Author: bugman
Date: Sat Feb 19 14:52:26 2011
New Revision: 12582
URL: http://svn.gna.org/viewcvs/relax?rev=12582&view=rev
Log:
Merged revisions 9274,9442,9445,9455,9661-9695,9697-9699,9701-9703,9705 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
........
r9274 | bugman | 2009-07-22 15:54:49 +0200 (Wed, 22 Jul 2009) | 5 lines
Created the bmrblib.kinetics.general_relaxation module.
Much work is still to be done.
........
r9442 | bugman | 2009-09-03 14:29:19 +0200 (Thu, 03 Sep 2009) | 17 lines
Updates for Python3k.
The command used was:
2to3 -w \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
This is from the docs/2to3_checklist document. One print statement change
in pystarlib/TagTable.py
had to be manually fixed afterwards, as the end arg to the print statement
does not exist in all
python 2.x versions.
........
r9445 | bugman | 2009-09-03 14:41:00 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the specific_fns.__all__ list.
........
r9455 | bugman | 2009-09-03 15:24:48 +0200 (Thu, 03 Sep 2009) | 19 lines
More updates for Python3k.
The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
This is from the docs/2to3_checklist document.
........
r9661 | bugman | 2009-10-08 17:44:25 +0200 (Thu, 08 Oct 2009) | 3 lines
Bug fix for the Relaxation_v3_1.__init__() method - incorrect variable name.
........
r9662 | bugman | 2009-10-08 17:46:22 +0200 (Thu, 08 Oct 2009) | 3 lines
More variable name bug fixes.
........
r9663 | bugman | 2009-10-08 17:48:49 +0200 (Thu, 08 Oct 2009) | 5 lines
Split the Relaxation_v3_1 class into Relaxation_v3_2.
The general relaxation saveframe category is not in v3.1!
........
r9664 | bugman | 2009-10-08 17:49:31 +0200 (Thu, 08 Oct 2009) | 3 lines
Fixed the inheritance of Relaxation_v3_2.
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r9665 | bugman | 2009-10-08 17:51:22 +0200 (Thu, 08 Oct 2009) | 3 lines
Fixes for the Relaxation_v3_1 saveframe class. This should set up all the
v3.1 relaxation classes.
........
r9666 | bugman | 2009-10-08 18:05:53 +0200 (Thu, 08 Oct 2009) | 5 lines
Added better versioning support to be able to switch to NMR-STAR v3.2 in
the future.
This will be easier for completing the general relaxation saveframe without
breakage.
........
r9667 | bugman | 2009-10-08 18:45:55 +0200 (Thu, 08 Oct 2009) | 5 lines
Wrote add() methods for the Relaxation_v3_1 and Relaxation_v3_2 classes.
This defined a stable API abstracting the saveframe structure from the user
of bmrblib.
........
r9668 | bugman | 2009-10-08 18:47:22 +0200 (Thu, 08 Oct 2009) | 3 lines
Each Relaxation_v3_* class calls the base class __init__() method.
........
r9669 | bugman | 2009-10-08 18:50:04 +0200 (Thu, 08 Oct 2009) | 5 lines
Clean up of the relaxation data bmrb_write() method.
The abstracted bmrblib API is now being called for all relaxation data.
........
r9670 | bugman | 2009-10-08 18:51:35 +0200 (Thu, 08 Oct 2009) | 3 lines
Fixes for the calls to the base class __init__() methods.
........
r9671 | bugman | 2009-10-08 18:52:36 +0200 (Thu, 08 Oct 2009) | 3 lines
Removed the initialisation of the non-existent v3.0 relaxation saveframes.
........
r9672 | bugman | 2009-10-08 18:56:37 +0200 (Thu, 08 Oct 2009) | 3 lines
More fixes for the base class __init__() calling, and removed the placement
of datanode into self.
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r9673 | bugman | 2009-10-08 18:58:44 +0200 (Thu, 08 Oct 2009) | 3 lines
Removed the NMR-STAR version arg to the data specific bmrb_write() methods.
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r9674 | bugman | 2009-10-08 18:59:44 +0200 (Thu, 08 Oct 2009) | 3 lines
Fixes for the incorrectly named object 'star' (should have been 'self'!)
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r9675 | bugman | 2009-10-08 19:02:25 +0200 (Thu, 08 Oct 2009) | 5 lines
Changes to generic_fns.relax_data.bmrb_read() for an abstracted bmrblib API.
This part of the API doesn't exist yet.
........
r9676 | bugman | 2009-10-08 19:04:05 +0200 (Thu, 08 Oct 2009) | 3 lines
Fix for bmrb_read(). The object is called 'star.relaxation', not
'star.relaxation_data'.
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r9677 | bugman | 2009-10-08 19:05:03 +0200 (Thu, 08 Oct 2009) | 3 lines
Removed a useless, now abstracted loop over the relaxation data types from
bmrb_read().
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r9678 | bugman | 2009-10-08 19:13:22 +0200 (Thu, 08 Oct 2009) | 5 lines
Wrote the loop() method for the abstracted relaxation data bmrblib API.
This loops over and returns all relaxation data, regardless of saveframe.
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r9679 | bugman | 2009-10-08 19:14:49 +0200 (Thu, 08 Oct 2009) | 3 lines
Added a version 3.2 specific loop() method for the general relaxation
saveframe.
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r9680 | bugman | 2009-10-09 12:01:55 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
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r9681 | bugman | 2009-10-09 12:11:09 +0200 (Fri, 09 Oct 2009) | 3 lines
The saveframe objects are no longer private. This was causing major bugs!
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r9682 | bugman | 2009-10-09 12:12:16 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
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r9683 | bugman | 2009-10-09 12:23:47 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the BMRB system tests to check versions 3.0, 3.1, and 3.2 of the
NMR-STAR definition.
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r9684 | bugman | 2009-10-09 12:44:10 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
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r9685 | bugman | 2009-10-09 12:44:59 +0200 (Fri, 09 Oct 2009) | 3 lines
Redesigned pack_data() to handle sequence generation.
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r9686 | bugman | 2009-10-09 12:50:52 +0200 (Fri, 09 Oct 2009) | 3 lines
Changed the NMR-STAR version number in the script (for stand alone testing).
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r9687 | bugman | 2009-10-09 13:00:28 +0200 (Fri, 09 Oct 2009) | 3 lines
Significant updates to the BMRB user function module, including the
addition of the version arg.
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r9688 | bugman | 2009-10-09 13:02:37 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the BMRB read/write system test to set the NMR-STAR dictionary
version.
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r9689 | bugman | 2009-10-09 13:10:03 +0200 (Fri, 09 Oct 2009) | 3 lines
A number of changes to create the infrastructure for v3.0 and lower of the
NMR-STAR dictionary format.
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r9690 | bugman | 2009-10-09 13:11:15 +0200 (Fri, 09 Oct 2009) | 5 lines
Bug fix for the non-version specific NMR-STAR dictionary.
The CSA saveframe was incorrectly setup.
........
r9691 | bugman | 2009-10-09 13:15:43 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the missing 'ChiSquaredVal' to the tag_names structure for the base
class.
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r9692 | bugman | 2009-10-09 13:24:34 +0200 (Fri, 09 Oct 2009) | 5 lines
Introduced the version arg to the bmrb.read() user function.
This is mainly useful for debugging.
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r9693 | bugman | 2009-10-09 13:25:31 +0200 (Fri, 09 Oct 2009) | 5 lines
Modified the BMRB read/write system test to use the bmrb.read() version arg.
Also reverted the default version number to 3.1.
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r9694 | bugman | 2009-10-09 13:29:58 +0200 (Fri, 09 Oct 2009) | 5 lines
Fix for the NMR_STAR_v3_2 class set up.
This should have been using Relaxation_v3_2.
........
r9695 | bugman | 2009-10-09 13:39:58 +0200 (Fri, 09 Oct 2009) | 6 lines
Shifted pystarlib into bmrblib.
The pystarlib software is only used by bmrblib. This also prepares for
bmrblib to be spun off as
a stand alone project.
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r9697 | bugman | 2009-10-09 15:48:19 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
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r9698 | bugman | 2009-10-09 15:49:42 +0200 (Fri, 09 Oct 2009) | 5 lines
Reworked the entire GeneralRelaxation saveframe code.
Now a rudimentary NMR-STAR v3.2 formatted file is able to be produced and
read back in.
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r9699 | bugman | 2009-10-09 16:15:00 +0200 (Fri, 09 Oct 2009) | 3 lines
Updated the GeneralRelaxation saveframe to be more in the NMR-STAR v3.1
style.
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r9701 | bugman | 2009-10-09 18:15:15 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the translate() method to handle not doing anything.
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r9702 | bugman | 2009-10-09 18:32:18 +0200 (Fri, 09 Oct 2009) | 5 lines
The software saveframe is now being created.
This information does not need to be read from the BMRB file.
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r9703 | bugman | 2009-10-09 18:38:35 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the missing Task tag to the Software saveframe.
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r9705 | bugman | 2009-10-09 18:45:26 +0200 (Fri, 09 Oct 2009) | 3 lines
The SVN repository version number is now sent into the Software saveframe.
........
Added:
1.3/bmrblib/experimental_details/software.py
- copied unchanged from r9703,
branches/bmrb/bmrblib/experimental_details/software.py
1.3/bmrblib/kinetics/general_relaxation.py
- copied, changed from r9274,
branches/bmrb/bmrblib/kinetics/general_relaxation.py
1.3/bmrblib/nmr_star_dict_v3_2.py
- copied unchanged from r9703,
branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
1.3/bmrblib/pystarlib/
- copied from r9703, branches/bmrb/bmrblib/pystarlib/
1.3/generic_fns/bmrb_saveframes.py
- copied, changed from r9703,
branches/bmrb/generic_fns/bmrb_saveframes.py
Removed:
1.3/pystarlib/
Modified:
1.3/ (props changed)
1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py
1.3/bmrblib/assembly_supercategory/entity.py
1.3/bmrblib/base_classes.py
1.3/bmrblib/kinetics/heteronucl_NOEs.py
1.3/bmrblib/kinetics/heteronucl_NOEs_v3_1.py
1.3/bmrblib/kinetics/heteronucl_T1_relaxation.py
1.3/bmrblib/kinetics/heteronucl_T2_relaxation.py
1.3/bmrblib/kinetics/relaxation.py
1.3/bmrblib/misc.py
1.3/bmrblib/nmr_star_dict.py
1.3/bmrblib/nmr_star_dict_v3_1.py
1.3/bmrblib/thermodynamics/order_parameters.py
1.3/generic_fns/bmrb.py
1.3/generic_fns/mol_res_spin.py
1.3/generic_fns/relax_data.py
1.3/prompt/bmrb.py
1.3/specific_fns/model_free/__init__.py
1.3/specific_fns/model_free/bmrb.py
1.3/test_suite/system_tests/bmrb.py
1.3/test_suite/system_tests/scripts/bmrb_rw.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/assembly_supercategory/entity.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/assembly_supercategory/entity.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/base_classes.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/base_classes.py?rev=12582&r1=12581&r2=12582&view=diff
Copied: 1.3/bmrblib/kinetics/general_relaxation.py (from r9274,
branches/bmrb/bmrblib/kinetics/general_relaxation.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/general_relaxation.py?p2=1.3/bmrblib/kinetics/general_relaxation.py&p1=branches/bmrb/bmrblib/kinetics/general_relaxation.py&r1=9274&r2=12582&rev=12582&view=diff
Modified: 1.3/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/heteronucl_NOEs.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/kinetics/heteronucl_NOEs_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/heteronucl_NOEs_v3_1.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/kinetics/heteronucl_T1_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/heteronucl_T1_relaxation.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/kinetics/heteronucl_T2_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/heteronucl_T2_relaxation.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/kinetics/relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/relaxation.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/misc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/misc.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/nmr_star_dict.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/nmr_star_dict_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/nmr_star_dict_v3_1.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/thermodynamics/order_parameters.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12582&r1=12581&r2=12582&view=diff
Copied: 1.3/generic_fns/bmrb_saveframes.py (from r9703,
branches/bmrb/generic_fns/bmrb_saveframes.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb_saveframes.py?p2=1.3/generic_fns/bmrb_saveframes.py&p1=branches/bmrb/generic_fns/bmrb_saveframes.py&r1=9703&r2=12582&rev=12582&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=12582&r1=12581&r2=12582&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=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12582&r1=12581&r2=12582&view=diff
Modified: 1.3/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/__init__.py?rev=12582&r1=12581&r2=12582&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=12582&r1=12581&r2=12582&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=12582&r1=12581&r2=12582&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=12582&r1=12581&r2=12582&view=diff
r12582 - in /1.3: ./ bmrblib/ bmrblib/NMR_parameters/ bmrblib/assembly_supercategory/ bmrblib/experimental_details/ bmrblib/...