relax SVN archive

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/spectral_errors

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@.../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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r8072 | bugman | 2008-12-01 10:47:02 +0100 (Mon, 01 Dec 2008) | 3 lines

Print out refinement of the __errors_repl() function.
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r8073 | bugman | 2008-12-01 10:51:10 +0100 (Mon, 01 Dec 2008) | 3 lines

Removal of the mean_and_error() method. This is now part of generic_fns.spectrum.
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r8074 | bugman | 2008-12-01 10:52:19 +0100 (Mon, 01 Dec 2008) | 5 lines

Some fixes for the back_calc() relax-fit method.

Not sure if this method will work yet!
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r8075 | bugman | 2008-12-01 10:53:49 +0100 (Mon, 01 Dec 2008) | 3 lines

Replaced all references to 'average peak intensity'. These are no longer averaged.
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r8076 | bugman | 2008-12-01 10:59:51 +0100 (Mon, 01 Dec 2008) | 3 lines

Some whitespace cleanups.
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r8077 | bugman | 2008-12-01 15:42:53 +0100 (Mon, 01 Dec 2008) | 5 lines

Fixed the setting of the spin specific peak intensity errors in __errors_repl().

This should be an array equal to cdp.sigma_I.
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r8078 | bugman | 2008-12-01 15:44:30 +0100 (Mon, 01 Dec 2008) | 3 lines

The proper spin specific peak intensity errors are now input into the relax-fit minimise() method.
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r8079 | bugman | 2008-12-01 15:54:59 +0100 (Mon, 01 Dec 2008) | 3 lines

Fix for the relax_fit.py system test script. The 'ave_int' value type is no more!
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r8080 | bugman | 2008-12-01 15:56:39 +0100 (Mon, 01 Dec 2008) | 5 lines

Another fix for the relax_fit.py system test script.

The state.save() user function has no 'file' arg.
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r8081 | bugman | 2008-12-01 15:59:05 +0100 (Mon, 01 Dec 2008) | 3 lines

Manually updated the relax_fit.py sample script to match the equivalent system test script.
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r8085 | bugman | 2008-12-01 16:20:36 +0100 (Mon, 01 Dec 2008) | 3 lines

Modified the specific base class method return_value() to handle peak heights by spectrum id.
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r8086 | bugman | 2008-12-01 16:23:58 +0100 (Mon, 01 Dec 2008) | 3 lines

Modified the NOE return_grace_string() method to handle unknown data types, i.e. spectrum ids.
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r8088 | bugman | 2008-12-01 18:56:47 +0100 (Mon, 01 Dec 2008) | 5 lines

Fix for the return_value() base class method.

The index should be tested against None!
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r8089 | bugman | 2008-12-01 19:12:52 +0100 (Mon, 01 Dec 2008) | 5 lines

Temporarily switched back to residue numbers for the X-axis in the Grace plots.

How the spin_id string can be handled in xmgrace needs to be investigated!
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r8090 | semor | 2008-12-01 20:23:44 +0100 (Mon, 01 Dec 2008) | 10 lines

Continued to add tests for the reading of an XEasy peak list.

Commented lines (154, 159, 162) refer to spins different than standard backbone amides (HN - N),
i.e. HE1 - NE1
HN - C
HE1 - C

Not sure yet how to implement the reading of these...
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Initialized merge tracking via "svnmerge" with revisions "1-7228" from
svn+ssh://bugman@.../svn/relax/branches/spectral_errors

Continued to add tests for the reading of an XEasy peak list.

Commented lines (154, 159, 162) refer to spins different than standard backbone amides (HN - N),
i.e. HE1 - NE1
HN - C
HE1 - C

Not sure yet how to implement the reading of these...

Temporarily switched back to residue numbers for the X-axis in the Grace plots.

How the spin_id string can be handled in xmgrace needs to be investigated!

Fix for the return_value() base class method.

The index should be tested against None!

Merged revisions 7866-7873,7876-7878,7937-7940,7942-7948,7952,7961-7963,7965-7968,7971-7973,7975-7983,7991-7992,7996,8014,8016,8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r7866 | bugman | 2008-10-20 22:11:40 +0200 (Mon, 20 Oct 2008) | 7 lines

Bug fix for the LaTeX table generating script.

This was identified by Tyler Reddy "TREDDY at dal dot ca" in the message at
https://mail.gna.org/public/relax-users/2008-10/msg00062.html (Message-id:
<20081020162741.yimh96r4oq2ow4w0@...>).
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r7867 | bugman | 2008-10-20 22:28:02 +0200 (Mon, 20 Oct 2008) | 3 lines

Duplicated the latex_mf_table.py sample script for the creation of a system test.
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r7868 | bugman | 2008-10-20 22:45:41 +0200 (Mon, 20 Oct 2008) | 3 lines

Comment fix in the latex_mf_table.py sample script.
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r7869 | bugman | 2008-10-20 22:46:37 +0200 (Mon, 20 Oct 2008) | 3 lines

Modified the latex_mf_table.py script for the test suite.
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r7870 | bugman | 2008-10-20 22:51:27 +0200 (Mon, 20 Oct 2008) | 3 lines

Activated the model-free results to LaTeX table sample script.
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r7871 | bugman | 2008-10-20 22:51:57 +0200 (Mon, 20 Oct 2008) | 3 lines

Missing import.
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r7872 | bugman | 2008-10-20 22:59:45 +0200 (Mon, 20 Oct 2008) | 3 lines

Fix for the test_latex_table() system test.
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r7873 | bugman | 2008-10-20 23:00:14 +0200 (Mon, 20 Oct 2008) | 3 lines

Fix for the latex_mf_table.py sample script. This matches the system test fix in r7872.
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r7876 | bugman | 2008-10-21 11:50:12 +0200 (Tue, 21 Oct 2008) | 11 lines

Fixes for the model-free LaTeX table generation sample script.

These fixes do not affect the system test result yet - as LaTeX compilation will not be part of the
test suite - but fix the LaTeX compilation. These will be ported back to the sample script.

The docstring has been modified as the booktabs package is needed for this table. The '&'
characters in the spin_id string have been escaped to avoid this being interpreted as a column
separator. The 'Residue' column has been renamed to 'Spin'. And finally missing model-free
parameter errors can be handled.
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r7877 | bugman | 2008-10-21 11:53:58 +0200 (Tue, 21 Oct 2008) | 24 lines

Ported the changes of r7876 from the test suite to the sample script.

The command used was:
svn merge -r7875:7876 test_suite/system_tests/scripts/latex_mf_table.py sample_scripts/latex_mf_table.py

The LaTeX document starting and ending commands have been removed from this revision!

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r7876 | bugman | 2008-10-21 11:50:12 +0200 (Tue, 21 Oct 2008) | 11 lines
Changed paths:
M /1.3/test_suite/system_tests/scripts/latex_mf_table.py

Fixes for the model-free LaTeX table generation sample script.

These fixes do not affect the system test result yet - as LaTeX compilation will not be part of the
test suite - but fix the LaTeX compilation. These will be ported back to the sample script.

The docstring has been modified as the booktabs package is needed for this table. The '&'
characters in the spin_id string have been escaped to avoid this being interpreted as a column
separator. The 'Residue' column has been renamed to 'Spin'. And finally missing model-free
parameter errors can be handled.
.....
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r7878 | bugman | 2008-10-21 15:17:17 +0200 (Tue, 21 Oct 2008) | 3 lines

Fixes for all the standard deviation and variance variable names.
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r7937 | bugman | 2008-10-22 22:25:33 +0200 (Wed, 22 Oct 2008) | 3 lines

Epydoc doctring indentation fixes.
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r7938 | bugman | 2008-10-22 22:47:56 +0200 (Wed, 22 Oct 2008) | 5 lines

Added module docstrings and __docformat__ variables to all of the prompt modules.

The __docformat__ string is set to 'plaintext' to make epydoc happy.
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r7939 | bugman | 2008-10-22 22:55:51 +0200 (Wed, 22 Oct 2008) | 5 lines

Lots of epydoc fixes.

This is mainly title underline fixes.
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r7940 | bugman | 2008-10-22 23:20:40 +0200 (Wed, 22 Oct 2008) | 3 lines

Massive epydoc fixes too all of the maths_fns modules!!!
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r7942 | bugman | 2008-10-23 16:44:53 +0200 (Thu, 23 Oct 2008) | 6 lines

Fix for the relax IO logging with the -l command line argument.

This is a partial fix for bug #12489 (https://gna.org/bugs/?12489). The teeing problem still has
to be fixed.
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r7943 | bugman | 2008-10-23 16:54:43 +0200 (Thu, 23 Oct 2008) | 3 lines

Converted the tee class method into a module function.
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r7944 | bugman | 2008-10-23 16:56:12 +0200 (Thu, 23 Oct 2008) | 3 lines

Epydoc'd the tee function docstring.
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r7945 | bugman | 2008-10-23 16:57:45 +0200 (Thu, 23 Oct 2008) | 3 lines

Docstring improvements for the log() function.
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r7946 | bugman | 2008-10-23 16:58:04 +0200 (Thu, 23 Oct 2008) | 3 lines

Removed a line of redundant code.
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r7947 | bugman | 2008-10-23 16:58:56 +0200 (Thu, 23 Oct 2008) | 3 lines

Added the missing import of relax_io.tee.
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r7948 | bugman | 2008-10-23 17:01:18 +0200 (Thu, 23 Oct 2008) | 5 lines

Final fixes for bug #12489 (https://gna.org/bugs/?12489).

The log() and tee() functions are now operational.
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r7952 | bugman | 2008-10-23 17:39:25 +0200 (Thu, 23 Oct 2008) | 9 lines

Fix for bug #12487 (https://gna.org/bugs/index.php?12487).

This bug was reported by Tyler Reddy (TREDDY at dal dot ca).

The problem was that missing XH bond vector data was being manifested as the spin.xh_vect object
being set to None. The overfit_deselect() function which is responsible for deselecting unsuitable
spins prior to optimisation was only checking if the object existed, not if it was None!
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r7961 | bugman | 2008-10-24 13:44:28 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check to the atom_loop() to make sure structural data is loaded.
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r7962 | bugman | 2008-10-24 13:56:38 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check for empty PDB files in the internal structural object.
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r7963 | bugman | 2008-10-24 14:22:44 +0200 (Fri, 24 Oct 2008) | 3 lines

Added another spin to try to catch a program bug (unsuccessfully).
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r7965 | semor | 2008-10-24 15:41:46 +0200 (Fri, 24 Oct 2008) | 5 lines

Introduced verifications for the '-t' and '-l' options not to erase the python script used.

This should fix bug 12498 (http://gna.org/bugs/?12498).
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r7966 | bugman | 2008-10-24 16:14:19 +0200 (Fri, 24 Oct 2008) | 3 lines

Created a system test using Tyler Reddy's bug report - bug #12487 (https://gna.org/bugs/?12487).
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r7967 | semor | 2008-10-24 16:19:17 +0200 (Fri, 24 Oct 2008) | 7 lines

Modified the '-l' and '-t' options so they check for an existing file and don't overwrite it.

This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@...)
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r7968 | semor | 2008-10-24 17:55:21 +0200 (Fri, 24 Oct 2008) | 7 lines

Still improved the detection of existing files not to be overwritten when logging or teeing.

This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@...)
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r7971 | bugman | 2008-11-10 23:17:17 +0100 (Mon, 10 Nov 2008) | 6 lines

Added a missing RelaxError import.

This was discovered when trying to replicate bug #12582 (https://gna.org/bugs/index.php?12582)
reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).
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r7972 | bugman | 2008-11-10 23:31:18 +0100 (Mon, 10 Nov 2008) | 3 lines

Added a system test for replicating bug #12582.
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r7973 | bugman | 2008-11-10 23:36:36 +0100 (Mon, 10 Nov 2008) | 9 lines

Fix for bug #12582 (https://gna.org/bugs/index.php?12582).

This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the frq_labels data structure in the SpinContainer was sometimes set to []
rather than the data structure being missing. Now the structure is being tested if it is either
None or [] before being accessed in the model-free return_units() method.
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r7975 | bugman | 2008-11-12 15:57:25 +0100 (Wed, 12 Nov 2008) | 3 lines

Converted some ints to bools.
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r7976 | bugman | 2008-11-12 20:57:14 +0100 (Wed, 12 Nov 2008) | 3 lines

Modified the system test to additionally catch bug #12591 (https://gna.org/bugs/index.php?12591).
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r7977 | bugman | 2008-11-12 20:59:05 +0100 (Wed, 12 Nov 2008) | 3 lines

Renamed the system test script.
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r7978 | bugman | 2008-11-12 20:59:27 +0100 (Wed, 12 Nov 2008) | 3 lines

Deleted the old system test script.
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r7979 | bugman | 2008-11-12 21:00:37 +0100 (Wed, 12 Nov 2008) | 3 lines

Fixes for the system test script rename of the previous commits.
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r7980 | bugman | 2008-11-12 21:18:03 +0100 (Wed, 12 Nov 2008) | 9 lines

Partial fix for bug #12591 (https://gna.org/bugs/index.php?12591).

This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

If no model is ever selected in the model_selection.select() function, then relax no longer fails.
The failure is however caused by another problem elsewhere within relax, so this fix is not
complete.
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r7981 | bugman | 2008-11-12 21:21:39 +0100 (Wed, 12 Nov 2008) | 9 lines

Final fix for bug #12591 (https://gna.org/bugs/index.php?12591).

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the global_index counter in the model-free model_loop() method was supposed to
be incremented at the start of the loop. The deselected spin skipping code was located before this
though, causing the counter to not be incremented!
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r7982 | bugman | 2008-11-12 21:35:26 +0100 (Wed, 12 Nov 2008) | 5 lines

Created a very simple system test to catch bug #12588 (https://gna.org/bugs/index.php?12588).

This bug was reported by Tyler Reddy (treddy at dal dot ca).
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r7983 | bugman | 2008-11-12 21:49:03 +0100 (Wed, 12 Nov 2008) | 8 lines

Fix for bug #12588 (https://gna.org/bugs/index.php?12588).

This bug was reported by Tyler Reddy (treddy at dal dot ca).

The problem was that the results.read() user function was not handling the directory name being part
of the file name argument. This can now be handled.
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r7991 | bugman | 2008-11-20 22:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines

Added a catch for bug #12607 (https://gna.org/bugs/?12607) to the bugs_12582_12591.py script.

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).
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r7992 | bugman | 2008-11-20 23:23:56 +0100 (Thu, 20 Nov 2008) | 8 lines

Fix for bug #12607 (https://gna.org/bugs/?12607).

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the fixed flag was being checked for all spins. However deselected spins
should be ignored.
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r7996 | bugman | 2008-11-21 09:45:57 +0100 (Fri, 21 Nov 2008) | 3 lines

Renamed the bugs_12582_12591.py system test script to include bug #12607.
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r8014 | bugman | 2008-11-21 18:35:42 +0100 (Fri, 21 Nov 2008) | 3 lines

The structure.load_spins() user function now tests if a structure has been loaded.
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r8016 | bugman | 2008-11-21 18:38:37 +0100 (Fri, 21 Nov 2008) | 3 lines

Added a missing RelaxError import.
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r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines

Wrote 8 system tests for reading various PDB files using the internal and Scientific python objects.
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r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines

Added a lactose PDB file and 2 system tests reading this file.
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r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines

Fix for the __atom_index() method. This is a partial fix for bug #12637 (https://gna.org/bugs/?12637).

The struct_index of None is now handled.
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r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the CHANGES file changes to the 1.3 line.

The command used was:
svn merge -r8059:8060 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES

Updated the CHANGES file for relax 1.3.3.
.....
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r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the user manual fixes of r8063 from the 1.3.3 tag.

The command used was:
svn merge -r8062:8063 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex

Fixed the spacing in the table of contents of the user manual.
.....
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Modified the NOE return_grace_string() method to handle unknown data types, i.e. spectrum ids.

Modified the specific base class method return_value() to handle peak heights by spectrum id.

Merged revisions 8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines

Wrote 8 system tests for reading various PDB files using the internal and Scientific python objects.
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r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines

Added a lactose PDB file and 2 system tests reading this file.
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r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines

Fix for the __atom_index() method. This is a partial fix for bug #12637 (https://gna.org/bugs/?12637).

The struct_index of None is now handled.
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r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the CHANGES file changes to the 1.3 line.

The command used was:
svn merge -r8059:8060 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES

Updated the CHANGES file for relax 1.3.3.
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r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the user manual fixes of r8063 from the 1.3.3 tag.

The command used was:
svn merge -r8062:8063 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex

Fixed the spacing in the table of contents of the user manual.
.....
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