Merged revisions 8091-8093,8095-8149,8152,8154-8157,8160,8180,8183,8186-8189,8191-8193 via svnmerge from
svn+ssh://bugman@.../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@.../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@.../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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r8093 | bugman | 2008-12-02 15:17:33 +0100 (Tue, 02 Dec 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/spectral_errors
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r8095 | semor | 2008-12-02 16:30:36 +0100 (Tue, 02 Dec 2008) | 5 lines
Added more system tests for the reading of an XEasy peak list with different spins.
Not sure if defining new functions was absolutely needed, but it works.
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r8096 | semor | 2008-12-02 21:38:19 +0100 (Tue, 02 Dec 2008) | 9 lines
Continued to implement the reading of the generic peak intensity file.
The code now calculates the number of delays (and associated intensities) input.
The remaining tasks include sorting the delays and intensities, which is different from when other
peak intensity files are used (e.g. XEasy, Sparky, nmrview) since the delays are part of the input
file header (in the case of the generic file).
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r8097 | semor | 2008-12-02 22:53:27 +0100 (Tue, 02 Dec 2008) | 7 lines
Continued the implementation of the reading of the generic peak intensity file.
The delays and intensities can now be read for the different peaks.
The remaining tasks include passing these information (delays + intensities) to relax...
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r8098 | bugman | 2008-12-03 14:10:03 +0100 (Wed, 03 Dec 2008) | 3 lines
Created a directory to store sequence data.
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r8099 | bugman | 2008-12-03 14:12:31 +0100 (Wed, 03 Dec 2008) | 8 lines
Added all the files necessary to reproduce bug #12670 (https://gna.org/bugs/index.php?12670).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
The script needs to be modified to point to the correct locations and needs to be activated as a
system test.
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r8100 | bugman | 2008-12-03 14:15:15 +0100 (Wed, 03 Dec 2008) | 5 lines
The script for reproducing bug #12670 (https://gna.org/bugs/index.php?12670) now works.
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
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r8101 | bugman | 2008-12-03 14:22:44 +0100 (Wed, 03 Dec 2008) | 5 lines
Activated the system test catching bug #12670 (https://gna.org/bugs/index.php?12670).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
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r8102 | bugman | 2008-12-03 14:27:06 +0100 (Wed, 03 Dec 2008) | 9 lines
Fix for bug #12670 (https://gna.org/bugs/index.php?12670).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
The problem was that the relaxation curve-fitting return_error() method was returning the global
cdp.sigma_I error structure - which does not exist for all error types - when it should have been
returning the spin specific error structure.
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r8103 | bugman | 2008-12-03 20:32:48 +0100 (Wed, 03 Dec 2008) | 6 lines
Added a system test for the creation of an XH bond vector distribution.
This test mimics the script used to create figure 7.8 of my PhD thesis
(http://eprints.infodiv.unimelb.edu.au/archive/00002799/).
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r8104 | bugman | 2008-12-03 20:36:17 +0100 (Wed, 03 Dec 2008) | 3 lines
Added the missing spin_loop() import.
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r8105 | bugman | 2008-12-03 20:53:44 +0100 (Wed, 03 Dec 2008) | 3 lines
A number of fixes for the create_vector_dist() function.
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r8106 | bugman | 2008-12-03 20:54:16 +0100 (Wed, 03 Dec 2008) | 3 lines
Converted the symmetry flag to a bool.
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r8107 | bugman | 2008-12-03 21:03:02 +0100 (Wed, 03 Dec 2008) | 5 lines
Bug fix for the create_vector_dist() function.
A structure needed to be added to the internal structural object.
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r8108 | bugman | 2008-12-03 21:10:26 +0100 (Wed, 03 Dec 2008) | 5 lines
Bug fixes for the PyMOL open_pdb() method.
This method was not handling the structural object properly.
................
r8109 | bugman | 2008-12-03 21:14:53 +0100 (Wed, 03 Dec 2008) | 6 lines
Bug fixes for the PyMOL cartoon() method.
As with the open_pdb() method, cartoon() was not handling the structural object correctly and was
not handling multiple structures.
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r8110 | bugman | 2008-12-03 21:17:30 +0100 (Wed, 03 Dec 2008) | 5 lines
Bug fix for the create_vector_dist() function.
The chain B of symmetry vectors was exactly the same as chain A and not mirrored.
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r8111 | bugman | 2008-12-03 21:20:47 +0100 (Wed, 03 Dec 2008) | 6 lines
Another bug fix for the create_vector_dist() function.
This time the atom number was not being incremented for chain B so that there are multiple atoms of
the same number in the PDB file.
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r8112 | bugman | 2008-12-03 21:22:20 +0100 (Wed, 03 Dec 2008) | 3 lines
Removed the PyMOL execution commands from the XH bond distribution PDB representation system test.
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r8113 | bugman | 2008-12-03 21:51:10 +0100 (Wed, 03 Dec 2008) | 5 lines
Bug fix for the centre_of_mass() function.
The spin id string is now created to correctly return the molecule, residue, and spin containers.
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r8114 | bugman | 2008-12-03 22:03:42 +0100 (Wed, 03 Dec 2008) | 5 lines
Fix for the centre_of_mass() function.
When no element entry is present in the PDB file, a RelaxError is thrown.
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r8115 | bugman | 2008-12-03 22:30:16 +0100 (Wed, 03 Dec 2008) | 6 lines
The centre_of_mass() function now only throws warnings rather than RelaxErrors.
This allows the CoM to be calculated even if a few elements are unknown or if the element record is
missing.
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r8116 | bugman | 2008-12-03 22:56:23 +0100 (Wed, 03 Dec 2008) | 3 lines
Added a sample script for the creation of the PDB representation of the XH bond vectors.
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r8117 | semor | 2008-12-04 02:09:50 +0100 (Thu, 04 Dec 2008) | 10 lines
Reverted revisions 8096 and 8097.
The command used was:
svn merge -r8097:8095 .
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-users/2008-12/msg00000.html
(Message ID: 7f080ed10812030146w7e73ce24r75d32121e5f1c05f@...)
................
r8118 | semor | 2008-12-04 02:14:08 +0100 (Thu, 04 Dec 2008) | 5 lines
Continued the implementation of the reading of the generic peak intensity file.
The good file is now input.
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r8119 | semor | 2008-12-04 02:22:24 +0100 (Thu, 04 Dec 2008) | 9 lines
Brought back revision 8096.
The command used was:
svn merge -r8095:8096 .
This was done since r8117 reverted accidentally both r8096 and r8097, while only r8097 had to be
reverted.
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r8120 | semor | 2008-12-04 02:30:38 +0100 (Thu, 04 Dec 2008) | 6 lines
Still more for the generic peak intensity support.
Added a column for the proton within the generic peak intensity file and modified the handling code
accordingly.
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r8121 | semor | 2008-12-04 02:46:41 +0100 (Thu, 04 Dec 2008) | 7 lines
Still more for the generic peak intensity support.
The intensity is now returned for the first delay only.
Further work is needed for the code to return all available intensities (for the different delays).
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r8122 | semor | 2008-12-04 02:48:29 +0100 (Thu, 04 Dec 2008) | 8 lines
Still more for the generic peak intensity support.
Changed the proton definition in the generic file to match the default value for simplicity of
coding at this time.
The test now passes for the reading of the intensity associated to the first delay only...
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r8123 | semor | 2008-12-04 03:21:37 +0100 (Thu, 04 Dec 2008) | 5 lines
Finalized the code for the reading of intensities from the generic file.
The test now passes after reading in multiple intensities from a single file.
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r8124 | semor | 2008-12-04 03:43:09 +0100 (Thu, 04 Dec 2008) | 3 lines
Deleted this now not needed file.
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r8125 | bugman | 2008-12-04 13:23:18 +0100 (Thu, 04 Dec 2008) | 7 lines
Seb, here is a challenge for the generic peak list reading code!
This includes a new valid peak intensity file and associated system test. In this case the spectrum
ids are given, along with an array specifying the intensity columns. This should cover much of what
I talked about in my post at https://mail.gna.org/public/relax-devel/2008-12/msg00016.html.
................
r8126 | bugman | 2008-12-04 14:45:28 +0100 (Thu, 04 Dec 2008) | 3 lines
Fix for the test_read_peak_list_generic2() system test.
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r8127 | semor | 2008-12-04 15:48:24 +0100 (Thu, 04 Dec 2008) | 7 lines
Added some printouts for the loading of the generic intensity file.
This is as suggested in a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-12/msg00016.html
(Message-id: <7f080ed10812040129pe2887deu339ae08b9021062a@...>)
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r8128 | bugman | 2008-12-04 16:16:15 +0100 (Thu, 04 Dec 2008) | 3 lines
A temporary directory is now created and deleted in the relaxation curve-fitting system tests.
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r8129 | bugman | 2008-12-04 16:22:11 +0100 (Thu, 04 Dec 2008) | 3 lines
The ubiquitin relaxation curve-fitting system test now dumps all files to the temp dir.
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r8130 | bugman | 2008-12-04 16:25:18 +0100 (Thu, 04 Dec 2008) | 5 lines
Fix for the 1UBQ_relax_fit.py system test script.
The directory arg to state.save() is 'dir_name'!
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r8131 | bugman | 2008-12-04 16:29:07 +0100 (Thu, 04 Dec 2008) | 3 lines
Expanded the system test for both bug #12670 and bug #12679.
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r8132 | bugman | 2008-12-04 16:36:02 +0100 (Thu, 04 Dec 2008) | 3 lines
Added code to check the Grace files created by the 1UBQ_relax_fit.py system test script.
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r8133 | bugman | 2008-12-04 16:37:20 +0100 (Thu, 04 Dec 2008) | 3 lines
Added a missing import causing a number of downstream system tests to fail.
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r8134 | bugman | 2008-12-04 16:45:33 +0100 (Thu, 04 Dec 2008) | 6 lines
Bug fix for the temp dir removal in the relaxation curve-fitting system tests.
The loading of program state was resetting the relax data store, so now the name is also kept in
self.
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r8135 | bugman | 2008-12-04 17:46:03 +0100 (Thu, 04 Dec 2008) | 7 lines
Partial fix for bug #12679 (https://gna.org/bugs/index.php?12679).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
The problem was that the data for the graph was numpy arrays, and only lists were being checked for.
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r8136 | bugman | 2008-12-04 18:13:21 +0100 (Thu, 04 Dec 2008) | 8 lines
Complete fix for bug #12679 (https://gna.org/bugs/index.php?12679).
This bug was reported by Michael Funk (mifu att nmr dot mpibpc dot mpg dot de).
The last issue was that when there multiple graphs, one per spin, the spin labels for the graphs
were set to the x-axis values rather than the spin_id.
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r8137 | semor | 2008-12-04 18:37:04 +0100 (Thu, 04 Dec 2008) | 8 lines
Modified the check for the spectrum_id being a string, a list is now accepted as well.
This is needed to implement the list of spectrum_id as in 'test_suite/system_tests/peak_lists.py'
(test_read_peak_list_generic2() function).
Should the RelaxStrError be changed to something like a RelaxStrListError ?
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r8138 | semor | 2008-12-04 19:30:11 +0100 (Thu, 04 Dec 2008) | 6 lines
Modified the autodetection code for the generic format.
This now recognizes the most generic format as in
'test_suite/shared_data/peak_lists/generic_intensity2.txt'.
................
r8139 | semor | 2008-12-04 19:33:11 +0100 (Thu, 04 Dec 2008) | 5 lines
Changed a RelaxError so it is more appropriated.
This is as proposed in the commit for r8137.
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r8140 | bugman | 2008-12-04 20:06:52 +0100 (Thu, 04 Dec 2008) | 5 lines
Fix for the value.read() user function.
The directory and 'sep' args were being ignored.
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r8141 | bugman | 2008-12-04 20:08:03 +0100 (Thu, 04 Dec 2008) | 5 lines
Fix for the spectrum.read_intensities() user function.
The sep arg was being ignored.
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r8142 | bugman | 2008-12-04 20:39:11 +0100 (Thu, 04 Dec 2008) | 3 lines
Created a new data pipe for relaxation dispersion analyses.
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r8143 | semor | 2008-12-04 20:44:25 +0100 (Thu, 04 Dec 2008) | 8 lines
Moved the 'spin_id = generate_spin_id(res_num=res_num, spin_name=X_name)' instance into the
different intensity_*() functions.
This is as suggested in a thread started by Edward at:
https://mail.gna.org/public/relax-devel/2008-12/msg00018.html
(Message-id: <7f080ed10812040706v3fadaa2eh2f475aa4ab611da7@...>)
................
r8144 | bugman | 2008-12-05 14:35:55 +0100 (Fri, 05 Dec 2008) | 3 lines
Modified the noe.spectrum_type() docstring to emphasis that it is for the steady-state NOE.
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r8145 | bugman | 2008-12-05 14:37:06 +0100 (Fri, 05 Dec 2008) | 3 lines
Modified the noe user function class docstring.
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r8146 | bugman | 2008-12-05 15:22:33 +0100 (Fri, 05 Dec 2008) | 3 lines
Wrote 2 arg unit tests for the noe.spectrum_type() user function.
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r8147 | bugman | 2008-12-05 15:37:07 +0100 (Fri, 05 Dec 2008) | 3 lines
Renamed the 2 unit tests committed at r8146.
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r8148 | bugman | 2008-12-05 16:05:49 +0100 (Fri, 05 Dec 2008) | 3 lines
Wrote 7 arg unit tests for the as of yet non-existent noe.read() user function.
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r8149 | semor | 2008-12-05 17:33:23 +0100 (Fri, 05 Dec 2008) | 10 lines
Introduced the generate_spin_id_data_array() function in the generic intensity file code.
The code now support a 'fake' generic format (with defined columns). Much more work is needed to
make this code more versatile to support 'any' format.
This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-12/msg00027.html
(Message-id: <7f080ed10812041223y1fe40665u90cfef9144cc5ca5@...>)
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r8152 | semor | 2008-12-05 20:42:50 +0100 (Fri, 05 Dec 2008) | 12 lines
Changed the generate_spin_id_data_array() arguments.
This follows a post by Ed at: https://mail.gna.org/public/relax-devel/2008-12/msg00032.html
(# Message-id: <7f080ed10812051130k7440d48cpf2902ca38dc5786f@...>)
Different arguments had been set in the idea of implementing complete automation for field
recognition for the generic file format... This might be implemented at a higher level as discussed
in a thread started at : https://mail.gna.org/public/relax-devel/2008-12/msg00029.html
(Message-id: <1228504156.9116.6.camel@...>)
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r8154 | bugman | 2008-12-05 20:51:38 +0100 (Fri, 05 Dec 2008) | 3 lines
Added a missing RelaxError import.
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r8155 | bugman | 2008-12-05 21:11:38 +0100 (Fri, 05 Dec 2008) | 3 lines
Implemented the interface of the noe.read() user function.
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r8156 | bugman | 2008-12-05 21:13:15 +0100 (Fri, 05 Dec 2008) | 3 lines
Missing import.
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r8157 | bugman | 2008-12-05 21:14:41 +0100 (Fri, 05 Dec 2008) | 3 lines
Fixes for 2 of the noe.read() user function arg unit tests.
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r8160 | bugman | 2008-12-08 14:47:42 +0100 (Mon, 08 Dec 2008) | 3 lines
Renamed the noe.read() user function to noe.read_constraints().
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r8180 | bugman | 2008-12-10 14:15:47 +0100 (Wed, 10 Dec 2008) | 6 lines
Bug fix for the vector_dist() function.
The PyMOL structure loading command should not use the file root but the full file name!!! A few
unused 'id' file root variables were also deleted.
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r8183 | bugman | 2008-12-10 18:35:05 +0100 (Wed, 10 Dec 2008) | 3 lines
Added a print out for the loading of PDB models.
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r8186 | bugman | 2008-12-10 18:46:37 +0100 (Wed, 10 Dec 2008) | 3 lines
Added tests of structure.load_spins() to all the structure system tests.
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r8187 | bugman | 2008-12-11 10:33:32 +0100 (Thu, 11 Dec 2008) | 10 lines
Partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
The problem fixed here is that of the missing molecule container. This was caused by the weirdness
of the Scientific python PDB reader splitting one modified lactose molecule into 2 molecules. The
lactose part was unnamed, while the modifier was named after the residues 'UNK'. The
generic_fns.mol_res_spin.return_molecule() function was having problems with this concept of the
first molecule unnamed and the second named. This is now fixed and the unnamed molecule can be
retrieved.
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r8188 | bugman | 2008-12-11 10:53:22 +0100 (Thu, 11 Dec 2008) | 8 lines
Another partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
This problem was trigged by the internal reader (where the problem lies) together with the
gromacs_phthalic_acid.pdb file. The issue was that the __fill_object_from_pdb() was operating on
all structures currently loaded into relax. Hence with the 2 models of this PDB file, the first
molecule had all the atoms of the first and second PDB models combined.
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r8189 | bugman | 2008-12-11 11:14:00 +0100 (Thu, 11 Dec 2008) | 9 lines
Final fixes for bug #12735 (https://gna.org/bugs/index.php?12735).
The last problem was again triggered by the Scientific python PDB reader weirdness. Residues ending
in '+' were being treated by the PDB reader as a different molecule. But then the molecule names
LYS+, ARG+, etc. were causing problems as '+' was being treated as regular expression when matching
molecule names. Therefore the '+' character has been stripped from all molecule, residue, and atom
names.
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r8191 | bugman | 2008-12-11 17:24:46 +0100 (Thu, 11 Dec 2008) | 8 lines
Fixes for bug #12573 (https://gna.org/bugs/index.php?12573).
This bug was reported by Jack Howarth (https://gna.org/users/jhowarth).
The problem was simply that the optimisation checks are exact and had to be slightly modified for
the Darwin kernel on 32 bit PowerPC.
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r8192 | bugman | 2008-12-11 17:48:43 +0100 (Thu, 11 Dec 2008) | 11 lines
Fixes for the 2 test_atom_loop_spin_selection2() unit tests.
This problem was reported by Jack Howarth (https://gna.org/users/jhowarth) in the post at
https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id:
<20081024141150.GA879@...>).
The problem was with the position array comparison as this was being converted to a string and then
compared. The string representations of the numpy arrays is obviously different on the intel vs.
powerpc chips.
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r8193 | bugman | 2008-12-11 18:09:51 +0100 (Thu, 11 Dec 2008) | 10 lines
Another PowerPC system test bug fix.
This problem was reported by Jack Howarth (https://gna.org/users/jhowarth) in the post at
https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id:
<20081024141150.GA879@...>).
The string.fromstring() function appears to be useless when switching between big and little endian
machines.
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