Author: bugman
Date: Sat Feb 19 14:47:48 2011
New Revision: 12581
URL: http://svn.gna.org/viewcvs/relax?rev=12581&view=rev
Log:
Merged revisions
8834-8860,8864-8878,8880-8881,8883-8892,8904-8908,8912-8915,8921-8922,8924,8930,8934,8937-8955,8959-8962,8964-8970,8973,8975
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
........
r8834 | bugman | 2009-02-21 23:50:56 +0100 (Sat, 21 Feb 2009) | 7 lines
Started to create the NMR-STAR dictionary object.
The object is in bmrblib.nmr_star_dict and acts as an abstraction layer
between pystarlib and the
specific analysis types. It also will translate the NMR-STAR dictionary
subset used by relax for
different versions of the definition. The object is far from complete
though.
........
r8835 | bugman | 2009-02-21 23:57:38 +0100 (Sat, 21 Feb 2009) | 3 lines
Renamed the pystarlib file object to self.data.
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r8836 | bugman | 2009-02-22 00:05:49 +0100 (Sun, 22 Feb 2009) | 3 lines
Fixed the call to pystarlib.File().
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r8837 | bugman | 2009-02-22 00:16:19 +0100 (Sun, 22 Feb 2009) | 3 lines
Small temporary fix for the file writing.
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r8838 | bugman | 2009-02-22 00:36:22 +0100 (Sun, 22 Feb 2009) | 3 lines
Shifted all the pystarlib code for the relaxation data into the NMR-STAR
dictionary object.
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r8839 | bugman | 2009-02-22 10:57:59 +0100 (Sun, 22 Feb 2009) | 3 lines
Shifted many tag names into class variables in preparation for inheritance
and multi-version support.
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r8840 | bugman | 2009-02-22 11:04:01 +0100 (Sun, 22 Feb 2009) | 3 lines
Created a package for the support of the supergroup 6 collection of
saveframes (kinetic data).
........
r8841 | bugman | 2009-02-22 11:14:22 +0100 (Sun, 22 Feb 2009) | 3 lines
Shifted the code for the relaxation data into
bmrblib.kinetics.heteronucl_T1_relaxation.
........
r8842 | bugman | 2009-02-22 13:15:43 +0100 (Sun, 22 Feb 2009) | 6 lines
Split up the T1 saveframe object.
The main object is now called HeteronuclT1Saveframe. The HeteronuclT1List
tag category has been
shifted into its own object, and the other tag categories will be created
next.
........
r8843 | bugman | 2009-02-22 13:25:13 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the HeteronuclT1Experiment tag category object.
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r8844 | bugman | 2009-02-22 13:29:20 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the unused HeteronuclT1Software tag category class.
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r8845 | bugman | 2009-02-22 13:34:08 +0100 (Sun, 22 Feb 2009) | 3 lines
Code simplification by placement of many objects into the saveframe
namespace.
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r8846 | bugman | 2009-02-22 13:40:08 +0100 (Sun, 22 Feb 2009) | 5 lines
Further object simplifications.
The __init__() methods have been shifted into the TagCategory base class in
bmrblib.tag_category.
........
r8847 | bugman | 2009-02-22 13:49:33 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the T1 tag category.
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r8848 | bugman | 2009-02-22 14:00:14 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the heteronucl_NOEs and heteronucl_T2_relaxation saveframes.
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r8849 | bugman | 2009-02-22 14:43:58 +0100 (Sun, 22 Feb 2009) | 3 lines
Shifted the tag name prefix creation code into
bmrblib.tag_category.TagCategory.
........
r8850 | bugman | 2009-02-22 14:53:45 +0100 (Sun, 22 Feb 2009) | 7 lines
Code rearrangement.
The BMRB read(), write(), and display() methods called by the user
functions has been shifted to
generic_fns. This allows bmrblib to be purely a package providing an API
for the NMR-STAR
dictionaries, with reading and writing done by pystarlib.
........
r8851 | bugman | 2009-02-22 15:05:06 +0100 (Sun, 22 Feb 2009) | 3 lines
Changed some imports in preparation for support for different NMR-STAR
versions.
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r8852 | bugman | 2009-02-22 15:31:48 +0100 (Sun, 22 Feb 2009) | 5 lines
Started to implement different NMR-STAR version support.
There are obvious design issues here, preventing this from working!
........
r8853 | bugman | 2009-02-22 15:37:57 +0100 (Sun, 22 Feb 2009) | 3 lines
Some class name changes.
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r8854 | bugman | 2009-02-22 16:23:56 +0100 (Sun, 22 Feb 2009) | 5 lines
Redesign for different NMR-STAR dictionary version support.
All class variables have been converted into dictionaries created upon
instantiation.
........
r8855 | bugman | 2009-02-22 18:56:52 +0100 (Sun, 22 Feb 2009) | 5 lines
Full implementation of v3.1 NMR-STAR support.
T2's are still missing, causing an import error.
........
r8856 | bugman | 2009-02-22 18:58:15 +0100 (Sun, 22 Feb 2009) | 3 lines
Added v3.1 support for the T2.
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r8857 | bugman | 2009-02-22 19:31:56 +0100 (Sun, 22 Feb 2009) | 6 lines
Improvements for the relaxation data storage tag categories.
Different NMR-STAR dictionary definitions are supported and the tag names
are now located in the
tag name dictionary.
........
r8858 | bugman | 2009-02-22 19:44:35 +0100 (Sun, 22 Feb 2009) | 3 lines
Values of 'None' are now translated to the '?' string.
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r8859 | bugman | 2009-02-22 19:47:09 +0100 (Sun, 22 Feb 2009) | 3 lines
Bug fix for the translate function. The old list was being overwritten.
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r8860 | bugman | 2009-02-22 19:48:45 +0100 (Sun, 22 Feb 2009) | 3 lines
The R2 and NOE data is now translated as well.
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r8864 | bugman | 2009-02-22 23:28:23 +0100 (Sun, 22 Feb 2009) | 3 lines
Updated the __all__ list.
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r8865 | bugman | 2009-02-22 23:33:38 +0100 (Sun, 22 Feb 2009) | 3 lines
Added directories for all the NMR-STAR dictionary supergroups.
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r8866 | bugman | 2009-02-22 23:36:40 +0100 (Sun, 22 Feb 2009) | 3 lines
Converted all directories into empty packages of the NMR-STAR dictionary
supergroups.
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r8867 | bugman | 2009-02-22 23:43:13 +0100 (Sun, 22 Feb 2009) | 3 lines
Bug fix for the __all__ list.
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r8868 | bugman | 2009-02-22 23:59:13 +0100 (Sun, 22 Feb 2009) | 3 lines
The BMRB NMR-STAR system test now tries to display some of the relaxation
data which should be read.
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r8869 | bugman | 2009-02-23 11:52:25 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the entity saveframe category.
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r8870 | bugman | 2009-02-23 14:01:18 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the v3.1 entity saveframe category.
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r8871 | bugman | 2009-02-23 14:10:02 +0100 (Mon, 23 Feb 2009) | 3 lines
Fixed some miss named variables (this has no effect).
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r8872 | bugman | 2009-02-23 19:59:27 +0100 (Mon, 23 Feb 2009) | 3 lines
Converted the entity saveframe code from the heteronuclear NOE code.
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r8873 | bugman | 2009-02-26 14:45:26 +0100 (Thu, 26 Feb 2009) | 3 lines
Added a check for the number of molecules for the entity saveframe
generation.
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r8874 | bugman | 2009-02-26 14:50:09 +0100 (Thu, 26 Feb 2009) | 3 lines
Shifted the non-function entity saveframe creation into the
generic_fns.mol_res_spin module.
........
r8875 | bugman | 2009-02-26 14:57:28 +0100 (Thu, 26 Feb 2009) | 3 lines
The entity saveframe is now enabled in the NMR_STAR object.
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r8876 | bugman | 2009-02-26 14:58:28 +0100 (Thu, 26 Feb 2009) | 3 lines
Bug fix.
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r8877 | bugman | 2009-02-26 15:14:54 +0100 (Thu, 26 Feb 2009) | 3 lines
Bug fix. The data is in self.sf and not in self!
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r8878 | bugman | 2009-02-26 15:21:28 +0100 (Thu, 26 Feb 2009) | 5 lines
Created the get_molecule_names() function.
This new function returns a list of all the molecule names.
bmrb_write_entity() now calls this.
........
r8880 | bugman | 2009-02-27 14:33:43 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecules are now looped over in preparation for the molecule assembly.
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r8881 | bugman | 2009-02-27 14:35:07 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed the useless ri_inc variable.
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r8883 | bugman | 2009-02-27 15:11:47 +0100 (Fri, 27 Feb 2009) | 7 lines
Added the missing _Heteronuclear_xx_list.ID tags.
This was pointed out by Eldon Ulrich <elu att bmrb dot wisc dot edu> in the
post at
https://mail.gna.org/public/relax-devel/2009-02/msg00025.html (Message-id:
<49A78ABD.2050505@xxxxxxxxxxxxx>).
........
r8884 | bugman | 2009-02-27 15:16:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule name is now correctly passed in.
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r8885 | bugman | 2009-02-27 15:56:25 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed some remnant args.
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r8886 | bugman | 2009-02-27 16:04:17 +0100 (Fri, 27 Feb 2009) | 3 lines
The _Entity.ID is now created.
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r8887 | bugman | 2009-02-27 17:18:38 +0100 (Fri, 27 Feb 2009) | 3 lines
Created 2 new functions, get_residue_names() and get_residue_nums().
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r8888 | bugman | 2009-02-27 17:20:49 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule type is now determined.
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r8889 | bugman | 2009-02-27 17:25:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The residue numbers are being stored in self now.
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r8890 | bugman | 2009-02-27 17:28:52 +0100 (Fri, 27 Feb 2009) | 5 lines
Switched from a RelaxError to 'non-polymer' for anything that isn't a
polymer.
A RelaxWarning is thrown so the user can check for FUBAR entries.
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r8891 | bugman | 2009-02-27 18:01:58 +0100 (Fri, 27 Feb 2009) | 3 lines
The translate function now converts all list data elements into strings.
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r8892 | bugman | 2009-02-27 18:02:22 +0100 (Fri, 27 Feb 2009) | 3 lines
The EntityCompIndex saveframe is now being created.
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r8904 | bugman | 2009-03-05 10:00:43 +0100 (Thu, 05 Mar 2009) | 3 lines
Shifted the relaxation data saveframe generation code into
generic_fns.relax_data.bmrb_write().
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r8905 | bugman | 2009-03-05 11:34:04 +0100 (Thu, 05 Mar 2009) | 3 lines
The data pipe is no longer needed.
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r8906 | bugman | 2009-03-05 11:48:09 +0100 (Thu, 05 Mar 2009) | 3 lines
Added a catch for spins with no relaxation data in bmrb_write().
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r8907 | bugman | 2009-03-05 15:07:18 +0100 (Thu, 05 Mar 2009) | 3 lines
The Entity saveframes are now being read and the sequence info recreated.
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r8908 | bugman | 2009-03-05 16:23:56 +0100 (Thu, 05 Mar 2009) | 6 lines
Simplified the tag name access.
Now the full tag names (category label + sep + tag name) is being generated
by TagCategory.__init__()
so that TagCategory.create_tag_label() doesn't need to be called by the
specific saveframes.
........
r8912 | bugman | 2009-03-06 11:33:35 +0100 (Fri, 06 Mar 2009) | 5 lines
Added checks for the residue names and numbers, and atom names.
They should not be None.
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r8913 | bugman | 2009-03-06 11:40:20 +0100 (Fri, 06 Mar 2009) | 5 lines
Added some checks for None before hitting the bmrblib code.
This gives more informative error messages.
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r8914 | bugman | 2009-03-06 11:51:53 +0100 (Fri, 06 Mar 2009) | 3 lines
Shifted the BMRB reading and writing test into a script and significantly
extended it.
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r8915 | bugman | 2009-03-06 13:43:06 +0100 (Fri, 06 Mar 2009) | 3 lines
Bug fix for the tearDown method. The reset was removing the temp file name!
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r8921 | bugman | 2009-03-06 15:42:34 +0100 (Fri, 06 Mar 2009) | 3 lines
Docstring fix.
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r8922 | bugman | 2009-03-06 15:48:36 +0100 (Fri, 06 Mar 2009) | 3 lines
Extraction of R1 data is now supported by the bmrblib API.
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r8924 | bugman | 2009-03-06 19:17:03 +0100 (Fri, 06 Mar 2009) | 3 lines
Start of the reading of relaxation data from the BMRB NMR-STAR files.
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r8930 | bugman | 2009-03-08 22:43:32 +0100 (Sun, 08 Mar 2009) | 3 lines
Added a call to pack_data() from bmrb_read().
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r8934 | bugman | 2009-03-08 23:38:36 +0100 (Sun, 08 Mar 2009) | 3 lines
Simplified the bmrb_read() function.
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r8937 | bugman | 2009-03-08 23:52:24 +0100 (Sun, 08 Mar 2009) | 3 lines
The gen_seq flag of pack_data() is now set in bmrb_read().
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r8938 | bugman | 2009-03-08 23:56:24 +0100 (Sun, 08 Mar 2009) | 5 lines
Bug fix for the T1.read() method.
The values and errors were being set to the residue number!
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r8939 | bugman | 2009-03-09 11:44:59 +0100 (Mon, 09 Mar 2009) | 3 lines
bmrb_read() now tries to read all relaxation data (from R2, R1, and NOE).
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r8940 | bugman | 2009-03-09 13:45:31 +0100 (Mon, 09 Mar 2009) | 5 lines
Shifted all the Rx data reading code into base classes in relax_base.py.
The R1, R2, and NOE now all use this abstracted code.
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r8941 | bugman | 2009-03-09 13:50:40 +0100 (Mon, 09 Mar 2009) | 3 lines
Added the saveframe category for model-free data.
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r8942 | bugman | 2009-03-09 15:10:26 +0100 (Mon, 09 Mar 2009) | 3 lines
The order_parameters saveframes are now created (although are missing all
the contents).
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r8943 | bugman | 2009-03-09 19:44:09 +0100 (Mon, 09 Mar 2009) | 3 lines
Support for all model-free parameters has been added to the BMRB library.
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r8944 | bugman | 2009-03-09 19:59:59 +0100 (Mon, 09 Mar 2009) | 3 lines
The model-free data is now being sent to the BMRB API.
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r8945 | bugman | 2009-03-10 10:48:14 +0100 (Tue, 10 Mar 2009) | 5 lines
Bug fix for the residue numbers.
This is CompIndexID and not SeqID!
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r8946 | bugman | 2009-03-10 11:09:26 +0100 (Tue, 10 Mar 2009) | 6 lines
Large code simplification via abstraction.
Most of the code from the create() method of the non-free TagTables has
been abstracted away into
the TagCategory.create_tag_table() method.
........
r8947 | bugman | 2009-03-10 11:26:10 +0100 (Tue, 10 Mar 2009) | 5 lines
Added the isotope arg to the relaxation data API parts.
The tag_setup() method has been abstracted back into the
kinetics.relax_base.Rx base class.
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r8948 | bugman | 2009-03-10 11:35:50 +0100 (Tue, 10 Mar 2009) | 3 lines
relax now dumps the spin isotope number into the Rx BMRB sections.
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r8949 | bugman | 2009-03-10 11:44:56 +0100 (Tue, 10 Mar 2009) | 3 lines
Added the HeteronuclRxListID tag elements. This just corresponds to the
self.rx_inc values.
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r8950 | bugman | 2009-03-10 14:17:38 +0100 (Tue, 10 Mar 2009) | 3 lines
Fixed the relaxation saveframe category values to be version specific.
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r8951 | bugman | 2009-03-10 14:19:36 +0100 (Tue, 10 Mar 2009) | 3 lines
Fixed the reading of relaxation data.
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r8952 | bugman | 2009-03-10 14:27:37 +0100 (Tue, 10 Mar 2009) | 3 lines
Made the model-free saveframe category name version specific.
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r8953 | bugman | 2009-03-10 14:45:09 +0100 (Tue, 10 Mar 2009) | 3 lines
Added the ID TagTable for the heteronuclear data (just a basic data
counter).
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r8954 | bugman | 2009-03-10 15:15:00 +0100 (Tue, 10 Mar 2009) | 3 lines
Shifted all the data ID code into the new BaseSaveframe base class.
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r8955 | bugman | 2009-03-10 15:19:03 +0100 (Tue, 10 Mar 2009) | 3 lines
Renamed the bmrblib.tag_category module to bmrblib.base_classes.
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r8959 | bugman | 2009-03-10 17:14:31 +0100 (Tue, 10 Mar 2009) | 5 lines
The CSA and bond length data is now collected, and the CSA part of the BMRB
API called.
The API call does not yet exist.
........
r8960 | bugman | 2009-03-10 17:28:49 +0100 (Tue, 10 Mar 2009) | 3 lines
Docstring fixes. These are not v3.1 files!
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r8961 | bugman | 2009-03-10 19:28:32 +0100 (Tue, 10 Mar 2009) | 3 lines
Created the CSA parts of the BMRB API.
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r8962 | bugman | 2009-03-10 19:29:06 +0100 (Tue, 10 Mar 2009) | 3 lines
The isotope number is now passed into the CSA part of the BMRB API.
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r8964 | bugman | 2009-03-11 14:03:55 +0100 (Wed, 11 Mar 2009) | 3 lines
Docstring addition - CSA must be in ppm.
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r8965 | bugman | 2009-03-11 15:12:01 +0100 (Wed, 11 Mar 2009) | 3 lines
The CSA is now sent in as ppm values.
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r8966 | bugman | 2009-03-11 15:16:12 +0100 (Wed, 11 Mar 2009) | 3 lines
Docstring and comment removal of 'NOE'.
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r8967 | bugman | 2009-03-11 15:22:06 +0100 (Wed, 11 Mar 2009) | 3 lines
Added the ID counter for the Order_param saveframe.
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r8968 | bugman | 2009-03-11 16:53:49 +0100 (Wed, 11 Mar 2009) | 3 lines
Docstring fixes and the addition of the rex_frq arg to add().
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r8969 | bugman | 2009-03-11 17:54:22 +0100 (Wed, 11 Mar 2009) | 7 lines
Added the new chi-squared tag.
This new tag is described in the document attached to the post
https://mail.gna.org/public/relax-devel/2009-03/msg00019.html (Message-id:
<49B7463E.7080109@xxxxxxxxxxxxx>).
........
r8970 | bugman | 2009-03-11 18:02:08 +0100 (Wed, 11 Mar 2009) | 7 lines
Updated the order_parameters saveframe to match the new NMR-STAR design.
The new design is described in the document attached to the post
https://mail.gna.org/public/relax-devel/2009-03/msg00019.html (Message-id:
<49B7463E.7080109@xxxxxxxxxxxxx>).
........
r8973 | bugman | 2009-03-12 17:25:11 +0100 (Thu, 12 Mar 2009) | 6 lines
Added a new module for abstracting the relaxation data part of the BMRB API.
This should automatically handle the change from heteronucl_NOEs,
heteronucl_T1_relaxation, and
heteronucl_T2_relaxation to the general_relaxation saveframe.
........
r8975 | bugman | 2009-03-12 18:55:46 +0100 (Thu, 12 Mar 2009) | 3 lines
Started to implement support for the General_relaxation saveframe category.
........
Added:
1.3/bmrblib/NMR_parameters/
- copied from r8881, branches/bmrb/bmrblib/NMR_parameters/
1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py
1.3/bmrblib/NMR_parameters/chem_shift_anisotropy_v3_1.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy_v3_1.py
1.3/bmrblib/assembly_supercategory/
- copied from r8881, branches/bmrb/bmrblib/assembly_supercategory/
1.3/bmrblib/base_classes.py
- copied unchanged from r8975, branches/bmrb/bmrblib/base_classes.py
1.3/bmrblib/citations/
- copied from r8881, branches/bmrb/bmrblib/citations/
1.3/bmrblib/entry_information/
- copied from r8881, branches/bmrb/bmrblib/entry_information/
1.3/bmrblib/experimental_details/
- copied from r8881, branches/bmrb/bmrblib/experimental_details/
1.3/bmrblib/kinetics/
- copied from r8860, branches/bmrb/bmrblib/kinetics/
1.3/bmrblib/kinetics/relax_base.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/kinetics/relax_base.py
1.3/bmrblib/kinetics/relaxation.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/kinetics/relaxation.py
1.3/bmrblib/misc.py
- copied, changed from r8860, branches/bmrb/bmrblib/misc.py
1.3/bmrblib/nmr_star_dict.py
- copied, changed from r8860, branches/bmrb/bmrblib/nmr_star_dict.py
1.3/bmrblib/nmr_star_dict_v3_1.py
- copied, changed from r8860,
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
1.3/bmrblib/structure/
- copied from r8881, branches/bmrb/bmrblib/structure/
1.3/bmrblib/thermodynamics/
- copied from r8881, branches/bmrb/bmrblib/thermodynamics/
1.3/bmrblib/thermodynamics/order_parameters.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/thermodynamics/order_parameters.py
1.3/bmrblib/thermodynamics/order_parameters_v3_1.py
- copied unchanged from r8975,
branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
1.3/generic_fns/bmrb.py
- copied unchanged from r8860, branches/bmrb/generic_fns/bmrb.py
1.3/test_suite/system_tests/scripts/bmrb_rw.py
- copied unchanged
[... 79 lines stripped ...]
r12581 - in /1.3: ./ bmrblib/ bmrblib/NMR_parameters/ bmrblib/assembly_supercategory/ bmrblib/citations/ bmrblib/entry_infor...