r21924 - /trunk/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Dec 10 09:51:04 2013
New Revision: 21924

URL: http://svn.gna.org/viewcvs/relax?rev=21924view=rev
Log:
Fix for wrong use of relax_fit.relax_time instead of relax_disp.relax_time.

Work in progress for Support Request #3044, 
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.

Modified:
trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21924r1=21923r2=21924view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 10 09:51:04 2013
@@ -2570,7 +2570,7 @@
 
self.interpreter.relax_disp.spin_lock_offset(spectrum_id=sp_id, 
offset=omega_rf_ppm)
 
 # Set the relaxation times (in s).
-self.interpreter.relax_fit.relax_time(time=time_sl, 
spectrum_id=sp_id)
+self.interpreter.relax_disp.relax_time(spectrum_id=sp_id, 
time=time_sl)
 
 # Set the spectrometer frequency.
 self.interpreter.spectrometer.frequency(id=sp_id, 
frq=set_sfrq, units='MHz')


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r21925 - /trunk/lib/dispersion/__init__.py

[edward]

Author: bugman
Date: Tue Dec 10 10:14:40 2013
New Revision: 21925

URL: http://svn.gna.org/viewcvs/relax?rev=21925view=rev
Log:
Added the ns_r1rho_3site module to the lib.dispersion package __all__ list.

This allows the unit tests to pass.


Modified:
trunk/lib/dispersion/__init__.py

Modified: trunk/lib/dispersion/__init__.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/__init__.py?rev=21925r1=21924r2=21925view=diff
==
--- trunk/lib/dispersion/__init__.py (original)
+++ trunk/lib/dispersion/__init__.py Tue Dec 10 10:14:40 2013
@@ -39,6 +39,7 @@
 'ns_mmq_2site',
 'ns_mmq_3site',
 'ns_r1rho_2site',
+'ns_r1rho_3site',
 'tap03',
 'tp02',
 'tsmfk01',


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r21926 - /trunk/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Dec 10 10:36:23 2013
New Revision: 21926

URL: http://svn.gna.org/viewcvs/relax?rev=21926view=rev
Log:
System test turned off until release is over.

Work in progress for Support Request #3044, 
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.

Modified:
trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21926r1=21925r2=21926view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 10 10:36:23 2013
@@ -2588,7 +2588,7 @@
 MODSEL = 'AIC'
 
 # Run the analysis.
-relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, 
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, 
modsel=MODSEL)
+#relax_disp.Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle, 
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, 
modsel=MODSEL)
 
 
 def test_r2eff_read(self):


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r21927 - /trunk/test_suite/gui_tests/relax_disp.py

[edward]

Author: bugman
Date: Tue Dec 10 11:17:10 2013
New Revision: 21927

URL: http://svn.gna.org/viewcvs/relax?rev=21927view=rev
Log:
Fix for the Relax_disp.test_bug_21076_multi_col_peak_list GUI test.

The peak intensity wizard is now closed at the end of the test so that 
subsequent tests can cleanly
operate.  Without closing this wizard, launching it a second time in another 
test will always fail.


Modified:
trunk/test_suite/gui_tests/relax_disp.py

Modified: trunk/test_suite/gui_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21927r1=21926r2=21927view=diff
==
--- trunk/test_suite/gui_tests/relax_disp.py (original)
+++ trunk/test_suite/gui_tests/relax_disp.py Tue Dec 10 11:17:10 2013
@@ -201,6 +201,9 @@
 
 # Now check that the first is set to 'Z_A0', since the keyword 'auto' 
was used for spectrum_id.
 self.assertEqual(cur_id, 'Z_A0')
+
+# Finally close the wizard to allow subsequent tests to be able to 
operate cleanly.
+wizard.Close()
 
 
 def test_hansen_trunc_data(self):


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r21928 - /trunk/lib/io.py

[edward]

Author: bugman
Date: Tue Dec 10 11:28:19 2013
New Revision: 21928

URL: http://svn.gna.org/viewcvs/relax?rev=21928view=rev
Log:
Capitalised 'Python' in the IO redirection messages.


Modified:
trunk/lib/io.py

Modified: trunk/lib/io.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/io.py?rev=21928r1=21927r2=21928view=diff
==
--- trunk/lib/io.py (original)
+++ trunk/lib/io.py Tue Dec 10 11:28:19 2013
@@ -243,9 +243,9 @@
 
 # Print out.
 if verbosity:
-print(Redirecting the sys.stdin IO stream to the python stdin IO 
stream.)
+print(Redirecting the sys.stdin IO stream to the Python stdin IO 
stream.)
 print(Redirecting the sys.stdout IO stream to the log file '%s'. % 
file_path)
-print(Redirecting the sys.stderr IO stream to both the python stderr 
IO stream and the log file '%s'. % file_path)
+print(Redirecting the sys.stderr IO stream to both the Python stderr 
IO stream and the log file '%s'. % file_path)
 
 # Set the logging IO streams.
 log_stdout = log_file
@@ -282,9 +282,9 @@
 
 # Print out.
 if verbosity:
-print(Redirecting the sys.stdin IO stream to the python stdin IO 
stream.)
-print(Redirecting the sys.stdout IO stream to both the python stdout 
IO stream and the log file '%s'. % file_path)
-print(Redirecting the sys.stderr IO stream to both the python stderr 
IO stream and the log file '%s'. % file_path)
+print(Redirecting the sys.stdin IO stream to the Python stdin IO 
stream.)
+print(Redirecting the sys.stdout IO stream to both the Python stdout 
IO stream and the log file '%s'. % file_path)
+print(Redirecting the sys.stderr IO stream to both the Python stderr 
IO stream and the log file '%s'. % file_path)
 
 # Set the tee IO streams.
 tee_stdout.split(stdout, tee_file)


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r21929 - /trunk/lib/dispersion/ns_mmq_3site.py

[edward]

Author: bugman
Date: Tue Dec 10 11:42:14 2013
New Revision: 21929

URL: http://svn.gna.org/viewcvs/relax?rev=21929view=rev
Log:
Epydoc docstring fix for the 
lib.dispersion.ns_mmq_3site.r2eff_ns_mmq_3site_sq_dq_zq() function.

This allows the API to be compiled correctly.


Modified:
trunk/lib/dispersion/ns_mmq_3site.py

Modified: trunk/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_3site.py?rev=21929r1=21928r2=21929view=diff
==
--- trunk/lib/dispersion/ns_mmq_3site.py (original)
+++ trunk/lib/dispersion/ns_mmq_3site.py Tue Dec 10 11:42:14 2013
@@ -270,11 +270,11 @@
 @keyword dw_AB: The combined chemical exchange difference between 
states A and B in rad/s.  It should be set to dwH for 1H SQ data, dw for 
heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
 @type dw_AB:float
 @keyword dw_AC: The combined chemical exchange difference between 
states A and C in rad/s.  It should be set to dwH for 1H SQ data, dw for 
heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
-@type dw_AB:float
+@type dw_AC:float
 @keyword dwH_AB:Unused - this is simply to match the 
r2eff_mmq_3site_mq() function arguments.
+@type dwH_AB:   float
+@keyword dwH_AC:Unused - this is simply to match the 
r2eff_mmq_3site_mq() function arguments.
 @type dwH_AC:   float
-@keyword dwH_AC:Unused - this is simply to match the 
r2eff_mmq_3site_mq() function arguments.
-@type dwH_AB:   float
 @keyword k_AB:  The rate of exchange from site A to B (rad/s).
 @type k_AB: float
 @keyword k_BA:  The rate of exchange from site B to A (rad/s).


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r21930 - /trunk/specific_analyses/relax_disp/optimisation.py

[edward]

Author: bugman
Date: Tue Dec 10 11:58:55 2013
New Revision: 21930

URL: http://svn.gna.org/viewcvs/relax?rev=21930view=rev
Log:
Bug fix for the dispersion grid_search_setup() optimisation function.

This function was not updated for the recent addition of the spin-lock or hard 
pulse offset
dimension in the specific_analyses.relax_disp.disp_data module (and hence all 
structures used by the
dispersion target functions).  The loop_exp_frq_point() function call has been 
replaced by a
loop_exp_frq_offset_point() function call to allow the 'R2eff' model parameters 
to be looped over.

For more details, see the thread 
http://thread.gmane.org/gmane.science.nmr.relax.scm/19685.  This
solution was mentioned at 
http://thread.gmane.org/gmane.science.nmr.relax.scm/19685/focus=4859.


Modified:
trunk/specific_analyses/relax_disp/optimisation.py

Modified: trunk/specific_analyses/relax_disp/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=21930r1=21929r2=21930view=diff
==
--- trunk/specific_analyses/relax_disp/optimisation.py (original)
+++ trunk/specific_analyses/relax_disp/optimisation.py Tue Dec 10 11:58:55 2013
@@ -35,7 +35,7 @@
 from lib.errors import RelaxError
 from lib.text.sectioning import subsection
 from multi import Memo, Result_command, Slave_command
-from specific_analyses.relax_disp.disp_data import has_disp_data, 
has_proton_mmq_cpmg, loop_exp, loop_exp_frq, loop_exp_frq_point, loop_frq, 
loop_offset, pack_back_calc_r2eff, return_cpmg_frqs, 
return_index_from_disp_point, return_index_from_exp_type, 
return_index_from_frq, return_offset_data, return_param_key_from_data, 
return_r1_data, return_r2eff_arrays, return_spin_lock_nu1, 
return_value_from_frq_index
+from specific_analyses.relax_disp.disp_data import has_disp_data, 
has_proton_mmq_cpmg, loop_exp, loop_exp_frq, loop_exp_frq_offset_point, 
loop_frq, loop_offset, pack_back_calc_r2eff, return_cpmg_frqs, 
return_index_from_disp_point, return_index_from_exp_type, 
return_index_from_frq, return_offset_data, return_param_key_from_data, 
return_r1_data, return_r2eff_arrays, return_spin_lock_nu1, 
return_value_from_frq_index
 from specific_analyses.relax_disp.parameters import assemble_param_vector, 
assemble_scaling_matrix, disassemble_param_vector, linear_constraints, 
loop_parameters, param_conversion, param_num
 from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ, 
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_LIST_CPMG, MODEL_CR72, MODEL_CR72_FULL, 
MODEL_DPL94, MODEL_LIST_MMQ, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_TAP03, MODEL_TP02
 from target_functions.relax_disp import Dispersion
@@ -179,8 +179,9 @@
 
 # The R2eff model.
 if cdp.model_type == 'R2eff':
-# Loop over each spectrometer frequency and dispersion point.
-for exp_type, frq, point in loop_exp_frq_point():
+# Loop over each experiment type, spectrometer frequency, offset 
and dispersion point.
+for exp_type, frq, offset, point in loop_exp_frq_offset_point():
+print exp_type, frq, point
 # Loop over the parameters.
 for param_name, param_index, si, r20_key in 
loop_parameters(spins=spins):
 # R2eff relaxation rate (from 1 to 40 s^-1).
@@ -278,6 +279,9 @@
 # Diagonal scaling of minimisation options.
 lower_new = []
 upper_new = []
+print lower
+print upper
+print scaling_matrix
 for i in range(n):
 lower_new.append(lower[i] / scaling_matrix[i, i])
 upper_new.append(upper[i] / scaling_matrix[i, i])


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r21931 - /trunk/specific_analyses/relax_disp/optimisation.py

[edward]

Author: bugman
Date: Tue Dec 10 12:05:45 2013
New Revision: 21931

URL: http://svn.gna.org/viewcvs/relax?rev=21931view=rev
Log:
Removed some debugging printouts accidentally committed in the last commit 
(r21930).


Modified:
trunk/specific_analyses/relax_disp/optimisation.py

Modified: trunk/specific_analyses/relax_disp/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=21931r1=21930r2=21931view=diff
==
--- trunk/specific_analyses/relax_disp/optimisation.py (original)
+++ trunk/specific_analyses/relax_disp/optimisation.py Tue Dec 10 12:05:45 2013
@@ -181,7 +181,6 @@
 if cdp.model_type == 'R2eff':
 # Loop over each experiment type, spectrometer frequency, offset 
and dispersion point.
 for exp_type, frq, offset, point in loop_exp_frq_offset_point():
-print exp_type, frq, point
 # Loop over the parameters.
 for param_name, param_index, si, r20_key in 
loop_parameters(spins=spins):
 # R2eff relaxation rate (from 1 to 40 s^-1).
@@ -279,9 +278,6 @@
 # Diagonal scaling of minimisation options.
 lower_new = []
 upper_new = []
-print lower
-print upper
-print scaling_matrix
 for i in range(n):
 lower_new.append(lower[i] / scaling_matrix[i, i])
 upper_new.append(upper[i] / scaling_matrix[i, i])


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r21932 - /trunk/test_suite/system_tests/relax_disp.py

[edward]

Author: bugman
Date: Tue Dec 10 12:13:22 2013
New Revision: 21932

URL: http://svn.gna.org/viewcvs/relax?rev=21932view=rev
Log:
Removed a printout from the Relax_disp.test_r1rho_kjaergaard GUI test as this 
is fatal for Python 3.


Modified:
trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21932r1=21931r2=21932view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 10 12:13:22 2013
@@ -2514,7 +2514,6 @@
 
 i = 0
 for spin, spin_id in spin_loop(return_id=True):
-print spin.name, spin.num, spin_id, spin.chemical_shift, cs[i]
 # Check the chemical shift.
 self.assertEqual(spin.chemical_shift, cs[i])
 


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r21933 - /trunk/specific_analyses/relax_disp/disp_data.py

[edward]

Author: bugman
Date: Tue Dec 10 12:27:52 2013
New Revision: 21933

URL: http://svn.gna.org/viewcvs/relax?rev=21933view=rev
Log:
Python 3 fixes for the relax_disp.r2eff_read_spin user function.

The check for the dispersion point column now only runs if that argument is 
set.  In addition, the
offset column is now also being checked.


Modified:
trunk/specific_analyses/relax_disp/disp_data.py

Modified: trunk/specific_analyses/relax_disp/disp_data.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21933r1=21932r2=21933view=diff
==
--- trunk/specific_analyses/relax_disp/disp_data.py (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py Tue Dec 10 12:27:52 2013
@@ -2076,8 +2076,11 @@
 new_ids = []
 for line in file_data:
 # Invalid columns.
-if disp_point_col  len(line):
+if disp_point_col != None and disp_point_col  len(line):
 warn(RelaxWarning(The data %s is invalid, no dispersion point 
column can be found. % line))
+continue
+if offset_col != None and offset_col  len(line):
+warn(RelaxWarning(The data %s is invalid, no offset column can be 
found. % line))
 continue
 if data_col  len(line):
 warn(RelaxWarning(The R2eff/R1rho data %s is invalid, no data 
column can be found. % line))


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r21934 - /tags/3.1.1/

[edward]

Author: bugman
Date: Tue Dec 10 14:05:58 2013
New Revision: 21934

URL: http://svn.gna.org/viewcvs/relax?rev=21934view=rev
Log:
relax version 3.1.1.

This is a minor feature release which adds support the 'NS MMQ 3-site linear', 
'NS MMQ 3-site',
'NS R1rho 3-site linear', and 'NS R1rho 3-site' relaxation dispersion models.  
There is also
improved support for R1rho data sets where multiple offsets and multiple 
spin-lock fields have been
collected for each spin.


Added:
tags/3.1.1/
  - copied from r21933, trunk/


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r21935 - /tags/3.1.1/docs/CHANGES

[edward]

Author: bugman
Date: Tue Dec 10 15:02:27 2013
New Revision: 21935

URL: http://svn.gna.org/viewcvs/relax?rev=21935view=rev
Log:
Updated the CHANGES file for relax version 3.1.1.


Modified:
tags/3.1.1/docs/CHANGES

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: tags/3.1.1/docs/CHANGES
URL: 
http://svn.gna.org/viewcvs/relax/tags/3.1.1/docs/CHANGES?rev=21935r1=21934r2=21935view=diff


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r21937 - /tags/3.1.1/version.py

[edward]

Author: bugman
Date: Tue Dec 10 15:03:53 2013
New Revision: 21937

URL: http://svn.gna.org/viewcvs/relax?rev=21937view=rev
Log:
Updated the version number to relax 3.1.1.


Modified:
tags/3.1.1/version.py

Modified: tags/3.1.1/version.py
URL: 
http://svn.gna.org/viewcvs/relax/tags/3.1.1/version.py?rev=21937r1=21936r2=21937view=diff
==
--- tags/3.1.1/version.py (original)
+++ tags/3.1.1/version.py Tue Dec 10 15:03:53 2013
@@ -35,7 +35,7 @@
 from status import Status; status = Status()
 
 
-version = repository checkout
+version = 3.1.1
 
 
 def revision():


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r21936 - /trunk/docs/CHANGES

[edward]

Author: bugman
Date: Tue Dec 10 15:03:31 2013
New Revision: 21936

URL: http://svn.gna.org/viewcvs/relax?rev=21936view=rev
Log:
Backported the relax 3.1.1 CHANGES file addition to trunk.

The command used was:
svn merge -r21934:21935 svn+ssh://bug...@svn.gna.org/svn/relax/tags/3.1.1 .


Modified:
trunk/docs/CHANGES

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: trunk/docs/CHANGES
URL: 
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=21936r1=21935r2=21936view=diff


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r21938 - /tags/3.1.1/docs/relax.pdf

[edward]

Author: bugman
Date: Tue Dec 10 15:18:00 2013
New Revision: 21938

URL: http://svn.gna.org/viewcvs/relax?rev=21938view=rev
Log:
Added the relax 3.1.1 manual to the repository.


Added:
tags/3.1.1/docs/relax.pdf   (with props)

Added: tags/3.1.1/docs/relax.pdf
URL: 
http://svn.gna.org/viewcvs/relax/tags/3.1.1/docs/relax.pdf?rev=21938view=auto
==
Binary file - no diff available.

Propchange: tags/3.1.1/docs/relax.pdf
--
svn:mime-type = application/octet-stream


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r21939 - /website/download.html

[edward]

Author: bugman
Date: Tue Dec 10 16:19:25 2013
New Revision: 21939

URL: http://svn.gna.org/viewcvs/relax?rev=21939view=rev
Log:
Updated the http://www.nmr-relax.com/download.html webpage for relax version 
3.1.1.


Modified:
website/download.html

Modified: website/download.html
URL: 
http://svn.gna.org/viewcvs/relax/website/download.html?rev=21939r1=21938r2=21939view=diff
==
--- website/download.html (original)
+++ website/download.html Tue Dec 10 16:19:25 2013
@@ -58,7 +58,7 @@
   div id=Current_release class=main_box
 h1Current release/h1
 
-pThe current stable release is a 
href=http://gna.org/forum/forum.php?forum_id=2407;relax version 3.1.0/a 
em(28 November 2013)/em./p
+pThe current stable release is a 
href=http://gna.org/forum/forum.php?forum_id=2407;relax version 3.1.1/a 
em(10 December 2013)/em./p
 
   prelax binaries have been pre-compiled for a number of computer 
architectures.  These are based on Python 2.7 but usually work with other 
Python versions.  If not, or if binaries for your system do not exist, please 
download the source release (note that the compilation of binary modules is not 
a prerequisite for using relax).  If the binary distribution file for your 
architecture does not correspond to the most up to date version of relax, 
please download the up-to-date source release instead.  If you would like to 
contribute binary packages for your specific architecture, please read the a 
href=http://www.nmr-relax.com/manual/Open_source_infrastructure.html;Open 
source infrastructure/a chapter of the relax manual for details./p
 
@@ -94,16 +94,16 @@
   tdstrongFile size (bytes)/strong/td
 /tr
 tr
-  tda 
href=http://download.gna.org/relax/relax-3.1.0.GNU-Linux.i686.tar.bz2; 
title=relaxrelax-3.1.0.GNU-Linux.i686.tar.bz2/a/td
-  tdttsmall51fa13f96b0dc7daf2bfd4235cca9b27/small/tt/td
-  tda 
href=http://download.gna.org/relax/relax-3.1.0.GNU-Linux.i686.tar.bz2.sig; 
title=relax GPG signaturesignature/a/td
-  td66020302/td
-/tr
-tr
-  tda 
href=http://download.gna.org/relax/relax-3.1.0.GNU-Linux.x86_64.tar.bz2; 
title=relaxrelax-3.1.0.GNU-Linux.x86_64.tar.bz2/a/td
-  tdttsmall7d64a6398931b1450b459b1478e4da32/small/tt/td
-  tda 
href=http://download.gna.org/relax/relax-3.1.0.GNU-Linux.x86_64.tar.bz2.sig; 
title=relax GPG signaturesignature/a/td
-  td66043590/td
+  tda 
href=http://download.gna.org/relax/relax-3.1.1.GNU-Linux.i686.tar.bz2; 
title=relaxrelax-3.1.1.GNU-Linux.i686.tar.bz2/a/td
+  tdttsmall03ea6f26ff9f46eebf6bf24e6f21b8aa/small/tt/td
+  tda 
href=http://download.gna.org/relax/relax-3.1.1.GNU-Linux.i686.tar.bz2.sig; 
title=relax GPG signaturesignature/a/td
+  td70854311/td
+/tr
+tr
+  tda 
href=http://download.gna.org/relax/relax-3.1.1.GNU-Linux.x86_64.tar.bz2; 
title=relaxrelax-3.1.1.GNU-Linux.x86_64.tar.bz2/a/td
+  tdttsmallfcdbdebc9431d604b79f1ed9c9d6b6d7/small/tt/td
+  tda 
href=http://download.gna.org/relax/relax-3.1.1.GNU-Linux.x86_64.tar.bz2.sig; 
title=relax GPG signaturesignature/a/td
+  td70825355/td
 /tr
   /tbody
 /table
@@ -137,10 +137,10 @@
   tdstrongFile size (bytes)/strong/td
 /tr
 tr
-  tda href=http://download.gna.org/relax/relax-3.1.0.Win32.zip; 
title=relaxrelax-3.1.0.Win32.zip/a/td
-  tdttsmall9c37a64a573bc0a88dda018a11347114/small/tt/td
-  tda href=http://download.gna.org/relax/relax-3.1.0.Win32.zip.sig; 
title=relax GPG signaturesignature/a/td
-  td70009574/td
+  tda href=http://download.gna.org/relax/relax-3.1.1.Win32.zip; 
title=relaxrelax-3.1.1.Win32.zip/a/td
+  tdttsmallc3b93840622cb8bf04406b683700efa2/small/tt/td
+  tda href=http://download.gna.org/relax/relax-3.1.1.Win32.zip.sig; 
title=relax GPG signaturesignature/a/td
+  td75349925/td
 /tr
   /tbody
 /table
@@ -180,10 +180,10 @@
   tdstrongFile size (bytes)/strong/td
 /tr
 tr
-  tda href=http://download.gna.org/relax/relax-3.1.0.Darwin.dmg; 
title=relaxrelax-3.1.0.Darwin.dmg/a/td
-  tdttsmall7a2c04b706e1063cb0fcef35a401fb62/small/tt/td
-  tda href=http://download.gna.org/relax/relax-3.1.0.Darwin.dmg.sig; 
title=relax GPG signaturesignature/a/td
-  td226598942/td
+  tda href=http://download.gna.org/relax/relax-3.1.1.Darwin.dmg; 
title=relaxrelax-3.1.1.Darwin.dmg/a/td
+  tdttsmallffa6f1512603805a0e57736f18417d98/small/tt/td
+  tda href=http://download.gna.org/relax/relax-3.1.1.Darwin.dmg.sig; 
title=relax GPG signaturesignature/a/td
+  td232104986/td
 /tr
   /tbody
 /table
@@ -235,16 +235,16 @@
   tdstrongFile size (bytes)/strong/td
 /tr
 tr
-  tda href=http://download.gna.org/relax/relax-3.1.0.src.tar.bz2; 
title=relaxrelax-3.1.0.src.tar.bz2/a/td
-  tdttsmallc737a5aa56641a7af5e9e79360a3e454/small/tt/td
-  tda href=http://download.gna.org/relax/relax-3.1.0.src.tar.bz2.sig; 
title=relax GPG 

r21940 - /website/manual/

[edward]

Author: bugman
Date: Tue Dec 10 16:31:33 2013
New Revision: 21940

URL: http://svn.gna.org/viewcvs/relax?rev=21940view=rev
Log:
Updated the HTML version of the relax manual to version 3.1.1.

This is for http://www.nmr-relax.com/manual/index.html.


Added:
website/manual/MMQ_CR72_model.html
website/manual/NS_3_site_R1_model.html
website/manual/NS_3_site_linear_R1_model.html
website/manual/NS_MMQ_2_site_model.html
website/manual/NS_MMQ_3_site_linear_model.html
website/manual/NS_MMQ_3_site_model.html
website/manual/img513.png   (with props)
website/manual/img514.png   (with props)
website/manual/img515.png   (with props)
website/manual/img516.png   (with props)
website/manual/img517.png   (with props)
website/manual/img518.png   (with props)
website/manual/img519.png   (with props)
website/manual/img520.png   (with props)
website/manual/img521.png   (with props)
website/manual/img522.png   (with props)
website/manual/img523.png   (with props)
website/manual/img524.png   (with props)
website/manual/img525.png   (with props)
website/manual/img526.png   (with props)
website/manual/img527.png   (with props)
website/manual/img528.png   (with props)
website/manual/img529.png   (with props)
website/manual/img530.png   (with props)
website/manual/img531.png   (with props)
website/manual/img532.png   (with props)
website/manual/img533.png   (with props)
website/manual/img534.png   (with props)
website/manual/img535.png   (with props)
website/manual/img536.png   (with props)
website/manual/img537.png   (with props)
website/manual/img538.png   (with props)
website/manual/img539.png   (with props)
website/manual/img540.png   (with props)
website/manual/img541.png   (with props)
website/manual/img542.png   (with props)
website/manual/img543.png   (with props)
website/manual/img544.png   (with props)
website/manual/img545.png   (with props)
website/manual/img546.png   (with props)
website/manual/img547.png   (with props)
website/manual/img548.png   (with props)
website/manual/spectrum_read_spins.html
website/manual/structure_read_gaussian.html
Removed:
website/manual/MMQ_2_site_model.html
website/manual/MQ_CR72_model.html
Modified:
website/manual/Abbreviations.html
website/manual/About_this_document.html
website/manual/Access_internals_relax.html
website/manual/Advanced_topics.html
website/manual/All_model_free_models_script_mode_explanation.html
website/manual/All_model_free_models_script_mode_sample_script.html
website/manual/Alphabetical_listing_user_functions.html
website/manual/Analysing_dispersion_in_prompt_script_UI_mode.html
website/manual/Assigning_issue_yourself.html
website/manual/Becoming_committer.html
website/manual/Bibliography.html
website/manual/Branch_creation.html
website/manual/Branches.html
website/manual/Brownian_rotational_diffusion.html
website/manual/C_module_compilation.html
website/manual/Calculating_NOE.html
website/manual/Calculation_NOE_in_prompt_script_UI_mode.html
website/manual/Cleaning_up.html
website/manual/Closing_issue.html
website/manual/Coding_conventions.html
website/manual/Comments.html
website/manual/Committers.html
website/manual/Comparison_dispersion_analysis_software.html
website/manual/Compilation_API_documentation_HTML_version.html
website/manual/Compilation_user_manual_HTML_version.html
website/manual/Compilation_user_manual_PDF_version.html
website/manual/Components_Ri_prime_theta_equations.html
website/manual/Conjugate_gradient_methods.html
website/manual/Consistency_testing.html
website/manual/Consistency_testing_analysis_references.html
website/manual/Consistency_testing_in_prompt_script_UI_mode.html

website/manual/Consistency_testing_script_mode_calculation_error_propagation.html
website/manual/Consistency_testing_script_mode_data_pipe_spin.html
website/manual/Consistency_testing_script_mode_relaxation_data_loading.html
website/manual/Consistency_testing_script_mode_relaxation_interactions.html
website/manual/Consistency_testing_script_mode_sample_script.html

website/manual/Consistency_testing_script_mode_visualisation_data_output.html
website/manual/Constraint_algorithms.html
website/manual/Construction_Hessian.html
website/manual/Construction_gradient.html
website/manual/Construction_values_gradients_Hessians.html
website/manual/Contents.html
website/manual/Copying_modification_sublicencing_distribution_relax.html
website/manual/DPL94_2_site_fast_exchange_R1_model.html
website/manual/Dasha.html
website/manual/Data_analysis_tools.html
website/manual/Data_visualisation.html
website/manual/Defaults.html
website/manual/Dependencies.html
website/manual/Diagonal_scaling.html

r21941 - /website/api/index.html

[edward]

Author: bugman
Date: Tue Dec 10 16:34:04 2013
New Revision: 21941

URL: http://svn.gna.org/viewcvs/relax?rev=21941view=rev
Log:
Updated the version number to 3.1.1 on the webpage 
http://www.nmr-relax.com/api/.


Modified:
website/api/index.html

Modified: website/api/index.html
URL: 
http://svn.gna.org/viewcvs/relax/website/api/index.html?rev=21941r1=21940r2=21941view=diff
==
--- website/api/index.html (original)
+++ website/api/index.html Tue Dec 10 16:34:04 2013
@@ -30,7 +30,7 @@
 
pThe most recent version of the documentation is:/p
 ul
- lia href=http://www.nmr-relax.com/api/3.1/;relax 3.1.0 API 
documentation/a/li
+ lia href=http://www.nmr-relax.com/api/3.1/;relax 3.1.1 API 
documentation/a/li
 /ul
 
h2The relax library/h2
@@ -42,7 +42,7 @@
 pThe automatically generated API documentation is also available for 
earlier relax versions:/p
 
 ul
- lia href=http://www.nmr-relax.com/api/3.1/;relax 3.1.0 API 
documentation/a/li
+ lia href=http://www.nmr-relax.com/api/3.1/;relax 3.1.1 API 
documentation/a/li
  lia href=http://www.nmr-relax.com/api/3.0/;relax 3.0.2 API 
documentation/a/li
  lia href=http://www.nmr-relax.com/api/2.2/;relax 2.2.5 API 
documentation/a/li
  lia href=http://www.nmr-relax.com/api/2.1/;relax 2.1.2 API 
documentation/a/li


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r21942 - /website/api/3.1/

[edward]

Author: bugman
Date: Tue Dec 10 16:42:19 2013
New Revision: 21942

URL: http://svn.gna.org/viewcvs/relax?rev=21942view=rev
Log:
Updated the relax API documentation at http://www.nmr-relax.com/api/3.1/ to 
version 3.1.1.


Added:
website/api/3.1/lib.dispersion.mmq_cr72-module.html
website/api/3.1/lib.dispersion.mmq_cr72-pysrc.html
website/api/3.1/lib.dispersion.ns_mmq_2site-module.html
website/api/3.1/lib.dispersion.ns_mmq_2site-pysrc.html
website/api/3.1/lib.dispersion.ns_mmq_3site-module.html
website/api/3.1/lib.dispersion.ns_mmq_3site-pysrc.html
website/api/3.1/lib.dispersion.ns_r1rho_3site-module.html
website/api/3.1/lib.dispersion.ns_r1rho_3site-pysrc.html
website/api/3.1/lib.nmr-module.html
website/api/3.1/lib.nmr-pysrc.html
website/api/3.1/lib.periodic_table-module.html
website/api/3.1/lib.periodic_table-pysrc.html
website/api/3.1/lib.periodic_table.Table-class.html
website/api/3.1/toc-lib.dispersion.mmq_cr72-module.html
website/api/3.1/toc-lib.dispersion.ns_mmq_2site-module.html
website/api/3.1/toc-lib.dispersion.ns_mmq_3site-module.html
website/api/3.1/toc-lib.dispersion.ns_r1rho_3site-module.html
website/api/3.1/toc-lib.nmr-module.html
website/api/3.1/toc-lib.periodic_table-module.html
Removed:
website/api/3.1/lib.dispersion.mmq_2site-module.html
website/api/3.1/lib.dispersion.mmq_2site-pysrc.html
website/api/3.1/lib.dispersion.mq_cr72-module.html
website/api/3.1/lib.dispersion.mq_cr72-pysrc.html
website/api/3.1/toc-lib.dispersion.mmq_2site-module.html
website/api/3.1/toc-lib.dispersion.mq_cr72-module.html
Modified:
website/api/3.1/abc.ABCMeta-class.html
website/api/3.1/api-objects.txt
website/api/3.1/auto_analyses-module.html
website/api/3.1/auto_analyses-pysrc.html
website/api/3.1/auto_analyses.dauvergne_protocol-module.html
website/api/3.1/auto_analyses.dauvergne_protocol-pysrc.html
website/api/3.1/auto_analyses.dauvergne_protocol.Container-class.html

website/api/3.1/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html
website/api/3.1/auto_analyses.frame_order-module.html
website/api/3.1/auto_analyses.frame_order-pysrc.html
website/api/3.1/auto_analyses.frame_order.Frame_order_analysis-class.html
website/api/3.1/auto_analyses.noe-module.html
website/api/3.1/auto_analyses.noe-pysrc.html
website/api/3.1/auto_analyses.noe.NOE_calc-class.html
website/api/3.1/auto_analyses.relax_disp-module.html
website/api/3.1/auto_analyses.relax_disp-pysrc.html
website/api/3.1/auto_analyses.relax_disp.Relax_disp-class.html
website/api/3.1/auto_analyses.relax_fit-module.html
website/api/3.1/auto_analyses.relax_fit-pysrc.html
website/api/3.1/auto_analyses.relax_fit.Relax_fit-class.html
website/api/3.1/auto_analyses.stereochem_analysis-module.html
website/api/3.1/auto_analyses.stereochem_analysis-pysrc.html

website/api/3.1/auto_analyses.stereochem_analysis.Stereochem_analysis-class.html
website/api/3.1/bmrblib-module.html
website/api/3.1/bmrblib-pysrc.html
website/api/3.1/bmrblib.NMR_parameters-module.html
website/api/3.1/bmrblib.NMR_parameters-pysrc.html
website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy-module.html
website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy-pysrc.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropy-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropyExperiment-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropySoftware-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropy-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropySaveframe-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-module.html
website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-pysrc.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropyExperiment_v3_1-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropySoftware_v3_1-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropy_v3_1-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropySaveframe_v3_1-class.html

website/api/3.1/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropy_v3_1-class.html
website/api/3.1/bmrblib.assembly_supercategory-module.html
website/api/3.1/bmrblib.assembly_supercategory-pysrc.html
website/api/3.1/bmrblib.assembly_supercategory.entity-module.html
website/api/3.1/bmrblib.assembly_supercategory.entity-pysrc.html
website/api/3.1/bmrblib.assembly_supercategory.entity.Entity-class.html

website/api/3.1/bmrblib.assembly_supercategory.entity.EntityCompIndex-class.html

r21943 - /website/download.html

[edward]

Author: bugman
Date: Tue Dec 10 17:23:45 2013
New Revision: 21943

URL: http://svn.gna.org/viewcvs/relax?rev=21943view=rev
Log:
Updated the news announcement link for relax version 3.1.1 at 
http://www.nmr-relax.com/download.html.

The correct link is https://gna.org/forum/forum.php?forum_id=2423.


Modified:
website/download.html

Modified: website/download.html
URL: 
http://svn.gna.org/viewcvs/relax/website/download.html?rev=21943r1=21942r2=21943view=diff
==
--- website/download.html (original)
+++ website/download.html Tue Dec 10 17:23:45 2013
@@ -335,7 +335,7 @@
   tdstrongFile size (bytes)/strong/td
 /tr
 
-trtdema href=http://gna.org/forum/forum.php?forum_id=2421;Version 
3.1.1/a (2013-12-10)/em/td/tr
+trtdema href=http://gna.org/forum/forum.php?forum_id=2423;Version 
3.1.1/a (2013-12-10)/em/td/tr
 tr
   tda 
href=http://download.gna.org/relax/relax-3.1.1.GNU-Linux.i686.tar.bz2; 
title=relaxrelax-3.1.1.GNU-Linux.i686.tar.bz2/a/td
   tdttsmall03ea6f26ff9f46eebf6bf24e6f21b8aa/small/tt/td


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r21944 - in /trunk/specific_analyses/relax_disp: api.py disp_data.py

[edward]

Author: bugman
Date: Tue Dec 10 20:50:56 2013
New Revision: 21944

URL: http://svn.gna.org/viewcvs/relax?rev=21944view=rev
Log:
The average_intensity() dispersion function now accepts the offset argument.

This is for better support of combined offset and spin-lock varied R1rho-type 
data.  The argument is
then passed into the find_intensity_keys() function.


Modified:
trunk/specific_analyses/relax_disp/api.py
trunk/specific_analyses/relax_disp/disp_data.py

Modified: trunk/specific_analyses/relax_disp/api.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=21944r1=21943r2=21944view=diff
==
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Tue Dec 10 20:50:56 2013
@@ -151,8 +151,8 @@
 times = []
 for time in cdp.relax_time_list:
 # The data.
-values.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, point=point, time=time))
-errors.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, point=point, time=time, error=True))
+values.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, offset=offset, point=point, time=time))
+errors.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, offset=offset, point=point, time=time, error=True))
 times.append(time)
 
 # The scaling matrix in a diagonalised list form.
@@ -218,12 +218,12 @@
 continue
 
 # Average the reference intensity data and errors.
-ref_intensity = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, point=None, time=time)
-ref_intensity_err = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, point=None, time=time, error=True)
+ref_intensity = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, offset=offset, point=None, time=time)
+ref_intensity_err = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, offset=offset, point=None, time=time, error=True)
 
 # Average the intensity data and errors.
-intensity = average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, point=point, time=time)
-intensity_err = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, point=point, time=time, error=True)
+intensity = average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, offset=offset, point=point, time=time)
+intensity_err = average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)
 
 # Calculate the R2eff value.
 spin.r2eff[param_key] = calc_two_point_r2eff(relax_time=time, 
I_ref=ref_intensity, I=intensity)
@@ -379,8 +379,8 @@
 errors = []
 times = []
 for time in cdp.relax_time_list:
-values.append(average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, point=point, time=time, sim_index=sim_index))
-errors.append(average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, point=point, time=time, error=True))
+values.append(average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, 
sim_index=sim_index))
+errors.append(average_intensity(spin=spin, 
exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True))
 times.append(time)
 
 # The scaling matrix in a diagonalised list form.
@@ -1374,7 +1374,7 @@
 # Generate the data structure to return.
 errors = []
 for time in cdp.relax_time_list:
-errors.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, point=point, time=time, error=True))
+errors.append(average_intensity(spin=spin, exp_type=exp_type, 
frq=frq, offset=offset, point=point, time=time, error=True))
 
 # All other models.
 else:

Modified: trunk/specific_analyses/relax_disp/disp_data.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21944r1=21943r2=21944view=diff
==
--- trunk/specific_analyses/relax_disp/disp_data.py (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py Tue Dec 10 20:50:56 2013
@@ -84,7 +84,7 @@
 R20_KEY_FORMAT = %s - %.8f MHz
 
 
-def average_intensity(spin=None, exp_type=None, frq=None, point=None, 
time=None, sim_index=None, error=False):
+def average_intensity(spin=None, exp_type=None, frq=None, offset=None, 
point=None, time=None, sim_index=None, error=False):
 Return the average peak intensity for the spectrometer frequency, 
dispersion point, and relaxation time.
 
 This is for 

r21945 - /trunk/docs/latex/dispersion.tex

[edward]

Author: bugman
Date: Tue Dec 10 21:40:40 2013
New Revision: 21945

URL: http://svn.gna.org/viewcvs/relax?rev=21945view=rev
Log:
Improved the DPL94 dispersion model description in the manual.


Modified:
trunk/docs/latex/dispersion.tex

Modified: trunk/docs/latex/dispersion.tex
URL: 
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21945r1=21944r2=21945view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Dec 10 21:40:40 2013
@@ -115,7 +115,7 @@
 
 \begin{description}
 \item[`M61':]\index{relaxation dispersion!M61 model}  The \citet{Meiboom61} 
2-site fast exchange equation for on-resonance data with parameters 
$\{\Ronerhoprime, \dots, \Phiex, \kex\}$.  See Section~\ref{sect: dispersion: 
M61 model} on page~\pageref{sect: dispersion: M61 model}.
-\item[`DPL94':]\index{relaxation dispersion!DPL94 model}  The \citet{Davis94} 
2-site fast exchange equation for off-resonance data with parameters 
$\{\Ronerhoprime, \dots, \Phiex, \kex\}$.  See Section~\ref{sect: dispersion: 
DPL94 model} on page~\pageref{sect: dispersion: DPL94 model}.
+\item[`DPL94':]\index{relaxation dispersion!DPL94 model}  The \citet{Davis94} 
extension of the `M61' model for off-resonance data with parameters 
$\{\Ronerhoprime, \dots, \Phiex, \kex\}$.  See Section~\ref{sect: dispersion: 
DPL94 model} on page~\pageref{sect: dispersion: DPL94 model}.
 \item[`M61 skew':]\index{relaxation dispersion!M61 skew model}  The 
\citet{Meiboom61} 2-site equation for all time scales with $\pA \gg \pB$ and 
with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$.  This model is 
disabled by default in the dispersion auto-analysis.  See Section~\ref{sect: 
dispersion: M61 skew model} on page~\pageref{sect: dispersion: M61 skew model}.
 \item[`TP02':]\index{relaxation dispersion!TP02 model}  The 
\citet{TrottPalmer02} 2-site equation for all time scales with $\pA \gg \pB$ 
and with parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$.  See 
Section~\ref{sect: dispersion: TP02 model} on page~\pageref{sect: dispersion: 
TP02 model}.
 \item[`TAP03':]\index{relaxation dispersion!TAP03 model}  The \citet{Trott03} 
off-resonance 2-site analytic equation for all time scales with the weak 
condition $\pA \gg \pB$ and with parameters $\{\Ronerhoprime, \dots, \pA, \dw, 
\kex\}$.


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