Author: bugman
Date: Thu Aug 21 08:54:22 2014
New Revision: 25133
URL: http://svn.gna.org/viewcvs/relax?rev=25133&view=rev
Log:
Merged revisions 25096-25132 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
................
r25096 | tlinnet | 2014-08-20 16:01:39 +0200 (Wed, 20 Aug 2014) | 6 lines
Inserted return of True/False flags from function which convert models.
The flag tells if:
- flag if 'No Rex' model for R1rho off-resonance was translated.
- flag if 'No Rex' model for R1rho off-resonance was inserted.
- flag if R1rho off-resonance was translated to 'R1 fit' models if no R1
data was found.
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r25097 | tlinnet | 2014-08-20 16:01:41 +0200 (Wed, 20 Aug 2014) | 1 line
Changes to systemtest, after the number of returns from function has been
altered.
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r25098 | tlinnet | 2014-08-20 16:01:43 +0200 (Wed, 20 Aug 2014) | 4 lines
Inserted into relax_disp auto_analyses, to convert the input models.
This will convert/insert the correct 'No Rex' to the corresponding 'No Rex'
model for R1rho off-resonance models.
It will also translate to the corresponding 'R1 fit' model, if no 'R1 data'
has been loaded with relax_data.read() function.
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r25099 | tlinnet | 2014-08-20 16:09:37 +0200 (Wed, 20 Aug 2014) | 3 lines
Lowering of precision in systemtest
Relax_disp.test_r1rho_kjaergaard_missing_r1().
This is due to 64/32 bit issues, between analysing on Linux computer, and
testing on Mac computer.
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r25100 | tlinnet | 2014-08-20 16:09:40 +0200 (Wed, 20 Aug 2014) | 8 lines
Made the GUI selection of models for relaxation dispersion more simple.
After the implementation of a function which will translate the models, the
'No Rex' model will be converted to the 'No Rex' model for R1rho
off-resonance.
Also the corresponding 'R1 fit' model will be chosen istead, if R1 data has
not been loaded.
This makes the model selection easier in the GUI interface.
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r25101 | tlinnet | 2014-08-20 16:19:35 +0200 (Wed, 20 Aug 2014) | 3 lines
Bugfix for Relax_disp.test_bug_21715_clustered_indexerror, where only
'R2eff', 'No Rex' is analysed.
This special case was not tested inte the translating function.
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r25102 | tlinnet | 2014-08-20 16:46:32 +0200 (Wed, 20 Aug 2014) | 1 line
Shortening the text in the auto_analysis, and raises a warning if R1 data
has not been loaded.
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r25103 | tlinnet | 2014-08-20 18:09:29 +0200 (Wed, 20 Aug 2014) | 6 lines
Rewrote the logic of the key-word 'optimise_r2eff' in the auto analyses of
relax disp.
If R2eff result file exist in the 'pre_run_dir', this is loaded.
If the results contain both values, and errors, then no optimisation is
performed on the R2eff model.
Unless the 'optimise_r2eff' flag is raised, which is not standard.
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r25104 | tlinnet | 2014-08-20 18:09:32 +0200 (Wed, 20 Aug 2014) | 1 line
Fix to systemtest, after changing the keyword to the auto analyses.
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r25105 | bugman | 2014-08-20 18:12:04 +0200 (Wed, 20 Aug 2014) | 5 lines
Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system
test on MS Windows.
This is for 32-bit MS Windows systems where the parameter checks need to be
loosened.
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r25106 | bugman | 2014-08-20 18:13:10 +0200 (Wed, 20 Aug 2014) | 5 lines
Fixes for the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test on MS
Windows.
This is for 32-bit MS Windows systems where the parameter checks need to be
loosened.
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r25107 | bugman | 2014-08-20 18:24:03 +0200 (Wed, 20 Aug 2014) | 9 lines
Created the specific_analyses.relax_disp.data.is_r1_optimsed() function.
This follows from an idea for handling R1 optimisation in the tread at
http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736.
This relaxation dispersion function can be used anywhere that requires the
knowledge that R1 values
should be fitted during optimisation or if loaded values should be used.
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r25108 | bugman | 2014-08-20 18:53:18 +0200 (Wed, 20 Aug 2014) | 5 lines
Implemented the very basic relax_disp.r1_fit user function.
This is as discussed at
http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6737.
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r25109 | bugman | 2014-08-20 19:07:00 +0200 (Wed, 20 Aug 2014) | 6 lines
Implemented the specific_analyses.relax_disp.parameters.r1_setup() function.
This matches the description at
http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6739
and http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736.
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r25110 | bugman | 2014-08-20 19:11:12 +0200 (Wed, 20 Aug 2014) | 3 lines
Spelling fix for the is_r1_optimised() function name.
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r25111 | tlinnet | 2014-08-20 19:16:05 +0200 (Wed, 20 Aug 2014) | 6 lines
Revert of commit r25002 in branches/R1_fitting.
This was not the correct implementation, since copying of 'R2eff' is
not really a "parameter", which can be "fitted" in the sence of the
dispersion models.
Rather, R2eff should be copied, with value.copy() function.
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r25112 | tlinnet | 2014-08-20 19:16:07 +0200 (Wed, 20 Aug 2014) | 1 line
Implemented to the back_end of the value.copy, a "force" flag to overwrite
destination value.
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r25113 | tlinnet | 2014-08-20 19:16:09 +0200 (Wed, 20 Aug 2014) | 1 line
Implemented to the front_end of the value.copy, a "force" flag to overwrite
destination value.
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r25114 | tlinnet | 2014-08-20 19:16:10 +0200 (Wed, 20 Aug 2014) | 1 line
Copying the R2eff value from the reading of R2eff results in the auto
analyses of relax_disp.
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r25115 | bugman | 2014-08-20 19:18:17 +0200 (Wed, 20 Aug 2014) | 3 lines
Fix for the misspelled is_r1_optimised() function.
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r25116 | bugman | 2014-08-20 19:21:05 +0200 (Wed, 20 Aug 2014) | 8 lines
The r1_fit flag is stored in the Disp_minimise_command class and passed
into the target function.
This matches the details at
http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736.
The specific_analyses.relax_disp.optimisation.Disp_minimise_command class
calls is_r1_optimised()
and stores the result. This is then passed into the relaxation dispersion
target function class.
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r25117 | tlinnet | 2014-08-20 19:33:41 +0200 (Wed, 20 Aug 2014) | 1 line
Modified that 'NS CPMG 2-site expanded' will be preferred before 'NS CPMG
2-site 3D' and 'NS CPMG 2-site star'.
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r25118 | bugman | 2014-08-20 19:33:47 +0200 (Wed, 20 Aug 2014) | 7 lines
Fixes for indentation accidentally committed at r25108.
This can be seen at
http://thread.gmane.org/gmane.science.nmr.relax.scm/22858.
A Vim command was accidentally typed which removed one level of indentation.
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r25119 | tlinnet | 2014-08-20 19:47:51 +0200 (Wed, 20 Aug 2014) | 3 lines
Modified the nesting for 'NS MMQ 3-site linear'.
'NS MMQ 3-site linear' should be able to nest from 'NS MMQ 3-site'.
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r25120 | tlinnet | 2014-08-20 21:06:27 +0200 (Wed, 20 Aug 2014) | 1 line
Fix to unit test, after MODEL_NS_CPMG_2SITE_EXPANDED has been preferred
over other numerical CPMG models.
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r25121 | tlinnet | 2014-08-20 21:06:29 +0200 (Wed, 20 Aug 2014) | 17 lines
Modified to unit test, that when model:
MODEL_PARAMS_NS_R1RHO_3SITE
nest from:
MODEL_PARAMS_NS_R1RHO_2SITE
the conversion should be:
'r2', 'r2'
'pA', 'pA'
'dw_AB', 'dw'
'kex_AB', 'kex'
'pB', '1 - pA'
'dw_BC', 'dw'
'kex_BC', 'kex'
'kex_AC', 'kex'
Here '1 - pA' is a special conversion flag.
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r25122 | tlinnet | 2014-08-20 21:06:31 +0200 (Wed, 20 Aug 2014) | 1 line
Implemented the special flag '1 - pA', when nesting parameters from models
with fewer chemical sites.
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r25123 | tlinnet | 2014-08-20 21:06:33 +0200 (Wed, 20 Aug 2014) | 1 line
Implemented the nesting of parameters from a model with fewer chemical
sites when nesting for NS R1rho 3sites.
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r25124 | tlinnet | 2014-08-20 21:06:37 +0200 (Wed, 20 Aug 2014) | 2 lines
Inserted systemtest Relax_disp.test_model_nesting_and_param() which will
go through all models, and then through all it nested models, testing that
all parameters have a conversion.
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r25125 | tlinnet | 2014-08-20 21:33:23 +0200 (Wed, 20 Aug 2014) | 2 lines
Modified systemtest Relax_disp.test_model_nesting_and_param() to only
print, when the
converted parameter is different from the original parameter.
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r25126 | tlinnet | 2014-08-20 21:33:26 +0200 (Wed, 20 Aug 2014) | 2 lines
Fix for parameter conversion when model is:
MODEL_PARAMS_NS_R1RHO_3SITE or MODEL_PARAMS_NS_R1RHO_3SITE_LINEAR.
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r25127 | tlinnet | 2014-08-20 21:48:37 +0200 (Wed, 20 Aug 2014) | 5 lines
Fix for parameter conversion for:
MODEL_PARAMS_NS_MMQ_3SITE
and
MODEL_PARAMS_NS_MMQ_3SITE_LINEAR
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r25128 | tlinnet | 2014-08-20 22:01:05 +0200 (Wed, 20 Aug 2014) | 23 lines
Reverted r25024, related to Linear Constraints change.
The command used was:
svn merge -r25024:r25023 .
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r25024 | tlinnet | 2014-08-15 15:11:00 +0200 (Fri, 15 Aug 2014) | 11
lines
Modified the Linear Constraints for the exchange rates.
For CPMG, the maximum kex should be 10^4, and for R1rho it should be
10^5.
This is altered from the value of 10^6.
The suggested restraints for 'kex' follows from article, on page 224:
Nuclear Magnetic Resonance Methods for Quantifying
Microsecond-to-Millisecond Motions in Biological Macromolecules.
Palmer-III, Arthur G., Kroenke, Christopher D., Loria, J. Patrick
Nucl. Magn. Reson. Biol. Macromol. B, 2001, Vol: 339, pages 204-238.
U{DOI:
10.1016/S0076-6879(01)39315-1<http://dx.doi.org/10.1016/S0076-6879%2801%2939315-1>}
........
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r25129 | tlinnet | 2014-08-20 22:03:00 +0200 (Wed, 20 Aug 2014) | 13 lines
Reverted r25025, related to Linear Constraints change.
The command used was:
svn merge -r25025:r25024 .
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r25025 | tlinnet | 2014-08-15 15:11:03 +0200 (Fri, 15 Aug 2014) | 1 line
Small fix for systemtest, where precision is lowered on digit after
altering the linear constraints.
........
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r25130 | tlinnet | 2014-08-20 22:06:40 +0200 (Wed, 20 Aug 2014) | 12 lines
Reverted r25027, related to Linear Constraints change.
The command used was:
svn merge -r25027:r25026 .
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r25027 | tlinnet | 2014-08-15 15:11:09 +0200 (Fri, 15 Aug 2014) | 1 line
Modification to the relax manual, regarding the Linear Constraints for
the exchange rate.
........
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r25131 | tlinnet | 2014-08-20 23:03:50 +0200 (Wed, 20 Aug 2014) | 1 line
Fixes to unit tests, after parameter conversion have been corrected.
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r25132 | tlinnet | 2014-08-20 23:03:53 +0200 (Wed, 20 Aug 2014) | 1 line
Replaced that folder names for writing out results should be with replaced
with underscores "_".
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Added:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/non_clustered/No_Rex/
- copied from r25132,
trunk/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/non_clustered/No_Rex/
Removed:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/non_clustered/No
Rex/results.bz2
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp.py
branches/frame_order_cleanup/docs/latex/dispersion.tex
branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py
branches/frame_order_cleanup/pipe_control/value.py
branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py
branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
branches/frame_order_cleanup/specific_analyses/relax_disp/uf.py
branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
branches/frame_order_cleanup/target_functions/relax_disp.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
branches/frame_order_cleanup/user_functions/relax_disp.py
branches/frame_order_cleanup/user_functions/value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/latex/dispersion.tex?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/analyses/auto_relax_disp.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/pipe_control/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/value.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/data.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/model.py?rev=25133&r1=25132&r2=25133&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py?rev=25133&r1=25132&r2=25133&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/uf.py?rev=25133&r1=25132&r2=25133&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/variables.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/target_functions/relax_disp.py?rev=25133&r1=25132&r2=25133&view=diff
Removed:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/non_clustered/No
Rex/results.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/non_clustered/No%20Rex/results.bz2?rev=25132&view=auto
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=25133&r1=25132&r2=25133&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_specific_analyses/_relax_disp/test_model.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/relax_disp.py?rev=25133&r1=25132&r2=25133&view=diff
Modified: branches/frame_order_cleanup/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/value.py?rev=25133&r1=25132&r2=25133&view=diff
r25133 - in /branches/frame_order_cleanup: ./ auto_analyses/ docs/latex/ gui/analyses/ pipe_control/ specific_analyses/relax...