Author: bugman
Date: Mon Dec 20 16:42:29 2010
New Revision: 11919
URL: http://svn.gna.org/viewcvs/relax?rev=11919&view=rev
Log:
Merged revisions 11879,11886,11888,11890-11896,11900,11904-11915 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11879 | bugman | 2010-12-17 17:10:39 +0100 (Fri, 17 Dec 2010) | 3 lines
Added a check that the script ends in '*.py'.
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r11886 | bugman | 2010-12-17 19:59:11 +0100 (Fri, 17 Dec 2010) | 9 lines
Fix for bug #17343 (https://gna.org/bugs/?17343).
This bug was reported by Vitaly Vostri <vvostri att gmail dott com>, also
in the mailing list
message https://mail.gna.org/public/relax-users/2010-12/msg00005.html.
The 'CH2' and 'OT' atoms have been added to the internal PDB reader, for
those incomplete PDB files
in which the element column is missing.
........
r11888 | bugman | 2010-12-17 20:19:26 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for script execution - the extension check for '.py' was incorrect!
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r11890 | bugman | 2010-12-17 20:41:01 +0100 (Fri, 17 Dec 2010) | 6 lines
Added test data and a script for testing the reading of CCPN Analysis 2.1
sparky peak lists.
This is data from bug #17341 (https://gna.org/bugs/?17341) submitted by
Madeleine Strickland <M dot
Strickland att bristol dot ac dott uk>.
........
r11891 | bugman | 2010-12-17 20:51:17 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for bug #17344 (https://gna.org/bugs/index.php?17344), the broken
grace.view() user function.
This has been broken since January, and is released in relax 1.3.5, but no
one seems to have
noticed :S
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r11892 | bugman | 2010-12-17 20:51:48 +0100 (Fri, 17 Dec 2010) | 3 lines
The grace executable file is now set to '' in the CCPN analysis peak list
system test.
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r11893 | bugman | 2010-12-17 21:11:13 +0100 (Fri, 17 Dec 2010) | 5 lines
Implemented and activated the CCPN Analysis 2.1 peak list reading system
test.
This is to catch bug #17341 (https://gna.org/bugs/index.php?17341).
........
r11894 | bugman | 2010-12-17 22:59:29 +0100 (Fri, 17 Dec 2010) | 3 lines
Decreased the number of MC sims to speed up the CCPN Analysis peak list
reading system test.
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r11895 | bugman | 2010-12-17 22:59:53 +0100 (Fri, 17 Dec 2010) | 3 lines
Bug fix for the CCPN Analysis peak list system test.
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r11896 | bugman | 2010-12-17 23:37:16 +0100 (Fri, 17 Dec 2010) | 6 lines
Added support for CCPN Analysis 2.1 peak lists (exported in Sparky format).
This is a fix for bug #17341 (https://gna.org/bugs/index.php?17341)
reported by Madeleine Strickland
<M dott Strickland att bristol dot ac dot uk>.
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r11900 | bugman | 2010-12-19 15:43:54 +0100 (Sun, 19 Dec 2010) | 7 lines
Removed the 2 from CH2 in the atom list in the element determining function.
This is in response to Vitaly Vostrikov's <vvostri att gmail dott com>
message at Message-id:
<AANLkTimYA4H7=WbMwzgpxaTJ6_nArKu=ed9VNdXCSuDB@xxxxxxxxxxxxxx>,
https://mail.gna.org/public/relax-users/2010-12/msg00013.html.
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r11904 | bugman | 2010-12-20 14:05:59 +0100 (Mon, 20 Dec 2010) | 6 lines
Added a system test for reading relax 1.2.x version results files.
This is from Sebastian Morin's PSE-4 data, truncated, and is to catch the
bug of not being able to
handle simulations.
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r11905 | bugman | 2010-12-20 14:18:21 +0100 (Mon, 20 Dec 2010) | 5 lines
Fix for bug #17361 (https://gna.org/bugs/index.php?17361).
The chi2_sim structure should have been initialised to a list, not a
dictionary.
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r11906 | bugman | 2010-12-20 14:30:16 +0100 (Mon, 20 Dec 2010) | 6 lines
Another fix for bug #17361 (https://gna.org/bugs/index.php?17361) the
loading 1.2.x sim data.
This time the global structures were too large - the lists were being
appended to for each spin and
simulation, rather than only each simulation.
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r11907 | bugman | 2010-12-20 14:46:26 +0100 (Mon, 20 Dec 2010) | 3 lines
For the 1.2 results files, the model information is now being setup even if
None.
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r11908 | bugman | 2010-12-20 15:06:02 +0100 (Mon, 20 Dec 2010) | 3 lines
Bug fix for the relaxation data add_data_to_spin() function - missing data
was not properly eliminated.
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r11909 | bugman | 2010-12-20 15:37:26 +0100 (Mon, 20 Dec 2010) | 3 lines
Completed the test_read_results_1_2_pse() model-free system test for
reading relax 1.2.x results.
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r11910 | bugman | 2010-12-20 15:47:46 +0100 (Mon, 20 Dec 2010) | 5 lines
Last fix for bug #17361 (https://gna.org/bugs/index.php?17361) the loading
1.2.x sim data.
The frequency information is now correctly updated when data is missing.
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r11911 | bugman | 2010-12-20 16:02:00 +0100 (Mon, 20 Dec 2010) | 3 lines
Updated some test data for the unit tests.
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r11912 | bugman | 2010-12-20 16:15:19 +0100 (Mon, 20 Dec 2010) | 3 lines
Added a system test to check that relax save files cannot be loaded as
results files.
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r11913 | bugman | 2010-12-20 16:15:56 +0100 (Mon, 20 Dec 2010) | 3 lines
Added a check to make sure the relax save states can not be loaded by
results.read().
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r11914 | bugman | 2010-12-20 16:28:56 +0100 (Mon, 20 Dec 2010) | 6 lines
Reverted r11913 as this was completely wrong and broke the reading of
results files.
The command used was:
svn merge -r11913:11912 .
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r11915 | bugman | 2010-12-20 16:33:45 +0100 (Mon, 20 Dec 2010) | 17 lines
Reverted r11912 as this system test was useless and incorrect.
There is currently no way to see the difference between a save state and a
results file unless there
are multiple pipes.
The command used was:
svn merge -r11912:11911 .
.....
r11912 | bugman | 2010-12-20 16:15:19 +0100 (Mon, 20 Dec 2010) | 3 lines
Changed paths:
M /1.3/test_suite/system_tests/results.py
Added a system test to check that relax save files cannot be loaded as
results files.
.....
........
Added:
branches/multi_processor_merge/test_suite/shared_data/peak_lists/ccpn_analysis/
- copied from r11915,
1.3/test_suite/shared_data/peak_lists/ccpn_analysis/
branches/multi_processor_merge/test_suite/shared_data/results_files/pse_trunc.bz2
- copied unchanged from r11915,
1.3/test_suite/shared_data/results_files/pse_trunc.bz2
branches/multi_processor_merge/test_suite/system_tests/scripts/peak_lists/
- copied from r11915, 1.3/test_suite/system_tests/scripts/peak_lists/
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/generic_fns/relax_data.py
branches/multi_processor_merge/generic_fns/spectrum.py
branches/multi_processor_merge/generic_fns/structure/internal.py
branches/multi_processor_merge/prompt/grace.py
branches/multi_processor_merge/prompt/interpreter.py
branches/multi_processor_merge/specific_fns/model_free/results.py
branches/multi_processor_merge/test_suite/shared_data/saved_states/basic_single_pipe.bz2
branches/multi_processor_merge/test_suite/system_tests/model_free.py
branches/multi_processor_merge/test_suite/system_tests/peak_lists.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/relax_data.py?rev=11919&r1=11918&r2=11919&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=11919&r1=11918&r2=11919&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/internal.py?rev=11919&r1=11918&r2=11919&view=diff
Modified: branches/multi_processor_merge/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/grace.py?rev=11919&r1=11918&r2=11919&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=11919&r1=11918&r2=11919&view=diff
Modified: branches/multi_processor_merge/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/model_free/results.py?rev=11919&r1=11918&r2=11919&view=diff
Modified:
branches/multi_processor_merge/test_suite/shared_data/saved_states/basic_single_pipe.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/shared_data/saved_states/basic_single_pipe.bz2?rev=11919&r1=11918&r2=11919&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=11919&r1=11918&r2=11919&view=diff
Modified: branches/multi_processor_merge/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/peak_lists.py?rev=11919&r1=11918&r2=11919&view=diff
r11919 - in /branches/multi_processor_merge: ./ generic_fns/ generic_fns/structure/ prompt/ specific_fns/model_free/ test_su...