Author: bugman
Date: Thu Dec 11 18:23:06 2008
New Revision: 8196
URL: http://svn.gna.org/viewcvs/relax?rev=8196&view=rev
Log:
Merged revisions
8091-8093,8095-8149,8152,8154-8157,8160,8180,8183,8186-8189,8191-8193 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r8091 | bugman | 2008-12-02 15:13:42 +0100 (Tue, 02 Dec 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-7228" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spectral_errors
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r8092 | bugman | 2008-12-02 15:16:54 +0100 (Tue, 02 Dec 2008) | 554 lines
Merged revisions
7881-7915,7925,7936,7950-7951,7953-7960,7964,7985-7990,7993-7995,7998-8010,8013,8023-8025,8037-8055,8069-8081,8085-8086,8088-8090
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spectral_errors
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r7881 | bugman | 2008-10-21 16:01:01 +0200 (Tue, 21 Oct 2008) | 3 lines
Created the empty user function class 'spectrum'.
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r7882 | bugman | 2008-10-21 16:03:37 +0200 (Tue, 21 Oct 2008) | 6 lines
Deleted the prompt.spectrum module.
The prompt.noe module will be renamed to this as its only functions are
the same as the spectrum
user function class.
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r7883 | bugman | 2008-10-21 16:04:32 +0200 (Tue, 21 Oct 2008) | 6 lines
Renamed the noe module to spectrum.
The noe module only contains user functions will are to be merged into
the spectrum user function
class, hence will be deleted anyway.
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r7884 | bugman | 2008-10-21 16:05:24 +0200 (Tue, 21 Oct 2008) | 3 lines
Renamed the class in the old prompt.noe module.
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r7885 | bugman | 2008-10-21 16:06:18 +0200 (Tue, 21 Oct 2008) | 3 lines
Deleted the old NOE user function class from the interpreter namespace.
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r7886 | bugman | 2008-10-21 16:31:48 +0200 (Tue, 21 Oct 2008) | 3 lines
Renamed 'spectrum_type' to the more generic 'spectrum_id'.
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r7887 | bugman | 2008-10-21 16:38:34 +0200 (Tue, 21 Oct 2008) | 3 lines
Docstring updates for spectrum.read().
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r7888 | bugman | 2008-10-21 16:39:01 +0200 (Tue, 21 Oct 2008) | 3 lines
Renamed spectrum.read() to spectrum.read_intensities().
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r7889 | bugman | 2008-10-21 16:45:27 +0200 (Tue, 21 Oct 2008) | 5 lines
Deletion of the format argument from the spectrum.read_intensities() user
function.
To compensate for this, relax will be modified to auto-detect the file
format.
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r7890 | bugman | 2008-10-21 16:49:49 +0200 (Tue, 21 Oct 2008) | 3 lines
Fixed docstrings and user function print outs.
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r7891 | bugman | 2008-10-21 16:53:04 +0200 (Tue, 21 Oct 2008) | 3 lines
Switched from calls to noe_obj to generic_fns.intensity.
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r7892 | bugman | 2008-10-21 17:22:49 +0200 (Tue, 21 Oct 2008) | 7 lines
Added new arguments and improved the spectrum.read_intensities()
docstring.
The mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col,
and sep args have been
added to support the generic intensity file format. This format has also
had a description in the
docstring written.
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r7893 | bugman | 2008-10-21 17:25:06 +0200 (Tue, 21 Oct 2008) | 3 lines
Shifted the relax_fit.mean_and_error() user function interface to
spectrum.mean_and_error().
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r7894 | bugman | 2008-10-21 17:25:43 +0200 (Tue, 21 Oct 2008) | 3 lines
Renamed spectrum.mean_and_error() to spectrum.error_analysis().
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r7895 | bugman | 2008-10-21 17:42:29 +0200 (Tue, 21 Oct 2008) | 3 lines
spectrum.error_analysis() now calls
generic_fns.intensity.error_analysis().
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r7896 | bugman | 2008-10-21 18:34:31 +0200 (Tue, 21 Oct 2008) | 5 lines
Rewrote the spectrum.error_analysis() user function docstring.
This is still missing 3 sections for error analysis with the volume
integration methods.
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r7897 | bugman | 2008-10-21 18:35:59 +0200 (Tue, 21 Oct 2008) | 3 lines
Renamed the generic_fns.intensity module to generic_fns/spectrum.
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r7898 | bugman | 2008-10-21 18:37:22 +0200 (Tue, 21 Oct 2008) | 3 lines
Import fix for generic_fns.spectrum.
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r7899 | bugman | 2008-10-21 18:38:19 +0200 (Tue, 21 Oct 2008) | 3 lines
Import error fix.
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r7900 | bugman | 2008-10-21 18:38:47 +0200 (Tue, 21 Oct 2008) | 3 lines
Another import error fix.
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r7901 | bugman | 2008-10-22 10:41:28 +0200 (Wed, 22 Oct 2008) | 3 lines
Finished of the massive docstring of the spectrum.error_analysis() user
function.
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r7902 | bugman | 2008-10-22 10:44:40 +0200 (Wed, 22 Oct 2008) | 3 lines
Created the skeleton module for arg unit tests of the spectrum user
function class.
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r7903 | bugman | 2008-10-22 11:16:31 +0200 (Wed, 22 Oct 2008) | 3 lines
Created the new error class RelaxNoneIntListIntError.
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r7904 | bugman | 2008-10-22 11:19:32 +0200 (Wed, 22 Oct 2008) | 3 lines
Wrote 15 arg unit tests for the spectrum user functions.
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r7905 | bugman | 2008-10-22 11:20:10 +0200 (Wed, 22 Oct 2008) | 3 lines
Modified the int_col arg to spectrum.read_intensities() to allow for
lists of integers.
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r7906 | bugman | 2008-10-22 11:25:22 +0200 (Wed, 22 Oct 2008) | 3 lines
Renamed spectrum.error() to spectrum.baseplane_rmsd().
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r7907 | bugman | 2008-10-22 11:31:14 +0200 (Wed, 22 Oct 2008) | 3 lines
Created the spectrum.integration_points() user function interface.
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r7908 | bugman | 2008-10-22 11:33:44 +0200 (Wed, 22 Oct 2008) | 3 lines
Wrote 3 arg unit tests for the spectrum.integration_points() user
function.
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r7909 | bugman | 2008-10-22 11:35:28 +0200 (Wed, 22 Oct 2008) | 3 lines
Fix for the N arg check of the spectrum.integration_points() user
function.
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r7910 | bugman | 2008-10-22 11:36:09 +0200 (Wed, 22 Oct 2008) | 3 lines
Fix for 2 arg unit tests of the spectrum.integration_points() user
function.
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r7911 | bugman | 2008-10-22 11:37:08 +0200 (Wed, 22 Oct 2008) | 3 lines
Fixes for the arg unit tests of the spectrum.baseplane_rmsd() user
function.
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r7912 | bugman | 2008-10-22 11:56:55 +0200 (Wed, 22 Oct 2008) | 3 lines
Added the int_method arg to the spectrum.read_intensities() user function.
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r7913 | bugman | 2008-10-22 12:04:38 +0200 (Wed, 22 Oct 2008) | 3 lines
Wrote the int_method arg unit test of the spectrum.read_intensities()
user function.
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r7914 | bugman | 2008-10-22 12:24:56 +0200 (Wed, 22 Oct 2008) | 3 lines
Fix for the user function class documentation.
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r7915 | bugman | 2008-10-22 12:36:21 +0200 (Wed, 22 Oct 2008) | 6 lines
Renamed relax_fit.read() to relax_fit.relax_time() and significantly
decreased its functionality.
Most of relax_fit.read() is now in spectrum.read_intensities() and hence
this functionality has been
axed. All that is left is the associating of a spectrum to a time point.
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r7925 | bugman | 2008-10-22 18:14:40 +0200 (Wed, 22 Oct 2008) | 3 lines
Added 3 arg unit tests for the relax_fit user function class.
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r7936 | bugman | 2008-10-22 19:26:53 +0200 (Wed, 22 Oct 2008) | 3 lines
Removed some unused imports.
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r7950 | bugman | 2008-10-23 17:09:03 +0200 (Thu, 23 Oct 2008) | 3 lines
Added module docstrings and __docformat__ variables to the 'spectrum'
prompt module.
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r7951 | bugman | 2008-10-23 17:15:19 +0200 (Thu, 23 Oct 2008) | 5 lines
Created a new noe user function class, unrelated to the previously
deleted one.
This contains the single user function, noe.spectrum_type().
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r7953 | bugman | 2008-10-23 17:56:58 +0200 (Thu, 23 Oct 2008) | 3 lines
Fix for the initial spectrum.read_intensities() print out, the int_method
arg was not being shown.
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r7954 | bugman | 2008-10-23 17:58:15 +0200 (Thu, 23 Oct 2008) | 3 lines
Updated the relax_fit.py system test script for the new spectrum user
function class.
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r7955 | bugman | 2008-10-23 17:59:19 +0200 (Thu, 23 Oct 2008) | 5 lines
Expanded the relax_fit.py system test script to include the creation of a
number of files.
These include files of Rx values, the results file, grace files, and the
saved state file.
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r7956 | bugman | 2008-10-23 18:01:58 +0200 (Thu, 23 Oct 2008) | 5 lines
Updated the relax_fit.py sample script to match the changes of r7954 to
the system test script.
The script now uses the new spectrum user function class.
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r7957 | bugman | 2008-10-23 18:10:59 +0200 (Thu, 23 Oct 2008) | 3 lines
Fixed the args and docstring for the generic_fns.spectrum.read() function.
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r7958 | bugman | 2008-10-23 18:23:42 +0200 (Thu, 23 Oct 2008) | 6 lines
The peak list type is now automatically determined.
The new autodetect_format() function was written, and the top half of the
read() function was
modified to handle the auto-detection.
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r7959 | bugman | 2008-10-23 18:32:08 +0200 (Thu, 23 Oct 2008) | 3 lines
Destroyed assign_func() and shifted all the data storage back to
generic_fns.spectrum.read().
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r7960 | bugman | 2008-10-23 18:57:53 +0200 (Thu, 23 Oct 2008) | 3 lines
Fixes for the peak list system tests, using the new
spectrum.read_intensities() user function.
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r7964 | bugman | 2008-10-24 15:40:05 +0200 (Fri, 24 Oct 2008) | 6 lines
Renamed and converted the read() method to relax_time().
The method now simply creates a structure in the relax data store
matching cdp.spectrum_ids and
storing the associated relaxation time periods.
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r7985 | bugman | 2008-11-20 21:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines
Changed the default integration method from None to 'height'.
Height integration, when done properly is better than volumes for peak
intensities ;)
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r7986 | bugman | 2008-11-20 21:56:17 +0100 (Thu, 20 Nov 2008) | 3 lines
Cleaned up a warning string.
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r7987 | bugman | 2008-11-20 21:58:12 +0100 (Thu, 20 Nov 2008) | 3 lines
Changed the warning message once more.
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r7988 | bugman | 2008-11-20 22:05:04 +0100 (Thu, 20 Nov 2008) | 5 lines
Fix for the test_read_sparky() system test.
The relax_fit.read() call was replaced with spectrum.read_intensities().
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r7989 | bugman | 2008-11-20 22:09:43 +0100 (Thu, 20 Nov 2008) | 6 lines
Modified the script to create the basic_heights_T2_ncyc1.bz2 saved state
and regenerated this file.
The spectrum.read_intensities() user function is now used, and the new
format of the spin specific
'intensities' data structure is in the saved state.
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r7990 | bugman | 2008-11-20 22:18:47 +0100 (Thu, 20 Nov 2008) | 5 lines
Another fix for the test_read_sparky() system test.
This fixes the checking of the new spin specific 'intensities' data
structure.
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r7993 | bugman | 2008-11-20 23:31:32 +0100 (Thu, 20 Nov 2008) | 5 lines
Fixes for the 4 peak list reading system tests.
The spin specific intensities structure is now a simple list.
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r7994 | bugman | 2008-11-20 23:39:41 +0100 (Thu, 20 Nov 2008) | 3 lines
Modified the noe.py system test script to use the new 'spectrum' user
functions.
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r7995 | bugman | 2008-11-20 23:40:45 +0100 (Thu, 20 Nov 2008) | 5 lines
Modified the noe.py sample script to use the new 'spectrum' user
functions.
This copies the changes of r7994 which were made to the equivalent system
test.
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r7998 | bugman | 2008-11-21 09:54:55 +0100 (Fri, 21 Nov 2008) | 5 lines
Renamed spectrum_type to spectrum_id in the NOE set_error() method.
This method may have to remain for the Monte Carlo simulations?
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r7999 | bugman | 2008-11-21 09:57:35 +0100 (Fri, 21 Nov 2008) | 5 lines
Copied the NOE set_error() function to
generic_fns.spectrum.baseplane_rmsd().
The class method has been converted to a module function.
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r8000 | bugman | 2008-11-21 10:03:55 +0100 (Fri, 21 Nov 2008) | 3 lines
Updated the baseplane_rmsd() function to it's new purpose.
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r8001 | bugman | 2008-11-21 10:04:45 +0100 (Fri, 21 Nov 2008) | 3 lines
Added a missing bracket.
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r8002 | bugman | 2008-11-21 10:06:35 +0100 (Fri, 21 Nov 2008) | 3 lines
The current data pipe is now aliased.
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r8003 | bugman | 2008-11-21 10:13:41 +0100 (Fri, 21 Nov 2008) | 3 lines
Fixes for the baseplane_rmsd() function.
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r8004 | bugman | 2008-11-21 10:15:04 +0100 (Fri, 21 Nov 2008) | 5 lines
Fix for the noe.py system test script.
The spectrum.baseplane_rmsd() user function was receiving the wrong
arguments.
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r8005 | bugman | 2008-11-21 10:31:10 +0100 (Fri, 21 Nov 2008) | 3 lines
Fix for a RelaxError call in baseplane_rmsd().
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r8006 | bugman | 2008-11-21 10:33:31 +0100 (Fri, 21 Nov 2008) | 3 lines
Added some tests to the NOE calculate() method.
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r8007 | bugman | 2008-11-21 10:37:46 +0100 (Fri, 21 Nov 2008) | 3 lines
Modified the NOE overfit_deselect() for the new peak intensity data
structures.
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r8008 | bugman | 2008-11-21 10:50:20 +0100 (Fri, 21 Nov 2008) | 5 lines
Created a new warning class, RelaxDeselectWarning.
This is to be used by all overfit_deselect methods!
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r8009 | bugman | 2008-11-21 10:51:55 +0100 (Fri, 21 Nov 2008) | 5 lines
Updated the NOE overfit_deselect() method to use RelaxDeselectWarning.
Deselected spins are skipped and the checks are now in an if-elif block.
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r8010 | bugman | 2008-11-21 11:22:47 +0100 (Fri, 21 Nov 2008) | 3 lines
Added the spectrum.error_analysis() user fn call to both the NOE sample
script and system test.
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r8013 | bugman | 2008-11-21 13:38:36 +0100 (Fri, 21 Nov 2008) | 3 lines
Initialisation of the error_analysis() function.
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r8023 | bugman | 2008-11-25 15:17:22 +0100 (Tue, 25 Nov 2008) | 5 lines
Added a catch for missing data in the grace.write() user function back
end.
A RelaxWarning is now thrown saying that an empty file will be created.
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r8024 | bugman | 2008-11-25 15:18:51 +0100 (Tue, 25 Nov 2008) | 3 lines
Slight modification to the missing data RelaxWarning message.
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r8025 | bugman | 2008-11-26 10:57:42 +0100 (Wed, 26 Nov 2008) | 3 lines
Wrote the interface for the spectrum.replicated() user function.
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r8037 | bugman | 2008-11-27 14:02:41 +0100 (Thu, 27 Nov 2008) | 5 lines
Partial implementation of the error_analysis() code
The 2 categories now supported are both peak height and volumes when no
spectra are replicated.
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r8038 | bugman | 2008-11-27 14:06:48 +0100 (Thu, 27 Nov 2008) | 3 lines
Fixes for the volume integration with no replicated spectra.
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r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines
Modified the NOE system test to call the noe.spectrum_type() user
function.
The spectrum_ids have also been changed to avoid user confusion (when
these changes are ported to
the sample script).
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r8040 | bugman | 2008-11-27 14:15:42 +0100 (Thu, 27 Nov 2008) | 17 lines
Manually ported r8039 from the system test to the sample script.
The command used was:
svn merge -r8038:8039 test_suite/system_tests/scripts/noe.py
sample_scripts/noe.py
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r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
M /branches/spectral_errors/test_suite/system_tests/scripts/noe.py
Modified the NOE system test to call the noe.spectrum_type() user
function.
The spectrum_ids have also been changed to avoid user confusion (when
these changes are ported to
the sample script).
.....
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r8041 | bugman | 2008-11-27 14:19:37 +0100 (Thu, 27 Nov 2008) | 3 lines
Activated the 'noe' user function class.
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r8042 | bugman | 2008-11-27 14:20:44 +0100 (Thu, 27 Nov 2008) | 5 lines
Fix for the noe.spectrum_type() user function.
The spectrum_type should be a string, not a number.
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r8043 | bugman | 2008-11-27 15:05:04 +0100 (Thu, 27 Nov 2008) | 6 lines
Split up the error_analysis() function.
The two functions __errors_height_no_repl() and __errors_volume_no_repl()
have been created. The
other 4 analysis types will be added as functions later.
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r8044 | bugman | 2008-11-27 16:22:56 +0100 (Thu, 27 Nov 2008) | 3 lines
Wrote the NOE spectrum_type() method.
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r8045 | bugman | 2008-11-27 16:29:02 +0100 (Thu, 27 Nov 2008) | 3 lines
Modified the NOE calculation code for the new spectra setup.
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r8046 | bugman | 2008-11-27 17:41:34 +0100 (Thu, 27 Nov 2008) | 3 lines
Added a check for the value of int_method in the
spectrum.read_intensities() user function.
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r8047 | bugman | 2008-11-27 17:47:45 +0100 (Thu, 27 Nov 2008) | 5 lines
Fix for the relax_fit.py system test script.
The spectrum.read_intensities() user function arg int_method was
incorrectly set.
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r8048 | bugman | 2008-11-27 17:49:50 +0100 (Thu, 27 Nov 2008) | 3 lines
Removed some debugging code.
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r8049 | bugman | 2008-11-27 18:06:29 +0100 (Thu, 27 Nov 2008) | 5 lines
Fixes for all the peak list reading tests.
The int_method arg to spectrum.read_intensities() was incorrectly set to
'heights'.
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r8050 | bugman | 2008-11-27 18:12:39 +0100 (Thu, 27 Nov 2008) | 3 lines
The duplicated spectra are now specified in the relax_fit.py system test
script.
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r8051 | bugman | 2008-11-27 18:14:00 +0100 (Thu, 27 Nov 2008) | 5 lines
Fixes for the relax_fit.py sample script.
This includes fixes for spectrum.read_intensities() and the use of
spectrum.replicated().
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r8052 | bugman | 2008-11-28 10:48:35 +0100 (Fri, 28 Nov 2008) | 3 lines
Implemented the replicated() function.
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r8053 | bugman | 2008-11-28 10:49:01 +0100 (Fri, 28 Nov 2008) | 3 lines
Removed some debugging print outs.
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r8054 | bugman | 2008-11-28 14:54:34 +0100 (Fri, 28 Nov 2008) | 3 lines
Fixes for the error_analysis() function. Replicated spectra are stored
in 'cdp.replicates'.
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r8055 | bugman | 2008-11-28 18:02:42 +0100 (Fri, 28 Nov 2008) | 5 lines
Started to implement the __errors_repl() function.
This is a highly modified form of the relaxation curve-fitting
mean_and_error() method.
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r8069 | bugman | 2008-12-01 09:37:13 +0100 (Mon, 01 Dec 2008) | 3 lines
Fix for the calculation of the average variance.
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r8070 | bugman | 2008-12-01 10:40:11 +0100 (Mon, 01 Dec 2008) | 5 lines
A number of fixes for the __errors_repl() function.
The variance and sd structures are now correctly created, and the
variances properly averaged.
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r8071 | bugman | 2008-12-01 10:42:42 +0100 (Mon, 01 Dec 2008) | 3 lines
The spin specific error structure intensity_err is now set for each
selected spin.
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r8196 - in /branches/j_couplings: ./ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ specific_fns/ te...