Author: bugman
Date: Tue Nov 23 11:33:07 2010
New Revision: 11697
URL: http://svn.gna.org/viewcvs/relax?rev=11697&view=rev
Log:
Merged revisions
11552,11565,11567,11571-11572,11574,11587-11588,11591,11594,11597,11607,11609,11618,11627-11628,11631,11661,11663-11685,11688
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11552 | bugman | 2010-09-14 16:34:11 +0200 (Tue, 14 Sep 2010) | 3 lines
Created a directory for relax graphics. The first files here are the relax
logo and icons.
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r11565 | bugman | 2010-09-15 19:36:15 +0200 (Wed, 15 Sep 2010) | 3 lines
The Ref.cite_html() method can now handle missing data.
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r11567 | bugman | 2010-09-15 19:43:22 +0200 (Wed, 15 Sep 2010) | 3 lines
Ref.cite_html() no longer adds the DOI web address in front of normal web
links!
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r11571 | bugman | 2010-09-16 09:59:26 +0200 (Thu, 16 Sep 2010) | 3 lines
Initialised the reference for the relax GUI paper.
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r11572 | bugman | 2010-09-16 10:00:23 +0200 (Thu, 16 Sep 2010) | 3 lines
Fix for the Bieri et al. ref.
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r11574 | bugman | 2010-09-16 10:06:47 +0200 (Thu, 16 Sep 2010) | 3 lines
Citations now include the status if not 'published'.
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r11587 | bugman | 2010-09-16 18:20:20 +0200 (Thu, 16 Sep 2010) | 3 lines
Renamed the results_folder arg to results_dir in the NOE auto-analysis, and
rearranged the args.
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r11588 | bugman | 2010-09-16 18:22:30 +0200 (Thu, 16 Sep 2010) | 5 lines
Added a system test for the dauvergne_protocol auto-analysis code.
The test is not yet functional.
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r11591 | bugman | 2010-09-16 19:17:33 +0200 (Thu, 16 Sep 2010) | 6 lines
Modified the specific code API to remove a number of references to spin_id.
Some analysis types do not work on spins, so the spin_id args are being
replaced by data_id to
identify the data requested. For most methods, this will be the spin_id.
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r11594 | bugman | 2010-09-17 10:06:20 +0200 (Fri, 17 Sep 2010) | 3 lines
Shifted the debug and pedantic flags into the __main__ namespace for better
access from other modules.
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r11597 | bugman | 2010-09-17 10:30:22 +0200 (Fri, 17 Sep 2010) | 3 lines
Some fixes for the NOE auto-analysis.
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r11607 | bugman | 2010-09-17 15:57:10 +0200 (Fri, 17 Sep 2010) | 3 lines
Fix for the NOE auto-analysis - the spins are now named to the value of the
'heteronuc' arg.
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r11609 | bugman | 2010-09-17 18:02:20 +0200 (Fri, 17 Sep 2010) | 5 lines
Shifted the NOE specific analysis code into its own package.
This is in preparation for splitting up the module and adding new modules.
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r11618 | bugman | 2010-09-29 15:26:50 +0200 (Wed, 29 Sep 2010) | 3 lines
Added a catch for no data in the error analysis by replicated spectra.
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r11627 | bugman | 2010-10-06 12:46:39 +0200 (Wed, 06 Oct 2010) | 3 lines
Added some checks to the dauvergne_protocol mf analysis for the required
previously optimised results.
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r11628 | bugman | 2010-10-06 12:47:20 +0200 (Wed, 06 Oct 2010) | 3 lines
pipe.delete() without args will now delete all data pipes.
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r11631 | bugman | 2010-10-06 18:52:13 +0200 (Wed, 06 Oct 2010) | 3 lines
Missing import of __main__.
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r11661 | bugman | 2010-10-25 10:10:42 +0200 (Mon, 25 Oct 2010) | 3 lines
Added 6 system tests for the spheroidal diffusion tensor.
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r11663 | bugman | 2010-11-16 18:07:43 +0100 (Tue, 16 Nov 2010) | 5 lines
Fix for the relatively unused calc_tensor_diag() for oblate tensors.
The eigenvalues were incorrectly ordered for oblate spheroids.
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r11664 | bugman | 2010-11-17 15:04:52 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for a failing diffusion tensor unit test.
This was testing an unused element of the diffusion tensor data structure
incorrectly.
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r11665 | bugman | 2010-11-17 16:03:54 +0100 (Wed, 17 Nov 2010) | 5 lines
The rotation matrix for the spheroidal diffusion tensors is now correctly
generated.
Again this is a fix for currently unused code (it will be used for BMRB
support though).
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r11666 | bugman | 2010-11-17 16:15:35 +0100 (Wed, 17 Nov 2010) | 5 lines
Fixes for the diffusion tensor system tests.
The spheroidal tensors are now correctly checked.
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r11667 | bugman | 2010-11-17 16:15:57 +0100 (Wed, 17 Nov 2010) | 3 lines
Removed some debugging code.
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r11668 | bugman | 2010-11-17 16:45:32 +0100 (Wed, 17 Nov 2010) | 3 lines
Some rotation matrix check fixes for the diffusion tensor unit tests.
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r11669 | bugman | 2010-11-17 16:48:20 +0100 (Wed, 17 Nov 2010) | 3 lines
Dpar_unit is no longer passed into calc_rotation() for spheroidal
diffusion, as it is not needed.
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r11670 | bugman | 2010-11-17 17:01:24 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the updating of the rotation and tensor MC sim objects for the
spheroidal diffusion.
This problem was only recently introduced.
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r11671 | bugman | 2010-11-17 17:05:46 +0100 (Wed, 17 Nov 2010) | 3 lines
Similar fix as in r11670, but for setting MC sim data.
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r11672 | bugman | 2010-11-17 17:18:29 +0100 (Wed, 17 Nov 2010) | 3 lines
Some more fixes for handling the diffusion tensor data structure
'spheroid_type' variable properly.
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r11673 | bugman | 2010-11-17 19:14:57 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the creation of the oblate spheroid geometric object PDB file.
The x and z axes need to be swapped now for the oblate tensor.
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r11674 | bugman | 2010-11-17 19:23:43 +0100 (Wed, 17 Nov 2010) | 6 lines
For some reason, the diffusion tensor PDB file for the oblate tensor now
has a slight rotation.
This rotation is about the unique axis of the tensor, so this gives a
different PDB file, but the
representation is the same.
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r11675 | bugman | 2010-11-18 13:42:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Some small cosmetic changes to the spheroid diffusion tensor system tests.
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r11676 | bugman | 2010-11-18 13:51:23 +0100 (Thu, 18 Nov 2010) | 3 lines
The hardcoded variables in get_spheroid() are now keyword args.
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r11677 | bugman | 2010-11-18 14:03:01 +0100 (Thu, 18 Nov 2010) | 3 lines
Added 6 system tests for the initialisation of the prolate spheroid
diffusion tensor.
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r11678 | bugman | 2010-11-18 16:52:49 +0100 (Thu, 18 Nov 2010) | 6 lines
Fix for the spheroid diffusion tensors for a recently introduced bug.
The oblate and prolate check was failing as the 'spheroid_type' variable
was set to None after a
call to diffusion_tensor.init(). 'spheroid_type' is now automatically
updated if Da is changed.
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r11679 | bugman | 2010-11-18 17:08:23 +0100 (Thu, 18 Nov 2010) | 5 lines
The tensor is first twisted before rotating to PDB frame in the spheroid
diffusion tensor system tests.
The twisting rotation was not being correctly performed.
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r11680 | bugman | 2010-11-18 17:25:40 +0100 (Thu, 18 Nov 2010) | 5 lines
Renamed test_init_spheroid_as_ellipsoid() to
test_init_prolate_spheroid_as_ellipsoid().
The print outs of the system test have been slightly improved.
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r11681 | bugman | 2010-11-18 17:38:09 +0100 (Thu, 18 Nov 2010) | 3 lines
Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid
checks into a separate method.
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r11682 | bugman | 2010-11-18 18:20:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Added a new system test test_init_oblate_spheroid_as_ellipsoid().
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r11683 | bugman | 2010-11-18 18:25:51 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2
eigenvalues are the same.
This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into
diffusion_tensor.init().
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r11684 | bugman | 2010-11-18 18:29:29 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy,
Dxz, Dyz).
The eigenvalues were being converted to ints!
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r11685 | bugman | 2010-11-18 18:53:39 +0100 (Thu, 18 Nov 2010) | 6 lines
Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal
diffusion parameters.
The numpy eigenvalue decomposition has been replaced by SVD as the
eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The
test suite now passes fully.
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r11688 | bugman | 2010-11-19 14:46:34 +0100 (Fri, 19 Nov 2010) | 3 lines
Improved the diffusion tensor print out.
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Added:
branches/multi_processor_merge/graphics/
- copied from r11688, 1.3/graphics/
branches/multi_processor_merge/specific_fns/noe/
- copied from r11688, 1.3/specific_fns/noe/
branches/multi_processor_merge/test_suite/shared_data/relaxation_data/13259_bug_reproducing_data/
- copied from r11688,
1.3/test_suite/shared_data/relaxation_data/13259_bug_reproducing_data/
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/full_analysis_trunc.py
- copied unchanged from r11688,
1.3/test_suite/system_tests/scripts/model_free/full_analysis_trunc.py
Removed:
branches/multi_processor_merge/specific_fns/noe.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/auto_analyses/dauvergne_protocol.py
branches/multi_processor_merge/auto_analyses/noe.py
branches/multi_processor_merge/data/data_classes.py
branches/multi_processor_merge/data/diff_tensor.py
branches/multi_processor_merge/generic_fns/diffusion_tensor.py
branches/multi_processor_merge/generic_fns/pipes.py
branches/multi_processor_merge/generic_fns/spectrum.py
branches/multi_processor_merge/generic_fns/structure/geometric.py
branches/multi_processor_merge/info.py
branches/multi_processor_merge/prompt/interpreter.py
branches/multi_processor_merge/relax
branches/multi_processor_merge/relax_errors.py
branches/multi_processor_merge/relax_warnings.py
branches/multi_processor_merge/specific_fns/api_base.py
branches/multi_processor_merge/specific_fns/api_common.py
branches/multi_processor_merge/specific_fns/consistency_tests.py
branches/multi_processor_merge/specific_fns/frame_order.py
branches/multi_processor_merge/specific_fns/jw_mapping.py
branches/multi_processor_merge/specific_fns/model_free/main.py
branches/multi_processor_merge/specific_fns/relax_fit.py
branches/multi_processor_merge/test_suite/shared_data/structures/diff_tensors/spheroid.pdb
branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py
branches/multi_processor_merge/test_suite/system_tests/model_free.py
branches/multi_processor_merge/test_suite/unit_tests/_data/test_diff_tensor.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/auto_analyses/dauvergne_protocol.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/auto_analyses/noe.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/data_classes.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/diff_tensor.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/diffusion_tensor.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/pipes.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/spectrum.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/geometric.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/info.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/interpreter.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax_errors.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/relax_warnings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax_warnings.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/api_base.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/api_common.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/consistency_tests.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/frame_order.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/jw_mapping.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/model_free/main.py?rev=11697&r1=11696&r2=11697&view=diff
Removed: branches/multi_processor_merge/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/noe.py?rev=11696&view=auto
Modified: branches/multi_processor_merge/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/relax_fit.py?rev=11697&r1=11696&r2=11697&view=diff
Modified:
branches/multi_processor_merge/test_suite/shared_data/structures/diff_tensors/spheroid.pdb
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/shared_data/structures/diff_tensors/spheroid.pdb?rev=11697&r1=11696&r2=11697&view=diff
Modified:
branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py?rev=11697&r1=11696&r2=11697&view=diff
Modified: branches/multi_processor_merge/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/model_free.py?rev=11697&r1=11696&r2=11697&view=diff
Modified:
branches/multi_processor_merge/test_suite/unit_tests/_data/test_diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_data/test_diff_tensor.py?rev=11697&r1=11696&r2=11697&view=diff
r11697 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ graphics/ prompt/ s...