relax SVN archive

Ported r3293 from the 1.2 line.

The command used was:
svn merge -r3292:3293 svn+ssh://bugman@.../svn/relax/1.2/specific_fns/model_free.py specific_fns/model_free/model_free.py

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r3293 | bugman | 2007-05-09 00:59:17 +0200 (Wed, 09 May 2007) | 7 lines
Changed paths:
M /1.2/specific_fns/model_free.py

Bug fix.

The reading of model-free results files was failing for residues with the parameters vector of None
(as well as the parameter set set to None and the model-free equation set to None). This situation
occurs after model selection when the residue is deselected.
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Ported r3292 from the 1.2 line.

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r3292 | bugman | 2007-05-09 00:52:48 +0200 (Wed, 09 May 2007) | 5 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py

Bug fix for the full_analysis.py script.

The list of model-free models needed to be placed into 'self.runs' for model selection to work.
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Ported r3291 from the 1.2 line.

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r3291 | bugman | 2007-05-09 00:52:00 +0200 (Wed, 09 May 2007) | 6 lines
Changed paths:
M /1.2/docs/latex/model-free.tex

Renamed "Kay's paradigm" to "the diffusion seeded paradigm".

Kay's paradigm was accidentally mislabelled. This paradigm should have been stated to be the
diffusion seeded paradigm using the T1/T2 ratio to initially estimate the diffusion tensor!
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Ported r3287 from the 1.2 line.

The command used was:
svn merge -r3286:3287 svn+ssh://bugman@.../svn/relax/1.2

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r3287 | bugman | 2007-05-08 23:39:21 +0200 (Tue, 08 May 2007) | 9 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py

Improvements to the 'full_analysis.py' sample script.

The script's documentation has been shifted from the __init__() method docstring to the module
docstring.

All of the options which need to be modified by the user have been shifted to the top of the script
as global variables. This means that the user doesn't even need to look at the complex code to
operate the script.
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Hand ported r3302 from the 1.2 line, the fix for bug #9259 (https://gna.org/bugs/?9259).

The commands used where:
svn merge -r3301:3302 svn+ssh://bugman@.../svn/relax/1.2/maths_fns/jw_mapping.py maths_fns/jw_mapping.py
svn merge -r3301:3302 svn+ssh://bugman@.../svn/relax/1.2/test_suite/jw_mapping.py test_suite/system_tests/jw_mapping.py

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r3302 | bugman | 2007-06-20 09:29:52 +0200 (Wed, 20 Jun 2007) | 15 lines
Changed paths:
M /1.2/maths_fns/jw_mapping.py
M /1.2/test_suite/jw_mapping.py

Fix for bug #9259 (https://gna.org/bugs/?9259).

This fix was created by Sebastien Morin (sebastien dott morin dot 1 at ulaval dot ca) and attached
as the patch file 'patch_2007-06-19' attached to the bug report. The thread on the relax-devel
mailing list begins at https://mail.gna.org/public/relax-devel/2007-06/msg00001.html. The exact
source of the bug was identified here https://mail.gna.org/public/relax-devel/2007-06/msg00003.html.
An important explanation of SI vs. CGS units, frequency vs. angular frequency, and why the frequency
is converted to angular frequency by multiplying by 2pi is located here
https://mail.gna.org/public/relax-devel/2007-06/msg00012.html.

The bug was that the heteronuclear frequency wX was being overwritten by the proton frequency wH in
the reduced spectral density mapping code. Both the reduced spectral mapping code and the test
suite have been fixed by Seb.
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Fix for bug #9259 (https://gna.org/bugs/?9259).

This fix was created by Sebastien Morin (sebastien dott morin dot 1 at ulaval dot ca) and attached
as the patch file 'patch_2007-06-19' attached to the bug report. The thread on the relax-devel
mailing list begins at https://mail.gna.org/public/relax-devel/2007-06/msg00001.html. The exact
source of the bug was identified here https://mail.gna.org/public/relax-devel/2007-06/msg00003.html.
An important explanation of SI vs. CGS units, frequency vs. angular frequency, and why the frequency
is converted to angular frequency by multiplying by 2pi is located here
https://mail.gna.org/public/relax-devel/2007-06/msg00012.html.

The bug was that the heteronuclear frequency wX was being overwritten by the proton frequency wH in
the reduced spectral density mapping code. Both the reduced spectral mapping code and the test
suite have been fixed by Seb.

Merged revisions 3299 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r3299 | bugman | 2007-05-30 17:31:19 +0200 (Wed, 30 May 2007) | 9 lines

Fix for bug #9189 (https://gna.org/bugs/index.php?9189).

This bug was reported by Neil Syme (bmbnrs at leeds dot ac dot uk).

Two of the functions accessed when the second set of extended model-free formulae - using the
parameters {S2f, tf, S2s, ts} rather than the standard {S2, S2f, tf, ts} - do not exist. This were
changed to the correct functions (hopefully)!
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Blocked revisions 3260,3286,3290,3297 via svnmerge

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r3260 | macraild | 2007-04-03 19:19:34 +0200 (Tue, 03 Apr 2007) | 4 lines

A further attempt to make boolean mol-res-spin selection work. This is
still some way from a solution.
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r3286 | bugman | 2007-05-08 23:04:54 +0200 (Tue, 08 May 2007) | 15 lines

Hand ported r3285 from the 1.2 line, the fix for bug #8953 (https://gna.org/bugs/?8953).

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Fix for bug #8953 (https://gna.org/bugs/?8953).

The bug was introduced by a fix to the model-free results writing function. In relax versions 1.2.9
and below, no data about a residue was being stored in the results file if it was deselected. This
behaviour undesirable as a spin system could be deselected temporarily and later on reselected. If
this process is deliberately interrupted by using 'results.write()' followed by 'results.read()' to
resume, then there will be data loss.

The fix was simple: check for the presence of the 'data.num_ri' data structure.
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r3290 | bugman | 2007-05-09 00:50:45 +0200 (Wed, 09 May 2007) | 20 lines

Manually ported the relevent part of r3288 (the fix to bug #9101 (https://gna.org/bugs/?9101)).

The changes to errors.py and specific_fns/model_free.py were not ported.

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r3288 | bugman | 2007-05-08 23:48:05 +0200 (Tue, 08 May 2007) | 6 lines
Changed paths:
M /1.2/errors.py
M /1.2/specific_fns/model_free.py
M /1.2/specific_fns/relax_data.py

Fix for bug #9101 (https://gna.org/bugs/?9101).

The relax_data.read() user function was failing when the data or error column contained the text
'None' which is the default output for deselected spin systems in the exponential curve fitting
component of relax. This is now fixed.
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r3297 | bugman | 2007-05-30 17:04:16 +0200 (Wed, 30 May 2007) | 8 lines

Fix for bug #9238 (https://gna.org/bugs/?9238).

This fatal bug was reported by Sébastien Morin.

The fix was slightly different from that posted in the bug report as the factor of 2 pi was still
required.
........

Fix for bug #9189 (https://gna.org/bugs/index.php?9189).

This bug was reported by Neil Syme (bmbnrs at leeds dot ac dot uk).

Two of the functions accessed when the second set of extended model-free formulae - using the
parameters {S2f, tf, S2s, ts} rather than the standard {S2, S2f, tf, ts} - do not exist. This were
changed to the correct functions (hopefully)!

Hand ported r3297 from the 1.3 line - the fix for bug #9238.

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r3297 | bugman | 2007-05-30 17:04:16 +0200 (Wed, 30 May 2007) | 8 lines

Fix for bug #9238 (https://gna.org/bugs/?9238).

This fatal bug was reported by Sébastien Morin.

The fix was slightly different from that posted in the bug report as the factor of 2 pi was still
required.
.....