relax SVN archive

Merged revisions 3309 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r3309 | bugman | 2007-06-24 17:28:28 +0200 (Sun, 24 Jun 2007) | 8 lines

Automatic looping in the full_analysis.py script.

In response to the post by Douglas Kojetin <douglas dot kojetin att gmail dot com> at
https://mail.gna.org/public/relax-users/2007-06/msg00002.html, I have added the ability to
automatically loop over the optimisation rounds of the full_analysis.py script until convergence.
This is not turned on automatically by default as it is likely to require a bit of debugging.
........

Blocked revisions 3303-3308 via svnmerge

........
r3303 | bugman | 2007-06-20 11:09:54 +0200 (Wed, 20 Jun 2007) | 28 lines

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

.....
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.
.....
........
r3304 | bugman | 2007-06-24 16:56:25 +0200 (Sun, 24 Jun 2007) | 20 lines

Ported r3287 from the 1.2 line.

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

.....
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.
.....
........
r3305 | bugman | 2007-06-24 17:00:32 +0200 (Sun, 24 Jun 2007) | 14 lines

Ported r3291 from the 1.2 line.

.....
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!
.....
........
r3306 | bugman | 2007-06-24 17:03:23 +0200 (Sun, 24 Jun 2007) | 13 lines

Ported r3292 from the 1.2 line.

.....
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.
.....
........
r3307 | bugman | 2007-06-24 17:08:03 +0200 (Sun, 24 Jun 2007) | 18 lines

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

.....
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.
.....
........
r3308 | bugman | 2007-06-24 17:13:00 +0200 (Sun, 24 Jun 2007) | 18 lines

Ported r3294 from the 1.2 line.

The command used was:
svn merge -r3293:3294 svn+ssh://bugman@.../svn/relax/1.2/specific_fns/model_free.py specific_fns/model_free/model_free.py

.....
r3294 | bugman | 2007-05-09 00:59:45 +0200 (Wed, 09 May 2007) | 7 lines
Changed paths:
M /1.2/specific_fns/model_free.py

Bug fix.

The setting up of Monte Carlo simulations was failing because of the existance of the empty
parameter vector []. This situation occurs after model selection when the residue is deselected
(after the reading of a model-free results file).
.....
........

Automatic looping in the full_analysis.py script.

In response to the post by Douglas Kojetin <douglas dot kojetin att gmail dot com> at
https://mail.gna.org/public/relax-users/2007-06/msg00002.html, I have added the ability to
automatically loop over the optimisation rounds of the full_analysis.py script until convergence.
This is not turned on automatically by default as it is likely to require a bit of debugging.

Ported r3294 from the 1.2 line.

The command used was:
svn merge -r3293:3294 svn+ssh://bugman@.../svn/relax/1.2/specific_fns/model_free.py specific_fns/model_free/model_free.py

.....
r3294 | bugman | 2007-05-09 00:59:45 +0200 (Wed, 09 May 2007) | 7 lines
Changed paths:
M /1.2/specific_fns/model_free.py

Bug fix.

The setting up of Monte Carlo simulations was failing because of the existance of the empty
parameter vector []. This situation occurs after model selection when the residue is deselected
(after the reading of a model-free results file).
.....

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

.....
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.
.....

Ported r3292 from the 1.2 line.

.....
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.
.....

Ported r3291 from the 1.2 line.

.....
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!
.....

Ported r3287 from the 1.2 line.

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

.....
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.
.....

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

.....
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.
.....

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.