Author: bugman
Date: Sat Feb 19 15:12:38 2011
New Revision: 12585
URL: http://svn.gna.org/viewcvs/relax?rev=12585&view=rev
Log:
Merged revisions 11633,11638-11660 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
........
r11633 | bugman | 2010-10-06 18:55:05 +0200 (Wed, 06 Oct 2010) | 5 lines
Bug fix for the BMRB system tests.
The file paths were incorrect.
........
r11638 | bugman | 2010-10-15 17:53:49 +0200 (Fri, 15 Oct 2010) | 5 lines
Fixes for the BMRB system tests.
These tests were non-functional!
........
r11639 | bugman | 2010-10-15 18:05:22 +0200 (Fri, 15 Oct 2010) | 3 lines
Fixes for the file paths to sync with the 1.3 line.
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r11640 | bugman | 2010-10-15 18:05:59 +0200 (Fri, 15 Oct 2010) | 3 lines
Fix for all the BMRB related user functions - exec_info is now a private
variable.
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r11641 | bugman | 2010-10-19 15:33:49 +0200 (Tue, 19 Oct 2010) | 3 lines
Added checks and the RelaxNoModuleInstallError relax error to make sure
that bmrblib is installed.
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r11642 | bugman | 2010-10-19 20:05:32 +0200 (Tue, 19 Oct 2010) | 6 lines
The diffusion tensor saveframe is now being created in the BMRB submission
file.
This saveframe is not complete and contains no tensor information, as
bmrblib does not support this
yet.
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r11643 | bugman | 2010-10-20 20:04:43 +0200 (Wed, 20 Oct 2010) | 5 lines
Removed the v3.2 BMRB imports as these no longer exist.
There is no 3.2 version!
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r11644 | bugman | 2010-10-21 00:17:29 +0200 (Thu, 21 Oct 2010) | 3 lines
Removed the BMRB NMR-STAR v3.2 system test and started to add data checks
for the old and new pipes.
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r11645 | bugman | 2010-10-21 20:08:53 +0200 (Thu, 21 Oct 2010) | 6 lines
Advancements for the diffusion tensor support in the BMRB file.
All of the tensor data is now being written out, and a very incomplete
bmrb_read() function has been
added.
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r11646 | bugman | 2010-10-21 22:35:20 +0200 (Thu, 21 Oct 2010) | 3 lines
The diffusion tensor bmrb_read() function is now complete and the tensor is
being created.
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r11647 | bugman | 2010-10-21 23:42:05 +0200 (Thu, 21 Oct 2010) | 3 lines
The prolate diffusion tensors are now correctly created from the BMRB files.
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r11648 | bugman | 2010-10-22 00:42:54 +0200 (Fri, 22 Oct 2010) | 3 lines
The reading of entity information from the BMRB file is fixed.
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r11649 | bugman | 2010-10-22 01:30:29 +0200 (Fri, 22 Oct 2010) | 5 lines
Fixes for the citations BMRB writing.
The author structure is now split up before sending to the saveframe class.
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r11650 | bugman | 2010-10-22 11:33:46 +0200 (Fri, 22 Oct 2010) | 3 lines
The spectrometer frequency is now converted to MHz before being sent to
BMRBlib.
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r11651 | bugman | 2010-10-22 15:18:18 +0200 (Fri, 22 Oct 2010) | 3 lines
The saveframe description for the relax scripts now says that they are
relax scripts.
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r11652 | bugman | 2010-10-22 17:59:25 +0200 (Fri, 22 Oct 2010) | 3 lines
The relaxation data reading is functional again, matching the new design of
bmrblib.
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r11653 | bugman | 2010-10-22 19:21:54 +0200 (Fri, 22 Oct 2010) | 3 lines
The restoration of the data from BMRB files into data pipes is now fully
tested in the system tests.
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r11654 | bugman | 2010-10-22 19:53:19 +0200 (Fri, 22 Oct 2010) | 3 lines
Caught when no diffusion tensor data is yielded by the bmrblib loop()
method.
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r11655 | bugman | 2010-10-22 22:11:38 +0200 (Fri, 22 Oct 2010) | 3 lines
A few system and unit test fixes broken by recent rearrangements of the
diffusion tensor code.
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r11656 | bugman | 2010-10-22 23:10:00 +0200 (Fri, 22 Oct 2010) | 6 lines
Fix for the test_read() unit test of generic_fns.relax_data.read().
The relaxation data structures are now handled differently in this branch
and all data structures
have the same from for all spins, even if data is missing.
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r11657 | bugman | 2010-10-25 09:56:03 +0200 (Mon, 25 Oct 2010) | 3 lines
Restored the reversal of the rotation matrix when determining Euler angles
for a tensor in the PDB frame.
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r11658 | bugman | 2010-10-25 10:04:58 +0200 (Mon, 25 Oct 2010) | 5 lines
Shifted the core of the model-free _select_model() method into _model_map().
This allows other parts of the code to translate model names to model-free
equations and parameters.
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r11659 | bugman | 2010-10-25 10:07:51 +0200 (Mon, 25 Oct 2010) | 5 lines
Removed the model-free and CSA info from the blacklisted spin variables.
This is to test the implementation of model-free and CSA BMRB saveframe
reading.
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r11660 | bugman | 2010-10-25 10:08:53 +0200 (Mon, 25 Oct 2010) | 3 lines
Implemented the reading of model-free and CSA BMRB saveframes from NMR-STAR
files.
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Modified:
1.3/ (props changed)
1.3/generic_fns/bmrb.py
1.3/generic_fns/diffusion_tensor.py
1.3/generic_fns/exp_info.py
1.3/generic_fns/mol_res_spin.py
1.3/generic_fns/relax_data.py
1.3/prompt/bmrb.py
1.3/prompt/molecule.py
1.3/prompt/relax_data.py
1.3/prompt/spin.py
1.3/relax_errors.py
1.3/specific_fns/model_free/bmrb.py
1.3/specific_fns/model_free/main.py
1.3/test_suite/system_tests/angles.py
1.3/test_suite/system_tests/bmrb.py
1.3/test_suite/system_tests/scripts/bmrb_rw.py
1.3/test_suite/unit_tests/diffusion_tensor_testing_base.py
1.3/test_suite/unit_tests/relax_data_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/exp_info.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/relax_data.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_errors.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/bmrb.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/angles.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/bmrb.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/bmrb_rw.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/test_suite/unit_tests/diffusion_tensor_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/diffusion_tensor_testing_base.py?rev=12585&r1=12584&r2=12585&view=diff
Modified: 1.3/test_suite/unit_tests/relax_data_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/relax_data_testing_base.py?rev=12585&r1=12584&r2=12585&view=diff
r12585 - in /1.3: ./ generic_fns/ prompt/ specific_fns/model_free/ test_suite/system_tests/ test_suite/system_tests/scripts/...