Author: bugman
Date: Thu Oct 16 23:57:25 2008
New Revision: 7792
URL: http://svn.gna.org/viewcvs/relax?rev=7792&view=rev
Log:
Merged revisions 7594-7791 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r7595 | bugman | 2008-10-11 18:15:19 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted all the Dasha class methods into module functions.
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r7596 | bugman | 2008-10-11 18:18:08 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the Dasha user function class prompt interface to the new design.
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r7597 | bugman | 2008-10-11 18:40:20 +0200 (Sat, 11 Oct 2008) | 3 lines
Created 7 arg unit tests for all fns of the dasha user function class.
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r7598 | bugman | 2008-10-11 18:41:47 +0200 (Sat, 11 Oct 2008) | 5 lines
Missing import bug fix.
This was identified by the arg unit tests of 7597.
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r7599 | bugman | 2008-10-11 18:43:02 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixes for the Dasha user function print outs.
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r7600 | bugman | 2008-10-11 20:45:03 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create() function to the new design.
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r7601 | bugman | 2008-10-11 21:09:54 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create_script() function to the new design.
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r7602 | bugman | 2008-10-11 21:16:30 +0200 (Sat, 11 Oct 2008) | 3 lines
Created the 2 new API functions: first_residue_num() and last_residue_num().
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r7603 | bugman | 2008-10-11 21:20:18 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the execute() function to the new design.
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r7604 | bugman | 2008-10-11 21:25:49 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the extract() function to the new design.
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r7605 | bugman | 2008-10-11 22:03:02 +0200 (Sat, 11 Oct 2008) | 6 lines
Fixes for the copy() and read() functions.
The specific set() function was destroyed at r4822, well at least shifted to
generic_fns.value.set_spin_params().
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r7606 | bugman | 2008-10-11 22:16:08 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixed the creation of the Dasha script.
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r7607 | bugman | 2008-10-11 22:17:22 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the extract() method. The current data pipe was missing.
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r7608 | bugman | 2008-10-11 22:18:42 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the extract() docstring.
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r7609 | bugman | 2008-10-11 22:35:06 +0200 (Sat, 11 Oct 2008) | 6 lines
Switched to using os.popen3 for executing Dasha.
This allows STDOUT and STDERR to be caught and sent to relax's STDOUT and
STDERR. Hence Dasha's
output is caught by the system tests, etc.
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r7610 | bugman | 2008-10-11 22:36:49 +0200 (Sat, 11 Oct 2008) | 5 lines
Bug fix for the minimisation set() function.
The variable 'index' no longer exists as it is replace by the SpinContainer
instance.
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r7611 | bugman | 2008-10-11 22:42:51 +0200 (Sat, 11 Oct 2008) | 3 lines
Modified the Dasha system test script to use the temporary directory.
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r7612 | bugman | 2008-10-11 22:46:23 +0200 (Sat, 11 Oct 2008) | 3 lines
The Dasha system test script can now run outside of the system test
framework.
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r7613 | bugman | 2008-10-11 22:47:48 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixed the call to results.write() in the Dasha system test script.
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r7614 | bugman | 2008-10-11 22:49:03 +0200 (Sat, 11 Oct 2008) | 3 lines
Comment fix.
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r7615 | bugman | 2008-10-11 23:04:16 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create() args to keyword args and the docstring to epydoc
format.
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r7616 | bugman | 2008-10-11 23:04:36 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the constraints flag to a bool.
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r7617 | bugman | 2008-10-11 23:06:13 +0200 (Sat, 11 Oct 2008) | 3 lines
The Modelfree4 execution system test script can now be run outside of the
test suite framework.
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r7618 | bugman | 2008-10-11 23:07:00 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the palmer.create() print out.
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r7619 | bugman | 2008-10-11 23:07:51 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the check of the constraints arg in palmer.create().
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r7620 | bugman | 2008-10-11 23:14:16 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the last pieces of create() to the new design.
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r7621 | bugman | 2008-10-11 23:21:05 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_mfin() to the new design.
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r7622 | bugman | 2008-10-11 23:34:53 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_mfdata() to the new design.
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r7623 | bugman | 2008-10-11 23:47:44 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create_mfmodel() and create_mfpar() functions to the new
design.
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r7624 | bugman | 2008-10-11 23:51:37 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_run() to the new design.
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r7625 | bugman | 2008-10-11 23:55:21 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted execute() to the new design.
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r7626 | bugman | 2008-10-12 00:03:01 +0200 (Sun, 12 Oct 2008) | 5 lines
Bug fix for the palmer.py sample script.
The model_selection() user function args were wrong.
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r7627 | bugman | 2008-10-12 00:11:52 +0200 (Sun, 12 Oct 2008) | 3 lines
Many fixes for the Modelfree4 execution system test script.
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r7628 | bugman | 2008-10-12 00:51:36 +0200 (Sun, 12 Oct 2008) | 6 lines
Switched from os.spawnlp to os.popen3 for proper IO redirection.
This allows the system tests to capture Modelfree4's STDOUT and STDERR
streams, as they are fused
into relax's.
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r7629 | bugman | 2008-10-12 00:54:20 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the palmer.py sample script.
The model selection data pipe is created by the user function so it
shouldn't be created beforehand.
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r7630 | bugman | 2008-10-12 01:33:29 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the reset() user function - the generic_fns.reset module was
not properly imported.
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r7631 | bugman | 2008-10-12 11:23:07 +0200 (Sun, 12 Oct 2008) | 3 lines
Shifted the pipe creation from setUp() to the script to allow for stand
alone execution.
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r7632 | bugman | 2008-10-12 11:40:43 +0200 (Sun, 12 Oct 2008) | 3 lines
Created a system test for the saving, loading, saving, and loading again of
the system state.
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r7633 | bugman | 2008-10-12 11:47:14 +0200 (Sun, 12 Oct 2008) | 5 lines
Removed the state loadings which was uncovering a pickling issue.
This bug is now caught by its own system test.
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r7634 | bugman | 2008-10-12 11:48:16 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the call to the fix() user function.
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r7635 | bugman | 2008-10-12 11:57:44 +0200 (Sun, 12 Oct 2008) | 3 lines
Updated the ancient palmer.py sample script to the new design.
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r7636 | bugman | 2008-10-12 12:07:28 +0200 (Sun, 12 Oct 2008) | 3 lines
Removed all references to 'run' and removed some useless comments.
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r7637 | bugman | 2008-10-12 12:26:47 +0200 (Sun, 12 Oct 2008) | 5 lines
Created the new specific method model_desc() for returning a human readable
model description.
This will be used in the model selection printouts.
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r7638 | bugman | 2008-10-12 12:27:23 +0200 (Sun, 12 Oct 2008) | 3 lines
Shifted to the use of the model_loop().
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r7639 | bugman | 2008-10-12 12:38:48 +0200 (Sun, 12 Oct 2008) | 8 lines
Converted the rest of the model selection to the model_loop() design.
The following model-free methods have been converted to using the
model_loop():
duplicate_data()
model_statistics()
skip_function()
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r7640 | bugman | 2008-10-12 12:42:09 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the determination of the global_stats flag in model_statistics().
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r7641 | bugman | 2008-10-12 12:48:17 +0200 (Sun, 12 Oct 2008) | 3 lines
Renamed the duplicate_data() arg model_info to model_index.
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r7642 | bugman | 2008-10-12 13:00:50 +0200 (Sun, 12 Oct 2008) | 3 lines
Created the model_type() method to determine whether the model is local or
global.
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r7643 | bugman | 2008-10-12 13:02:29 +0200 (Sun, 12 Oct 2008) | 3 lines
Activated the specific model_type() method.
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r7644 | bugman | 2008-10-12 13:04:07 +0200 (Sun, 12 Oct 2008) | 3 lines
Removed the model_index arg from model_type().
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r7645 | bugman | 2008-10-12 13:05:50 +0200 (Sun, 12 Oct 2008) | 3 lines
Used the new model_type() specific method to differentiate between global
and local models.
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r7646 | bugman | 2008-10-12 13:24:48 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the setUp() method. The 'palmer' data pipe shouldn't be created!
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r7647 | bugman | 2008-10-12 15:17:44 +0200 (Sun, 12 Oct 2008) | 3 lines
Changes to the model selection print out.
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r7648 | bugman | 2008-10-12 16:09:04 +0200 (Sun, 12 Oct 2008) | 3 lines
Added checks to the Modelfree4 system test.
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r7649 | bugman | 2008-10-12 16:12:49 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the extract() function.
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r7650 | bugman | 2008-10-12 16:30:32 +0200 (Sun, 12 Oct 2008) | 5 lines
Removed the 'format' arg from results.write() and results.display().
This is no longer used as the only supported format is now XML.
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r7651 | bugman | 2008-10-12 17:05:21 +0200 (Sun, 12 Oct 2008) | 7 lines
Fixes for the relax data store singleton 'add()', 'to_xml()', and
'from_xml()' methods.
These were referring to the contents of the singleton as self, whereas in
reality with the current
temporary implementation it is stored in self.instance. Hence the
singleton wasn't operating on
itself.
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r7652 | bugman | 2008-10-12 17:07:57 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the extraction of mfout file data in the Modelfree4 system test.
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r7653 | bugman | 2008-10-12 17:09:00 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the Modelfree4 controlling sample script.
This matches the fixes of r7652.
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r7654 | bugman | 2008-10-12 17:22:45 +0200 (Sun, 12 Oct 2008) | 3 lines
Fixes for the checks of the test_palmer() system test.
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r7655 | bugman | 2008-10-12 17:30:11 +0200 (Sun, 12 Oct 2008) | 3 lines
Added some checks for the final mfout file.
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r7656 | bugman | 2008-10-12 17:40:28 +0200 (Sun, 12 Oct 2008) | 3 lines
Fixes for the checks of the final mfout reading.
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r7657 | bugman | 2008-10-12 17:47:28 +0200 (Sun, 12 Oct 2008) | 3 lines
Added checks for the global chi2 and tm value.
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r7658 | bugman | 2008-10-12 18:22:02 +0200 (Sun, 12 Oct 2008) | 3 lines
The global chi2 and tm value are now extracted from the mfout file.
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r7659 | bugman | 2008-10-12 18:23:12 +0200 (Sun, 12 Oct 2008) | 3 lines
Removed a debugging print out.
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r7660 | bugman | 2008-10-12 18:33:46 +0200 (Sun, 12 Oct 2008) | 6 lines
Fix for the loading of global data from the mfout file.
This only happens when a global model is optimised. The parameters and
chi2 value are in the mfout
file but are fixed or the sum of individual chi2 vals.
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r7661 | bugman | 2008-10-12 18:35:17 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for a typo in the global chi2 check.
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r7662 | bugman | 2008-10-12 18:37:04 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the check of the optimised tm value.
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r7663 | bugman | 2008-10-12 18:43:27 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for running Modelfree4 - the structure is properly copied in the
create_run() method.
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r7664 | bugman | 2008-10-12 18:45:21 +0200 (Sun, 12 Oct 2008) | 3 lines
More fixes for create_run().
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r7665 | bugman | 2008-10-12 18:46:27 +0200 (Sun, 12 Oct 2008) | 3 lines
Modified the Modelfree4 system test to use a PDB file and spheroid
diffusion tensor.
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r7666 | bugman | 2008-10-12 18:46:57 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the execute() method when a PDB file is being used.
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r7667 | bugman | 2008-10-12 18:57:33 +0200 (Sun, 12 Oct 2008) | 3 lines
Created a new script to test out the handling of Modelfree4 with PDB files
and spheroid diffusion.
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r7668 | bugman | 2008-10-12 18:58:28 +0200 (Sun, 12 Oct 2008) | 5 lines
Removed the reading of the PDB file and setting of a spheroid tensor.
This will be tested in a second system test.
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r7669 | bugman | 2008-10-12 19:00:13 +0200 (Sun, 12 Oct 2008) | 5 lines
Created a system test for Modelfree4 with the OMP data.
This runs the palmer_omp.py system test script.
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r7670 | bugman | 2008-10-12 19:03:26 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the create() method. Deselected spins should be skipped.
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r7671 | bugman | 2008-10-12 19:22:42 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the test_palmer_omp() system test.
The PDB file has no models in it!
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r7672 | bugman | 2008-10-12 19:26:35 +0200 (Sun, 12 Oct 2008) | 5 lines
Created a truncated OMP PDB file with only NH vectors of the first 15
residues.
The molmol residue name syntax has also been fixed to allow Modelfree4 to
be happy.
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r7673 | bugman | 2008-10-12 19:28:06 +0200 (Sun, 12 Oct 2008) | 3 lines
The Modelfree4 system test using the OMP data now uses the truncated and
more standard PDB file.
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r7674 | bugman | 2008-10-12 19:35:56 +0200 (Sun, 12 Oct 2008) | 3 lines
Updated the checks of the test_palmer_omp() system test to be specific to
that test.
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r7675 | bugman | 2008-10-12 19:38:10 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the spin names in the test_palmer_omp() system test checks.
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r7676 | bugman | 2008-10-12 19:48:55 +0200 (Sun, 12 Oct 2008) | 3 lines
The spheroidal diffusion tensor from the mfout file is now read and loaded
into the relax data store.
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r7677 | bugman | 2008-10-12 19:59:03 +0200 (Sun, 12 Oct 2008) | 8 lines
Important bug fix!!
The theta angle of the spheroidal diffusion tensor was being improperly
wrapped between 0 and pi.
This was causing the glide reflection symmetry to be broken, hence the
tensor was incorrect. The
result would be longer optimisation times for the spheroid tensors and more
iterations than
necessary in the full_analysis.py script.
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r7678 | bugman | 2008-10-12 21:34:09 +0200 (Sun, 12 Oct 2008) | 3 lines
Fixes for the OpenDX code to handle mapping of the global parameter space
(diff tensor, etc.).
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r7679 | bugman | 2008-10-12 21:37:28 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the dx.execute() user function - the correct args now are used.
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r7680 | bugman | 2008-10-12 21:40:22 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the backend of the dx.execute() user function.
The file arg was at some point renamed to file_prefix. The code now uses
this name change.
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r7681 | bugman | 2008-10-12 22:00:14 +0200 (Sun, 12 Oct 2008) | 6 lines
Reverted r7677. This was a false alarm!
The command used was:
svn merge -r7677:7676 .
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r7682 | bugman | 2008-10-12 22:14:47 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the setting of the theta and phi diff tensor angles from the
Modelfree4 mfout file.
The angles need to be passed in in radian units.
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r7683 | bugman | 2008-10-12 22:15:26 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the theta and phi angle checks in the test_palmer_omp() system test.
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r7684 | bugman | 2008-10-12 22:23:16 +0200 (Sun, 12 Oct 2008) | 6 lines
Fix for bug #12437 (https://gna.org/bugs/?12437).
The problem was that the 'from_xml' and 'to_xml' methods needed to be
blacklisted to prevent them
from being restored from the pickled state.
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r7685 | semor | 2008-10-13 17:10:52 +0200 (Mon, 13 Oct 2008) | 3 lines
Fixed the name of the NMRView program.
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r7686 | semor | 2008-10-13 17:32:25 +0200 (Mon, 13 Oct 2008) | 5 lines
Added a system test for the reading of a Sparky peak list.
This will help find the problems specific to NMRView peak list support...
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r7687 | semor | 2008-10-13 17:37:17 +0200 (Mon, 13 Oct 2008) | 5 lines
Fixed a problem raised when the number 0 would be given as relaxation delay.
A delay of 0.0 is now given for the intensities associated with the Sparky
peak list.
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r7688 | semor | 2008-10-13 18:03:23 +0200 (Mon, 13 Oct 2008) | 3 lines
Added the function for the NMRView peak list header handling.
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r7689 | semor | 2008-10-13 19:44:02 +0200 (Mon, 13 Oct 2008) | 3 lines
Fixed the extraction of the residue number, nucleus name and heteronucleus
name.
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r7690 | semor | 2008-10-13 19:44:38 +0200 (Mon, 13 Oct 2008) | 3 lines
Fixed the column number for the intensity.
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r7691 | semor | 2008-10-13 20:24:28 +0200 (Mon, 13 Oct 2008) | 3 lines
Fixed the test for the setting of Sparky and NMRView intensities.
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r7692 | semor | 2008-10-13 20:47:19 +0200 (Mon, 13 Oct 2008) | 3 lines
Added the framework for a XEasy system test.
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r7693 | bugman | 2008-10-14 12:27:56 +0200 (Tue, 14 Oct 2008) | 3 lines
Modified the test_palmer_omp() system test to take into account the bugs
fixed in Modelfree 4.20.
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r7694 | semor | 2008-10-14 18:10:16 +0200 (Tue, 14 Oct 2008) | 7 lines
Added the support for when a nmrview peak list contains unassigned peaks.
These peaks have an assignment field as '{}' in the peak list and are now
excluded.
Complemented the peak list sample accordingly.
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r7695 | semor | 2008-10-14 18:50:59 +0200 (Tue, 14 Oct 2008) | 7 lines
Added the support of unassigned peaks in Sparky formatted peak lists.
The unassigned peak show up as '?-?'.
Thanks to Ryan Hoffman and his bug report (https://gna.org/bugs/?11913).
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r7696 | bugman | 2008-10-14 21:10:31 +0200 (Tue, 14 Oct 2008) | 3 lines
Added an XEasy peak list, with peak heights as volumes, into the test suite
data store.
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r7697 | semor | 2008-10-14 21:25:20 +0200 (Tue, 14 Oct 2008) | 7 lines
Corrected two typos.
These were discovered by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00041.html (message ID:
7f080ed10810141215r72940a18hc09456a02d3f69ce@xxxxxxxxxxxxxx)
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r7698 | bugman | 2008-10-14 22:06:17 +0200 (Tue, 14 Oct 2008) | 5 lines
Added a RelaxError to tell the user that the Modelfree4 version being used
is buggy.
It also tells them that they must upgrade!
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r7699 | bugman | 2008-10-14 22:42:18 +0200 (Tue, 14 Oct 2008) | 6 lines
The relaxation curve time point can now be an integer to allow the time of
'0'.
See the post at
https://mail.gna.org/public/relax-devel/2008-10/msg00040.html (Message-id:
<7f080ed10810141213s2211d36fre56906e0ae5903e2@xxxxxxxxxxxxxx>).
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r7700 | bugman | 2008-10-14 22:43:20 +0200 (Tue, 14 Oct 2008) | 3 lines
Made sure that the relaxation curve fitting time point is stored as a float.
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r7701 | semor | 2008-10-14 23:33:38 +0200 (Tue, 14 Oct 2008) | 3 lines
Corrected the formatting of a few lines...
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r7702 | semor | 2008-10-15 00:01:04 +0200 (Wed, 15 Oct 2008) | 5 lines
Continued the implementation of the XEasy support system test.
Much more work is needed, though.
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r7703 | semor | 2008-10-15 00:20:08 +0200 (Wed, 15 Oct 2008) | 3 lines
Grouped the three peak list support tests into a single one.
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r7704 | bugman | 2008-10-15 00:43:39 +0200 (Wed, 15 Oct 2008) | 7 lines
Modified the Modelfree4 system tests to work with the Portland C compiler
Linux version.
[... 262 lines stripped ...]
r7792 - in /branches/spectral_errors: ./ data/ generic_fns/ opendx/ prompt/ sample_scripts/ specific_fns/ specific_fns/model...