Author: bugman
Date: Sat Feb 19 15:08:38 2011
New Revision: 12584
URL: http://svn.gna.org/viewcvs/relax?rev=12584&view=rev
Log:
Merged revisions
9795-9798,9801-9811,9813-9828,9833,9835-9862,9865-9869,9990,10116,10874,10876-10877,10880,10885,11264
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
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r9795 | bugman | 2009-10-27 14:07:24 +0100 (Tue, 27 Oct 2009) | 3 lines
Removed the artificial constraint for there being only 1 entity allowed.
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r9796 | bugman | 2009-10-27 14:41:42 +0100 (Tue, 27 Oct 2009) | 3 lines
Relaxation values and errors of ? are now handled and converted to None.
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r9797 | bugman | 2009-10-27 14:42:19 +0100 (Tue, 27 Oct 2009) | 3 lines
Missing relaxation data is now handled when creating the BMRB file.
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r9798 | bugman | 2009-10-27 15:12:27 +0100 (Tue, 27 Oct 2009) | 3 lines
The entity ID tag is now present in the general relaxation saveframe.
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r9801 | bugman | 2009-10-27 15:29:50 +0100 (Tue, 27 Oct 2009) | 3 lines
The translate function now handles numpy arrays.
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r9802 | bugman | 2009-10-27 15:46:54 +0100 (Tue, 27 Oct 2009) | 3 lines
Entity ID numbers are now supported throughout the relaxation data and
model-free saveframes.
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r9803 | bugman | 2009-10-27 15:52:18 +0100 (Tue, 27 Oct 2009) | 3 lines
Molecule names are converted to entity IDs and vice versa for BMRB writing
and reading.
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r9804 | bugman | 2009-10-27 15:56:39 +0100 (Tue, 27 Oct 2009) | 3 lines
An entity IDs fix for the general relaxation saveframe reading.
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r9805 | bugman | 2009-10-27 15:57:41 +0100 (Tue, 27 Oct 2009) | 3 lines
Removed a test for duplicated data - data can be duplicated!!!
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r9806 | bugman | 2009-10-27 15:58:11 +0100 (Tue, 27 Oct 2009) | 3 lines
Entity IDs are going into the model-free saveframe and missing parameter
errors are now handled.
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r9807 | bugman | 2009-10-27 16:14:33 +0100 (Tue, 27 Oct 2009) | 3 lines
All the relaxation data saveframes now contain all the equivalent data as
in general relaxation.
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r9808 | bugman | 2009-10-27 16:20:35 +0100 (Tue, 27 Oct 2009) | 3 lines
Added a catch for Rex error values of None.
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r9809 | bugman | 2009-10-27 16:34:45 +0100 (Tue, 27 Oct 2009) | 3 lines
Expansion of the chemical shift anisotropy saveframe.
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r9810 | bugman | 2009-10-27 16:42:02 +0100 (Tue, 27 Oct 2009) | 3 lines
Updated the v3.1 and earlier T1 and T2 saveframes for all the new info.
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r9811 | bugman | 2009-10-27 16:49:45 +0100 (Tue, 27 Oct 2009) | 3 lines
The entity IDs are being passed into the CSA saveframe.
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r9813 | bugman | 2009-10-27 20:58:05 +0100 (Tue, 27 Oct 2009) | 3 lines
Modified the citation label so that the multiple entries wouldn't have the
same name.
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r9814 | bugman | 2009-10-27 21:12:56 +0100 (Tue, 27 Oct 2009) | 3 lines
The relax citation ID is now going in as the BMRB citation label.
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r9815 | bugman | 2009-10-27 21:20:21 +0100 (Tue, 27 Oct 2009) | 5 lines
The SfFramecode tag is now being created for the citation saveframes.
This fixes deposition issues due to all citations having the same
entry_citation name.
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r9816 | bugman | 2009-10-27 21:23:57 +0100 (Tue, 27 Oct 2009) | 3 lines
Added a dummy title for the Sparky citation as this must be supplied.
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r9817 | bugman | 2009-10-27 22:59:45 +0100 (Tue, 27 Oct 2009) | 3 lines
The SfFramecode tag is now going into the heteronuclear NOE saveframe.
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r9818 | bugman | 2009-10-27 23:02:37 +0100 (Tue, 27 Oct 2009) | 3 lines
The base class add() methods are now receiving all args.
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r9819 | bugman | 2009-10-27 23:12:53 +0100 (Tue, 27 Oct 2009) | 3 lines
All the relaxation data info can now be set through the add() method.
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r9820 | bugman | 2009-10-27 23:14:19 +0100 (Tue, 27 Oct 2009) | 3 lines
The element name is now being placed into the relaxation data saveframes.
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r9821 | bugman | 2009-10-27 23:20:02 +0100 (Tue, 27 Oct 2009) | 3 lines
Added the SfFramecode tag to the general relaxation saveframe.
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r9822 | bugman | 2009-10-27 23:20:29 +0100 (Tue, 27 Oct 2009) | 3 lines
Variable renaming.
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r9823 | bugman | 2009-10-27 23:22:45 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the previous variable change.
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r9824 | bugman | 2009-10-27 23:36:49 +0100 (Tue, 27 Oct 2009) | 5 lines
The DataFileName tag is being created for the CSA saveframe.
This doesn't seem to be read by the ADIT-NMR system.
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r9825 | bugman | 2009-10-27 23:50:51 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the _Vendor.Electronic_address tag (previously incorrectly named).
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r9826 | bugman | 2009-10-28 11:05:19 +0100 (Wed, 28 Oct 2009) | 3 lines
Fix for the _General_Relaxation_list.Sf_category tag.
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r9827 | bugman | 2009-10-28 11:34:59 +0100 (Wed, 28 Oct 2009) | 5 lines
The tags for the 2 heteronuclNOE atoms are now supported.
The normal relaxation tags for the atom info are duplicated and called *_1
and *_2 for the 2 atoms.
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r9828 | bugman | 2009-10-28 11:38:20 +0100 (Wed, 28 Oct 2009) | 3 lines
Fix for the Seq_ID_2 tag in the heteronuclear NOE saveframe.
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r9833 | bugman | 2009-10-28 12:01:52 +0100 (Wed, 28 Oct 2009) | 5 lines
The attached atom info is been sent into the BMRB NMR-STAR file.
This is used in the heteronuclear NOE saveframe.
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r9835 | bugman | 2009-10-28 18:11:01 +0100 (Wed, 28 Oct 2009) | 5 lines
Expanded the entity saveframe.
The PolymerType, PolymerSeqOneLetterCode, and ThiolState are now supported.
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r9836 | bugman | 2009-10-28 18:20:02 +0100 (Wed, 28 Oct 2009) | 3 lines
Shifted a line of code to the correct place.
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r9837 | bugman | 2009-10-28 18:59:00 +0100 (Wed, 28 Oct 2009) | 5 lines
The polymer type and one letter code sequence are being placed into the
BMRB file.
The new molecule.type() user function has been created for this.
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r9838 | bugman | 2009-10-29 11:23:53 +0100 (Thu, 29 Oct 2009) | 3 lines
Added support for the method saveframe.
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r9839 | bugman | 2009-10-29 11:32:52 +0100 (Thu, 29 Oct 2009) | 3 lines
Added a number of new user function calls to the BMRB system test.
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r9840 | bugman | 2009-10-29 11:59:17 +0100 (Thu, 29 Oct 2009) | 3 lines
Created the bmrb.thiol_state() user function.
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r9841 | bugman | 2009-10-29 13:14:53 +0100 (Thu, 29 Oct 2009) | 3 lines
Removed the thiol state check as this can be anything.
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r9842 | bugman | 2009-10-29 13:15:31 +0100 (Thu, 29 Oct 2009) | 3 lines
The thiol state is now being put into the BMRB file.
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r9843 | bugman | 2009-10-29 14:31:33 +0100 (Thu, 29 Oct 2009) | 3 lines
Created the bmrb.script() user function for specifying the scripts used in
the analysis.
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r9844 | bugman | 2009-10-29 14:42:57 +0100 (Thu, 29 Oct 2009) | 3 lines
The method saveframes are now accessible from the API.
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r9845 | bugman | 2009-10-29 14:43:56 +0100 (Thu, 29 Oct 2009) | 3 lines
Missing import fix.
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r9846 | bugman | 2009-10-29 14:52:14 +0100 (Thu, 29 Oct 2009) | 3 lines
Fixes for the method saveframe. This should now work correctly.
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r9847 | bugman | 2009-10-29 14:53:14 +0100 (Thu, 29 Oct 2009) | 3 lines
The citation ID strings are now going into the script containers.
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r9848 | bugman | 2009-10-29 14:53:47 +0100 (Thu, 29 Oct 2009) | 3 lines
The scripts are now being placed by relax into the BMRB file.
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r9849 | bugman | 2009-10-29 14:55:05 +0100 (Thu, 29 Oct 2009) | 3 lines
The script name was being overwritten.
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r9850 | bugman | 2009-10-29 15:45:47 +0100 (Thu, 29 Oct 2009) | 5 lines
Changed how the built in citations are handled.
They are now all stored in the CITE dictionary.
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r9851 | bugman | 2009-10-29 15:58:39 +0100 (Thu, 29 Oct 2009) | 3 lines
The setting up of software and its citations is now functional again.
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r9852 | bugman | 2009-10-29 16:02:15 +0100 (Thu, 29 Oct 2009) | 3 lines
The _Method_file and _Method_param tag categories are now free tables.
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r9853 | bugman | 2009-10-29 16:23:02 +0100 (Thu, 29 Oct 2009) | 3 lines
Changed the method saveframe category name.
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r9854 | bugman | 2009-10-29 16:24:04 +0100 (Thu, 29 Oct 2009) | 14 lines
Reverted r9852.
The command used was:
svn merge -r9852:9851 .
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r9852 | bugman | 2009-10-29 16:02:15 +0100 (Thu, 29 Oct 2009) | 3 lines
Changed paths:
M /branches/bmrb/bmrblib/experimental_details/method.py
The _Method_file and _Method_param tag categories are now free tables.
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r9855 | bugman | 2009-10-29 17:26:35 +0100 (Thu, 29 Oct 2009) | 3 lines
Separated the software info from CITE into the SOFTWARE dictionary.
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r9856 | bugman | 2009-10-29 17:31:53 +0100 (Thu, 29 Oct 2009) | 3 lines
The directory info is being stored in the script container.
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r9857 | bugman | 2009-10-29 17:54:26 +0100 (Thu, 29 Oct 2009) | 5 lines
Added the model-free model selection and elimination and set theory papers
as citations.
These are also placed into the BMRB file.
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r9858 | bugman | 2009-10-29 17:56:17 +0100 (Thu, 29 Oct 2009) | 3 lines
The method saveframes containing scripts now refer to the citations
associated with that script.
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r9859 | bugman | 2009-10-29 18:25:45 +0100 (Thu, 29 Oct 2009) | 3 lines
Sometimes the spin container attached atom variable name is
'attached_proton' and not 'attached_atom'.
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r9860 | bugman | 2009-10-29 18:25:57 +0100 (Thu, 29 Oct 2009) | 3 lines
Fixes for the BMRB system test.
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r9861 | bugman | 2009-10-29 19:12:15 +0100 (Thu, 29 Oct 2009) | 3 lines
Suppressed a retarded warning message in pystarlib.
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r9862 | bugman | 2009-11-02 18:19:53 +0100 (Mon, 02 Nov 2009) | 6 lines
Removed the bmrblib package as this is now its own software project.
The BMRB library package (https://gna.org/projects/bmrblib/) is now a
dependency if BMRB file
creation or reading is required.
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r9865 | bugman | 2009-11-04 15:12:10 +0100 (Wed, 04 Nov 2009) | 3 lines
Added the specification of the peak intensity type to the BMRB system test.
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r9866 | bugman | 2009-11-04 15:18:15 +0100 (Wed, 04 Nov 2009) | 5 lines
The peak intensity type is now being passed into the BMRB file.
This doesn't work yet as the user function doesn't exist!
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r9867 | bugman | 2009-11-05 11:52:27 +0100 (Thu, 05 Nov 2009) | 3 lines
Added the interface for the relax_data.peak_intensity_type() user function.
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r9868 | bugman | 2009-11-05 13:23:26 +0100 (Thu, 05 Nov 2009) | 5 lines
The relax_data.peak_intensity_type() user function is now fully operational.
The BMRB system test has been repaired for the user function argument name
change.
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r9869 | bugman | 2009-11-05 13:48:57 +0100 (Thu, 05 Nov 2009) | 3 lines
Implemented the get_peak_intensity_type() method for returning that data.
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r9990 | bugman | 2009-11-27 10:50:50 +0100 (Fri, 27 Nov 2009) | 3 lines
Added bmrb_read() and bmrb_write() to the analysis specific base API.
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r10116 | bugman | 2010-01-06 18:15:24 +0100 (Wed, 06 Jan 2010) | 3 lines
Fixes for the rename of prompt.check to the arg_check module.
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r10874 | bugman | 2010-02-23 21:56:34 +0100 (Tue, 23 Feb 2010) | 3 lines
relax now can start without the presence of the bmrblib package
(http://gna.org/projects/bmrblib/).
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r10876 | bugman | 2010-02-23 22:02:55 +0100 (Tue, 23 Feb 2010) | 6 lines
Fix for the PipeContainer.from_xml() method.
The experimental information container was been searched for in the wrong
node (actually an
undeclared variable).
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r10877 | bugman | 2010-02-23 22:31:03 +0100 (Tue, 23 Feb 2010) | 5 lines
User function fixes to match the changes to the user function framework
The exec_info box is now being used.
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r10880 | bugman | 2010-02-24 00:15:26 +0100 (Wed, 24 Feb 2010) | 5 lines
Shifted to using the Info_box rather than the local CITE variable.
This is for the d'Auvergne and Gooley, 2003, 2006, and 2007 refs. The rest
will be converted later.
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r10885 | bugman | 2010-02-24 01:27:24 +0100 (Wed, 24 Feb 2010) | 5 lines
All references are now taken from the Info_box.bib dictionary
The CITE structure has therefore been deleted.
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r11264 | bugman | 2010-06-29 23:16:35 +0200 (Tue, 29 Jun 2010) | 3 lines
Started to create the diffusion tensor saveframe.
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Removed:
1.3/bmrblib/
Modified:
1.3/ (props changed)
1.3/data/exp_info.py
1.3/data/pipe_container.py
1.3/generic_fns/bmrb.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/specific_fns/api_base.py
1.3/specific_fns/model_free/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/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/exp_info.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/pipe_container.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12584&r1=12583&r2=12584&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=12584&r1=12583&r2=12584&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=12584&r1=12583&r2=12584&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=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/relax_data.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=12584&r1=12583&r2=12584&view=diff
Modified: 1.3/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_base.py?rev=12584&r1=12583&r2=12584&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=12584&r1=12583&r2=12584&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=12584&r1=12583&r2=12584&view=diff
r12584 - in /1.3: ./ bmrblib/ data/ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/scri...