://gna.org/support/index.php?3071 - Implementation of Tollinger/Kay dispersion model (2001)
Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>

Merged revisions 20582-20584,20587-20588,20590-20596,20620-20621,20623-20625 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20582 | bugman | 2013-08-13 17:58:03 +0200 (Tue, 13 Aug 2013) | 8 lines

Large change to the free file format GUI element for the user functions.

The GUI element used in the user function wizard windows has been modified to have both a 'default'
form, which is the previous design, and a 'mini' form which is now used for the user functions.
This mini form only uses 1 row, rather than the default of 6 or 8. It is a read only text element
with a button that launches the free file format window. The amount of space saved is huge.
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r20583 | bugman | 2013-08-13 18:03:42 +0200 (Tue, 13 Aug 2013) | 3 lines

Improved the text for the mini free file format GUI element.
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r20584 | bugman | 2013-08-13 18:12:04 +0200 (Tue, 13 Aug 2013) | 5 lines

Updated all of the user function GUI window sizes for the 'mini' free file format GUI element.

This allows much more text of the description to be displayed.
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r20587 | bugman | 2013-08-14 15:49:57 +0200 (Wed, 14 Aug 2013) | 5 lines

Fixes for the Palmer.test_palmer_omp system test for Modelfree4 version 4.20 gcc.

The gcc and pgf results were somehow switched!
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r20588 | bugman | 2013-08-14 16:11:51 +0200 (Wed, 14 Aug 2013) | 6 lines

Another fix for the Palmer.test_palmer_omp system test for Modelfree4.

The gcc and pgf compiled i386 Linux binaries of Modelfree4 version 4.20 actually give identical
results. Therefore the checks have been merged.
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r20590 | bugman | 2013-08-14 16:48:43 +0200 (Wed, 14 Aug 2013) | 8 lines

Reverted r20587 and r20588 as these were rubbish!

The command used was:
svn merge -rHEAD:r20586 .

There are gcc verses pdf Modelfree4 binary results for version 4.20.
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r20591 | bugman | 2013-08-14 18:19:38 +0200 (Wed, 14 Aug 2013) | 6 lines

Proper fix for the Palmer.test_palmer_omp for the different Modelfree4 binaries.

The gcc and pdf binaries are now properly detected and the slightly different results are now
correctly checked for.
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r20592 | bugman | 2013-08-14 18:53:13 +0200 (Wed, 14 Aug 2013) | 3 lines

Updated the Mac Framework setup document to help with scipy compilation problems.
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r20593 | bugman | 2013-08-14 18:54:19 +0200 (Wed, 14 Aug 2013) | 5 lines

Improved the Python seeking and module version print out script for symlinks.

This should now be much more capable of finding all Python versions on a system.
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r20594 | bugman | 2013-08-14 19:52:39 +0200 (Wed, 14 Aug 2013) | 8 lines

Added support for the Mac OS X Modelfree4 binary results to the Palmer.* system tests.

The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to
a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In
the Mac binaries, the results are instead written out to 4 significant figures. Therefore the
number of decimal places are much less than the Linux results.
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r20595 | bugman | 2013-08-14 19:55:57 +0200 (Wed, 14 Aug 2013) | 5 lines

Fix for the Palmer.test_palmer system test for older Python versions.

This is a problem introduced in the previous commit (r20594).
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r20596 | bugman | 2013-08-15 09:10:12 +0200 (Thu, 15 Aug 2013) | 24 lines

Syntax error fix for one of the unused scripts in the relax test suite shared data directories.

This problem was encountered by Jack Howarth <howarth att bromo dott med dott uc dott edu> and
communicated in a private message. The issue was found by fink. This script is never used and will
never be used again - it is only there for reference. How a syntax error was introduced is a
mystery. For reference, the full message is:

"""
While preparing fink packaging for the new relax 3.0.0 release, I noticed an error
in the python scripts. When installing relax-py27-3.0.0, I get the following error as
the the frame_order_pseudo_ellipse.py python script is compiled. What is the correct
syntax for that particular call to pymol.command?

Setting up relax-py27 (3.0.0-1) ...
Compiling /sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py ...
File "/sw/lib/relax-py27/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_pseudo_ellipse.py", line 154
pymol.command('show spheres'_pseudo_ellipse)
^
SyntaxError: invalid syntax

Thanks in advance for any clarification.
"""
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r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
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r20621 | bugman | 2013-08-16 20:19:19 +0200 (Fri, 16 Aug 2013) | 15 lines

Reverted r20620 as the checked out trunk copy was not up to date.

The command used was:
svn merge -r20620:r20619 .

.....
r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Changed paths:
M /trunk

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
.....
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r20623 | bugman | 2013-08-16 20:20:23 +0200 (Fri, 16 Aug 2013) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
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r20624 | bugman | 2013-08-16 20:30:10 +0200 (Fri, 16 Aug 2013) | 112 lines

Merged revisions 20579,20598-20619 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities

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r20579 | bugman | 2013-08-13 11:58:38 +0200 (Tue, 13 Aug 2013) | 6 lines

Modification of the spectrum.read_intensities user function front end.

The heteronuc and proton arguments have been eliminated. Instead the new dim argument is used to
associate the data with the spins of any dimension in the peak list.
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r20598 | bugman | 2013-08-15 12:01:52 +0200 (Thu, 15 Aug 2013) | 3 lines

Replaced the 'heteronuc' and 'proton' arguments of the spectrum.read_intensities user function backend with 'dim'.
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r20599 | bugman | 2013-08-16 17:15:24 +0200 (Fri, 16 Aug 2013) | 6 lines

Created the new lib.spectrum.objects module.

This will hold temporary data structures for representing peak lists and other spectral data. The
module currently contains the Peak_list class which is used to hold peak list data.
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r20600 | bugman | 2013-08-16 17:18:21 +0200 (Fri, 16 Aug 2013) | 3 lines

Started to shift the spectrum.read_intensities user function backend to use lib.spectrum.peak_list.
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r20601 | bugman | 2013-08-16 17:49:45 +0200 (Fri, 16 Aug 2013) | 3 lines

The pipe_control.spectrum.read_intensities() function now works with the Peak_list object.
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r20602 | bugman | 2013-08-16 17:50:26 +0200 (Fri, 16 Aug 2013) | 3 lines

The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function.
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r20603 | bugman | 2013-08-16 18:28:25 +0200 (Fri, 16 Aug 2013) | 3 lines

Fix for the lib.spectrum.objects.Peak_list object - the Assignment object was not initialised.
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r20604 | bugman | 2013-08-16 18:31:04 +0200 (Fri, 16 Aug 2013) | 3 lines

Small fix for how pipe_control.spectrum.read() uses the Peak_list object.
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r20605 | bugman | 2013-08-16 18:31:40 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.sparky.read_list_intensity() function now operates on the Peak_list object.
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r20606 | bugman | 2013-08-16 18:42:46 +0200 (Fri, 16 Aug 2013) | 3 lines

Changed the spectrum.read_intensities dim argument default to w2 and improved the long description.
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r20607 | bugman | 2013-08-16 18:44:54 +0200 (Fri, 16 Aug 2013) | 5 lines

Fix for the assignment handling in the lib.software.sparky.read_peak_list() function.

The first element is usually the indirect dimension or w2.
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r20608 | bugman | 2013-08-16 18:48:15 +0200 (Fri, 16 Aug 2013) | 5 lines

Fix for many of the Peak_list system tests for the user function argument changes.

The heteronuc and proton arguments have been replaced by the dim argument.
........
r20609 | bugman | 2013-08-16 18:57:15 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.xeasy.read_list_intensity() function now operates on the Peak_list object.
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r20610 | bugman | 2013-08-16 18:58:58 +0200 (Fri, 16 Aug 2013) | 3 lines

Small docstring change for lib.software.sparky.read_list_intensity().
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r20611 | bugman | 2013-08-16 19:02:03 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.nmrview.read_list_intensity() function now operates on the Peak_list object.
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r20612 | bugman | 2013-08-16 19:14:57 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.spectrum.peak_list.intensity_generic() function now operates on the Peak_list object.
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r20613 | bugman | 2013-08-16 19:16:39 +0200 (Fri, 16 Aug 2013) | 5 lines

Fixes for the pipe_control.spectrum.read() function.

An error was referencing a now non-existent variable and the docstring has been fixed.
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r20614 | bugman | 2013-08-16 19:17:01 +0200 (Fri, 16 Aug 2013) | 3 lines

Removal of a now unused list variable.
........
r20615 | bugman | 2013-08-16 19:34:45 +0200 (Fri, 16 Aug 2013) | 6 lines

The Peak_list object can now store peak intensity names.

This is for peak lists such as from NMRPipe seriersTab files where the peak list covers multiple
spectra.
........
r20616 | bugman | 2013-08-16 19:42:56 +0200 (Fri, 16 Aug 2013) | 3 lines

The NMRPipe seriesTab peak lists are now supported through the Peak_list object.
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r20617 | bugman | 2013-08-16 19:54:36 +0200 (Fri, 16 Aug 2013) | 3 lines

Unit test fixes for the spectrum.read_intensities user function argument changes.
........
r20618 | bugman | 2013-08-16 19:56:45 +0200 (Fri, 16 Aug 2013) | 3 lines

Fixes for a few system tests for the spectrum.read_intensities user function argument changes.
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r20619 | bugman | 2013-08-16 20:11:07 +0200 (Fri, 16 Aug 2013) | 3 lines

Fixes for a few GUI tests for the spectrum.read_intensities user function argument changes.
........
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r20625 | bugman | 2013-08-16 20:30:34 +0200 (Fri, 16 Aug 2013) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
................

Removal of the peak_intensities branch as it has been merged back to trunk.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/peak_intensities

Merged revisions 20579,20598-20619 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities

........
r20579 | bugman | 2013-08-13 11:58:38 +0200 (Tue, 13 Aug 2013) | 6 lines

Modification of the spectrum.read_intensities user function front end.

The heteronuc and proton arguments have been eliminated. Instead the new dim argument is used to
associate the data with the spins of any dimension in the peak list.
........
r20598 | bugman | 2013-08-15 12:01:52 +0200 (Thu, 15 Aug 2013) | 3 lines

Replaced the 'heteronuc' and 'proton' arguments of the spectrum.read_intensities user function backend with 'dim'.
........
r20599 | bugman | 2013-08-16 17:15:24 +0200 (Fri, 16 Aug 2013) | 6 lines

Created the new lib.spectrum.objects module.

This will hold temporary data structures for representing peak lists and other spectral data. The
module currently contains the Peak_list class which is used to hold peak list data.
........
r20600 | bugman | 2013-08-16 17:18:21 +0200 (Fri, 16 Aug 2013) | 3 lines

Started to shift the spectrum.read_intensities user function backend to use lib.spectrum.peak_list.
........
r20601 | bugman | 2013-08-16 17:49:45 +0200 (Fri, 16 Aug 2013) | 3 lines

The pipe_control.spectrum.read_intensities() function now works with the Peak_list object.
........
r20602 | bugman | 2013-08-16 17:50:26 +0200 (Fri, 16 Aug 2013) | 3 lines

The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function.
........
r20603 | bugman | 2013-08-16 18:28:25 +0200 (Fri, 16 Aug 2013) | 3 lines

Fix for the lib.spectrum.objects.Peak_list object - the Assignment object was not initialised.
........
r20604 | bugman | 2013-08-16 18:31:04 +0200 (Fri, 16 Aug 2013) | 3 lines

Small fix for how pipe_control.spectrum.read() uses the Peak_list object.
........
r20605 | bugman | 2013-08-16 18:31:40 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.sparky.read_list_intensity() function now operates on the Peak_list object.
........
r20606 | bugman | 2013-08-16 18:42:46 +0200 (Fri, 16 Aug 2013) | 3 lines

Changed the spectrum.read_intensities dim argument default to w2 and improved the long description.
........
r20607 | bugman | 2013-08-16 18:44:54 +0200 (Fri, 16 Aug 2013) | 5 lines

Fix for the assignment handling in the lib.software.sparky.read_peak_list() function.

The first element is usually the indirect dimension or w2.
........
r20608 | bugman | 2013-08-16 18:48:15 +0200 (Fri, 16 Aug 2013) | 5 lines

Fix for many of the Peak_list system tests for the user function argument changes.

The heteronuc and proton arguments have been replaced by the dim argument.
........
r20609 | bugman | 2013-08-16 18:57:15 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.xeasy.read_list_intensity() function now operates on the Peak_list object.
........
r20610 | bugman | 2013-08-16 18:58:58 +0200 (Fri, 16 Aug 2013) | 3 lines

Small docstring change for lib.software.sparky.read_list_intensity().
........
r20611 | bugman | 2013-08-16 19:02:03 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.software.nmrview.read_list_intensity() function now operates on the Peak_list object.
........
r20612 | bugman | 2013-08-16 19:14:57 +0200 (Fri, 16 Aug 2013) | 3 lines

The lib.spectrum.peak_list.intensity_generic() function now operates on the Peak_list object.
........
r20613 | bugman | 2013-08-16 19:16:39 +0200 (Fri, 16 Aug 2013) | 5 lines

Fixes for the pipe_control.spectrum.read() function.

An error was referencing a now non-existent variable and the docstring has been fixed.
........
r20614 | bugman | 2013-08-16 19:17:01 +0200 (Fri, 16 Aug 2013) | 3 lines

Removal of a now unused list variable.
........
r20615 | bugman | 2013-08-16 19:34:45 +0200 (Fri, 16 Aug 2013) | 6 lines

The Peak_list object can now store peak intensity names.

This is for peak lists such as from NMRPipe seriersTab files where the peak list covers multiple
spectra.
........
r20616 | bugman | 2013-08-16 19:42:56 +0200 (Fri, 16 Aug 2013) | 3 lines

The NMRPipe seriesTab peak lists are now supported through the Peak_list object.
........
r20617 | bugman | 2013-08-16 19:54:36 +0200 (Fri, 16 Aug 2013) | 3 lines

Unit test fixes for the spectrum.read_intensities user function argument changes.
........
r20618 | bugman | 2013-08-16 19:56:45 +0200 (Fri, 16 Aug 2013) | 3 lines

Fixes for a few system tests for the spectrum.read_intensities user function argument changes.
........
r20619 | bugman | 2013-08-16 20:11:07 +0200 (Fri, 16 Aug 2013) | 3 lines

Fixes for a few GUI tests for the spectrum.read_intensities user function argument changes.
........

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities

Merged revisions 20620-20621 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
........
r20621 | bugman | 2013-08-16 20:19:19 +0200 (Fri, 16 Aug 2013) | 15 lines

Reverted r20620 as the checked out trunk copy was not up to date.

The command used was:
svn merge -r20620:r20619 .

.....
r20620 | bugman | 2013-08-16 20:15:58 +0200 (Fri, 16 Aug 2013) | 3 lines
Changed paths:
M /trunk

Initialized merge tracking via "svnmerge" with revisions "1-20577" from
svn+ssh://bugman@.../svn/relax/branches/peak_intensities
.....
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