Author: bugman
Date: Tue Oct 9 01:01:34 2012
New Revision: 17777
URL: http://svn.gna.org/viewcvs/relax?rev=17777&view=rev
Log:
Merged revisions 17739-17774 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/tensor_data
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r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines
The diffusion tensor data structure has been completely converted into a
read-only structure.
The __setattr__() method now will always raise a RelaxError, and the
diffusion tensor simulation
data structure objects __setitem__() method will raise the same error.
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r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the initialisation of the diffusion tensor data structure, now that
it is read-only.
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r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines
The new diffusion tensor fixed() method has been created to allow the fixed
flag to be changed.
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r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines
Created the diffusion tensor data structure type() method for setting the
tensor type.
This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of
relax, as the structure is
now read only.
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r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines
Renamed the diffusion tensor data structure type() method to set_type().
This is because the type is stored as the 'type' object, clashing with the
method name.
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r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines
Converted the old diffusion tensor __setattr__() method into the set()
method.
This is the only way in which diffusion tensor parameters, errors and
simulations can be set.
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r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines
Improvements to the diffusion tensor set() method.
The parameters, errors and simulations are now properly differentiated and
stored.
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r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines
A number of private diffusion tensor objects and methods have switched to
the single leading '_' format.
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r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines
Removed all the unused imports from specific_fns.model_free.main.
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r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines
Redesigned how diffusion tensor simulation structures are handled.
The design is now much cleaner and works with all Python versions.
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r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines
Modified the setUp() method for the diffusion tensor system tests to use
the new design.
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r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines
The model-free specific analysis _disassemble_param_vector() method now
uses the new diffusion tensor design.
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r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the diffusion tensor __deepcopy__() replacement method for the new
design.
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r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines
The setting of list values for the DiffTensorSimList object now works
correctly.
The private _set() method now works correctly by calling the base class
method, and the normal
setting of diffusion tensor simulation values produces a RelaxError.
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r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the Diffusion_tensor.test_copy system test - the simulation
parameters are now read-only.
Instead, the diffusion tensor set() method needs to be called.
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r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines
Converted the diffusion tensor data structure from_xml() method to the new
tensor design.
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r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the diffusion tensor to_xml() method for the new design.
For some reason the methods of the Element class are no longer blacklisted.
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r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the model-free specific analysis duplicate_data() method for the
new design.
The diffusion tensor __mod_attr__ object is now called _mod_attr.
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r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines
Renamed the diffusion tensor fixed() method to set_fixed() to avoid
clashing with the 'fixed' object.
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r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines
The fix user function now uses the diffusion tensor set_fixed() method.
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r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines
The diffusion tensor bmrb_read() function now uses the set_fixed() method
instead of fixed().
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r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines
Converted the palmer.extract user function to use the new diffusion tensor
design.
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r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the XML output of the diffusion tensor - only the modifiable
parameters are output.
This was the previous behaviour and is needed for the test suite to pass.
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r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the fixing of parameters in the model-free analyses.
The diffusion tensor set_fixed() method is now used.
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r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines
Another fix for the diffusion_tensor.init user function - it was not
completely converted.
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r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the setup of the model-free Monte Carlo simulations for the new
diffusion tensor design.
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r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the setting of the diffusion tensor parameter errors in the
model-free specific analysis code.
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r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines
Another fix for the fold_angles() diffusion tensor function - again an
incomplete design conversion.
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r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the reading of relax 1.2 model-free results files for the diffusion
tensor structure redesign.
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r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines
Fix for the reading of model-free results files from relax 1.2 when
simulation data is missing.
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r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines
Updated all of the diffusion tensor unit tests to the new design.
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r17770 | bugman | 2012-10-08 22:36:00 +0200 (Mon, 08 Oct 2012) | 3 lines
Cleaned up the docstring of the diffusion tensor data object __setattr__()
method.
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r17771 | bugman | 2012-10-08 22:36:47 +0200 (Mon, 08 Oct 2012) | 3 lines
Removed the now unused _update_sim_append() method from the diffusion
tensor data structure.
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r17772 | bugman | 2012-10-08 22:38:18 +0200 (Mon, 08 Oct 2012) | 3 lines
Deleted the now unused _update_sim_set() method of the diffusion tensor
data structure.
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r17773 | bugman | 2012-10-08 22:49:38 +0200 (Mon, 08 Oct 2012) | 3 lines
Small clean ups of the diffusion tensor data structure code.
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r17774 | bugman | 2012-10-09 00:24:34 +0200 (Tue, 09 Oct 2012) | 7 lines
Mass conversion of the alignment tensor data structures to the same new
design as the diffusion tensor.
This large set of changes matches all of those revisions for the diffusion
tensor already committed in
this branch. The alignment tensor data structures are now read only, and
can only be modified via the
set() method. This is a much simplified design which works on all Python
versions.
........
Modified:
trunk/ (props changed)
trunk/data/align_tensor.py
trunk/data/diff_tensor.py
trunk/data/relax_xml.py
trunk/generic_fns/align_tensor.py
trunk/generic_fns/diffusion_tensor.py
trunk/generic_fns/fix.py
trunk/generic_fns/palmer.py
trunk/specific_fns/frame_order.py
trunk/specific_fns/model_free/main.py
trunk/specific_fns/model_free/mf_minimise.py
trunk/specific_fns/model_free/results.py
trunk/specific_fns/n_state_model.py
trunk/test_suite/system_tests/align_tensor.py
trunk/test_suite/system_tests/diffusion_tensor.py
trunk/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
trunk/test_suite/unit_tests/_data/test_align_tensor.py
trunk/test_suite/unit_tests/_data/test_diff_tensor.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/data/align_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/data/diff_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/data/relax_xml.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/data/relax_xml.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/align_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/diffusion_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/generic_fns/fix.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/fix.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/palmer.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/main.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/mf_minimise.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/results.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/n_state_model.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/align_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/diffusion_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified:
trunk/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/test_suite/unit_tests/_data/test_align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_data/test_align_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
Modified: trunk/test_suite/unit_tests/_data/test_diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_data/test_diff_tensor.py?rev=17777&r1=17776&r2=17777&view=diff
r17777 - in /trunk: ./ data/ generic_fns/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/ test_suite/system_...