Author: tlinnet
Date: Wed Dec 3 20:45:38 2014
New Revision: 26944
URL: http://svn.gna.org/viewcvs/relax?rev=26944&view=rev
Log:
Merged revisions
26782,26791,26794-26795,26798,26810,26819-26870,26874-26876,26885,26901-26902,26907,26925
via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
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(?\226?\136?\146R1*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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r26794 | bugman | 2014-11-27 21:48:08 +0100 (Thu, 27 Nov 2014) | 3 lines
Updated the target_functions package __all__ list to include the relax_fit*
modules.
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r26795 | bugman | 2014-11-27 21:50:50 +0100 (Thu, 27 Nov 2014) | 3 lines
Modified the package __all__ list checking unit test to accept *.so C
modules.
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r26798 | bugman | 2014-11-28 09:34:02 +0100 (Fri, 28 Nov 2014) | 9 lines
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.
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r26810 | bugman | 2014-11-28 19:03:16 +0100 (Fri, 28 Nov 2014) | 3 lines
Removal of an unused import in the relax_fit_zooming_grid.py system test
script.
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r26819 | bugman | 2014-11-29 09:44:49 +0100 (Sat, 29 Nov 2014) | 9 lines
Added a system test script for testing the saturation-recovery R1
experiment.
This was created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott
harvard dot edu>. The
file was taken from the saturation_recovery.tar.gaz file
(https://gna.org/task/download.php?file_id=22997) are attached to the task
at
http://gna.org/task/?7415. The only difference with the original script is
that the grace.view user
function calls have been removed, as these cannot be used in a system test.
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r26820 | bugman | 2014-11-29 09:48:13 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a copyright notice for Andras Boeszoermenyi for the newly added
saturation-recovery R1 script.
This change follows the discussion in the message
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26821 | bugman | 2014-11-29 09:55:57 +0100 (Sat, 29 Nov 2014) | 11 lines
Modified the relax_fit_saturation_recovery.py script to work as a system
test.
This is the script from Andras Boeszoermenyi <Andras_Boeszoermenyi att hms
dott harvard dot edu>.
The change follows from the discussion of
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
The status.install_path variable is now used to point to the location of
the files. The relax data
store ds.tmpdir variable is used for outputting all files. And commented
out user functions have
been deleted.
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r26822 | bugman | 2014-11-29 09:56:49 +0100 (Sat, 29 Nov 2014) | 6 lines
Reverted r26820 as this was incorrect.
The command used was:
svn merge -r26820:r26819 .
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r26823 | bugman | 2014-11-29 09:59:17 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a copyright notice for Andras Boeszoermenyi for the newly added
saturation-recovery R1 script.
This change follows the discussion in the message
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26824 | bugman | 2014-11-29 10:03:27 +0100 (Sat, 29 Nov 2014) | 6 lines
Created the Relax_fit.test_saturation_recovery system test.
This follows from the discussion of
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
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r26825 | bugman | 2014-11-29 10:10:56 +0100 (Sat, 29 Nov 2014) | 5 lines
Added the saturation recovery experiment to the relax_fit.select_model user
function.
This simply adds a new option and sets up a different parameter set [Rx,
Iinf].
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r26826 | bugman | 2014-11-29 10:12:15 +0100 (Sat, 29 Nov 2014) | 5 lines
Modified the Relax_fit.test_saturation_recovery system test script.
The relax_fit.select_model user function call now selects the 'sat' model.
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r26827 | bugman | 2014-11-29 10:13:10 +0100 (Sat, 29 Nov 2014) | 3 lines
Fix for the relax_fit.select_model user function backend for the 'sat'
model.
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r26828 | bugman | 2014-11-29 10:18:50 +0100 (Sat, 29 Nov 2014) | 6 lines
The exponential model name is now being passed into the target function
class.
The model as specified by the relax_fit.select_model user function is now
finally being sent into
the target function, in this case the Relax_fit_opt class in
target_functions.relax_fit_wrapper.
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r26829 | bugman | 2014-11-29 10:23:52 +0100 (Sat, 29 Nov 2014) | 3 lines
Small fix for the relax_fit.select_model user function.
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r26830 | bugman | 2014-11-29 10:26:15 +0100 (Sat, 29 Nov 2014) | 8 lines
Renamed all of the relaxation curve-fitting target functions.
This includes all of the C functions which are model specific, by appending
'_exp' to the current
names to now be func_exp, dfunc_exp, d2func_exp, jacobian_exp, and
jacobian_chi2_exp. And all of
the Relax_fit_opt target function class *_wrapper() methods to *_exp().
The target function class
is now only aliasing the *_exp() methods when the model is set to 'exp'.
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r26831 | bugman | 2014-11-29 10:27:28 +0100 (Sat, 29 Nov 2014) | 3 lines
Alphabetical ordering of the C function imports in the
target_functions.relax_fit_wrapper module.
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r26832 | bugman | 2014-11-29 11:14:31 +0100 (Sat, 29 Nov 2014) | 3 lines
Modified the relax_fit.test_saturation_recovery system test to check for
Iinf instead of I0.
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r26833 | bugman | 2014-11-29 11:16:08 +0100 (Sat, 29 Nov 2014) | 6 lines
Added support for the saturation recovery experiment to parameter
disassembly function.
This is in the disassemble_param_vector() function of the
specific_analyses.relax_fit.parameters
module. This function requires each experiment to be handled separately.
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r26834 | bugman | 2014-11-29 11:24:15 +0100 (Sat, 29 Nov 2014) | 16 lines
Implemented the target functions for the saturation recovery exponential
curve.
In the Python target function class Relax_fit_opt, the new func_sat(),
dfunc_sat() and d2func_sat()
methods have been created as wrappers for the new C functions. These are
aliased to func(), dfunc()
and d2func() in the __init__() method.
In the target_functions/exponential.c C file, the functions
exponential_sat(),
exponential_sat_dIinf(), exponential_sat_dR(), exponential_sat_dIinf2(),
exponential_sat_dR_dIinf()
and exponential_sat_dR2() have been created to implement the function,
gradient, and Hessian for the
equation I = Iinf * (1 - exp(-R.t)).
In the target_functions/relax_fit.c file, the functions func_sat(),
dfunc_sat(), d2func_sat(),
jacobian_sat() and jacobian_chi2_sat() have been created as duplications of
the *_exp() functions,
but pointing to the exponential_sat*() functions and using Iinf instead of
I0.
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r26835 | bugman | 2014-11-29 13:29:52 +0100 (Sat, 29 Nov 2014) | 3 lines
Split the saturation recovery exponential equations and partial derivatives
into their own C file.
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r26836 | bugman | 2014-11-29 13:43:44 +0100 (Sat, 29 Nov 2014) | 3 lines
Expansion and improvements for the relax_fit.select_model user function
documentation and printouts.
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r26837 | bugman | 2014-11-29 13:46:35 +0100 (Sat, 29 Nov 2014) | 5 lines
The relax_fit.relax_time and relax_fit.select_model user functions now have
wizard graphics.
The R1 graphic from graphics/analyses/r1_200x200.png is now being used.
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r26838 | bugman | 2014-11-29 13:49:48 +0100 (Sat, 29 Nov 2014) | 7 lines
Added support for the inversion recovery experiment to parameter
disassembly function.
This matches the change of r26833 for the saturation recovery experiment.
This is in the
disassemble_param_vector() function of the
specific_analyses.relax_fit.parameters module. This
function requires each experiment to be handled separately.
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r26839 | bugman | 2014-11-29 17:02:18 +0100 (Sat, 29 Nov 2014) | 5 lines
Expanded the relax_fit_saturation_recovery.py system test script.
This now calls the error_analysis.covariance_matrix user function to test
that code path.
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r26840 | bugman | 2014-11-29 17:04:00 +0100 (Sat, 29 Nov 2014) | 6 lines
Updated the relaxation curve-fitting covariance_matrix() API method to
handle all models.
The check for the 'exp' model type has been eliminated, and the parameter
vector is assembled using
the flexible assemble_param_vector() function rather than manually
constructing the vector.
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r26841 | bugman | 2014-11-29 17:06:20 +0100 (Sat, 29 Nov 2014) | 6 lines
The errors in the Relax_fit.test_saturation_recovery system test are now
reasonable.
They have been set to 5% of Iinf so that the chi-squared value during
optimisation is more
realistic.
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r26842 | bugman | 2014-11-29 17:19:16 +0100 (Sat, 29 Nov 2014) | 6 lines
Updated the relaxation curve-fitting get_param_names() API method to handle
all models.
This now simply returns the spin container 'params' list, allowing all
models to be properly
supported.
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r26843 | bugman | 2014-11-29 17:23:53 +0100 (Sat, 29 Nov 2014) | 6 lines
Big bug fix for the error_analysis.covariance_matrix user function.
The model_info structure is now being passed into the get_param_names() API
method, as required by
the API.
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r26844 | bugman | 2014-11-29 17:25:28 +0100 (Sat, 29 Nov 2014) | 6 lines
Another change for the relaxation curve-fitting covariance_matrix() API
method to handle all models.
The scaling matrix diagonalised list of 1.0 values now has the same number
of elements as there are
parameters.
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r26845 | bugman | 2014-11-29 17:30:51 +0100 (Sat, 29 Nov 2014) | 17 lines
Implemented the target functions for the inversion recovery exponential
curve.
In the Python target function class Relax_fit_opt, the new func_inv(),
dfunc_inv() and d2func_inv()
methods have been created as wrappers for the new C functions. These are
aliased to func(), dfunc()
and d2func() in the __init__() method.
The target_functions/exponential_inv.c C file has been created with the
functions exponential_inv(),
exponential_inv_d0(), exponential_inv_dIinf(), exponential_inv_dR(),
exponential_inv_dI02(),
exponential_inv_dIinf2(), exponential_inv_dI0_dIinf(),
exponential_inv_dR_dI0(),
exponential_inv_dR_dIinf() and exponential_inv_dR2() have been created to
implement the function,
gradient, and Hessian for the equation I(t) = Iinf - I0*exp(-R.t).
In the target_functions/relax_fit.c file, the functions func_inv(),
dfunc_inv(), d2func_inv(),
jacobian_inv() and jacobian_chi2_inv() have been created as duplications of
the *_exp() functions,
but pointing to the exponential_inv*() functions and adding the Iinf
dimension.
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r26846 | bugman | 2014-11-29 17:41:53 +0100 (Sat, 29 Nov 2014) | 5 lines
More editing of the relax_fit.select_model user function.
The IR and SR abbreviations have been added, and a lot of text cleaned up.
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r26847 | bugman | 2014-11-29 17:51:35 +0100 (Sat, 29 Nov 2014) | 7 lines
Improvement for the relax_fit.select_model user function in the GUI.
Unicode text is now being used to display the parameters as R_x and I_0 and
to show an infinity
symbol in the Iinf parameter. The Rx and Iinf parameters have been added
to lib.text.gui to allow
this.
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r26848 | bugman | 2014-11-29 18:18:12 +0100 (Sat, 29 Nov 2014) | 7 lines
Expanded the relaxation curve-fitting chapter of the manual to include
descriptions of the models.
A new section at the start of this chapter has been added to explain the
different models and their
equations. This was taken from the script mode section and expanded to
include the new saturation
recovery experiment.
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r26849 | bugman | 2014-11-29 18:35:43 +0100 (Sat, 29 Nov 2014) | 5 lines
Removed the relax_fit.select_model user function call from the relax_fit
auto-analysis.
This is to allow the user in a script, or in the GUI, to choose the model
themselves.
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r26850 | bugman | 2014-11-29 18:37:07 +0100 (Sat, 29 Nov 2014) | 6 lines
Added a button to the R1 and R2 GUI analyses for executing the
relax_fit.select_model user function.
This is just after the peak list GUI element and before the optimisation
settings. It allows
different curve types to be selected for the analysis.
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r26851 | bugman | 2014-11-29 18:55:20 +0100 (Sat, 29 Nov 2014) | 7 lines
Created the new specific_analyses.relax_fit.checks module.
This creates the check_model_setup Check object, following the check_*()
function design at
http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions.
This will be used to
make sure that the exponential curve model is set prior to executing
certain user functions.
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r26852 | bugman | 2014-11-29 18:58:17 +0100 (Sat, 29 Nov 2014) | 8 lines
Improved the checking in the relaxation curve-fitting analysis.
The new specific_analyses.relax_fit.checks.check_model_setup() function is
now called prior to
minimisation and in the get_param_names() API method to prevent Python
errors from occurring due to
missing data structures. In addition, the pipe_control.mol_res_spin module
function
exists_mol_res_spin_data() has been replaced with check_mol_res_spin_data().
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r26853 | bugman | 2014-11-29 19:00:38 +0100 (Sat, 29 Nov 2014) | 6 lines
Fix for the recently broken
Relax_fit.test_curve_fitting_height_estimate_error system test.
The relax_fit.select_model user function is now called as this is no longer
performed in the
auto-analysis.
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r26854 | bugman | 2014-11-29 19:01:43 +0100 (Sat, 29 Nov 2014) | 6 lines
Removed the text that the inversion recovery experiment is not implemented
yet.
This is in the documentation for the relax_fit.select_model user function
and is in preparation for
completing this.
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r26855 | bugman | 2014-11-29 19:03:46 +0100 (Sat, 29 Nov 2014) | 3 lines
Added the checks module to the specific_analyses.relax_fit package __all__
list.
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r26856 | bugman | 2014-11-29 19:23:11 +0100 (Sat, 29 Nov 2014) | 6 lines
Fixes for the relaxation dispersion analysis for the recent relaxation
curve-fitting analysis changes.
The Relax_fit_opt target function class requires the model argument to be
supplied to be correctly
set up.
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r26857 | bugman | 2014-11-29 19:40:35 +0100 (Sat, 29 Nov 2014) | 5 lines
Fixes for the unit tests of the target_functions.relax_fit C module.
This is for the recent renaming of all the C functions based on the model
type.
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r26858 | bugman | 2014-11-29 19:44:10 +0100 (Sat, 29 Nov 2014) | 5 lines
Fix for the Rx.test_r1_analysis GUI test.
A click on the relax_fit.select_model user function button is now being
simulated.
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r26859 | bugman | 2014-11-30 00:21:07 +0100 (Sun, 30 Nov 2014) | 3 lines
Created a directory for holding synthetic inversion recovery R1 data.
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r26860 | bugman | 2014-11-30 00:27:28 +0100 (Sun, 30 Nov 2014) | 14 lines
Copied synthetic inversion recovery Sparky peak lists from
S?\195?\169bastien Morin's inversion-recovery branch.
The commands used were:
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1100_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1500_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1950_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_1950_ms_bis.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_200_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_2450_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_450_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_750_ms.list
.
svn cp
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery/test_suite/shared_data/curve_fitting/T1_inv-recov_750_ms_bis.list
.
........
r26861 | bugman | 2014-11-30 00:30:52 +0100 (Sun, 30 Nov 2014) | 17 lines
Ported r13116 of S?\195?\169bastien Morin's inversion-recovery branch.
The command used was:
svn merge -r13115:r13116
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery .
.....
r13116 | semor | 2011-06-17 18:18:43 +0200 (Fri, 17 Jun 2011) | 5 lines
Changed paths:
A
/branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
(from
/branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_2param_neg.py:13114)
Created a system test script for the inversion-recovery function.
This is based on a copy of the script 'relax_fit_exp_2param_neg.py'.
.....
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r26862 | bugman | 2014-11-30 00:33:03 +0100 (Sun, 30 Nov 2014) | 15 lines
Ported r13133 of S?\195?\169bastien Morin's inversion-recovery branch.
The command used was:
svn up; svn merge -r13132:r13133
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery .
.....
r13133 | semor | 2011-06-20 19:05:09 +0200 (Mon, 20 Jun 2011) | 4 lines
Changed paths:
M
/branches/inversion-recovery/test_suite/system_tests/scripts/relax_fit_exp_3param_inv_neg.py
The 3-parameter curve fitting test script now uses the corresponding peak
lists.
.....
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r26863 | bugman | 2014-11-30 00:35:40 +0100 (Sun, 30 Nov 2014) | 14 lines
Ported r14430 of S?\195?\169bastien Morin's inversion-recovery branch.
The command used was:
svn merge -r14429:r14430
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/inversion-recovery .
.....
[... 281 lines stripped ...]
r26944 - in /branches/nmrglue: ./ auto_analyses/ devel_scripts/ docs/ docs/latex/ gui/analyses/ lib/ lib/structure/internal/...