Author: bugman
Date: Sat Feb 19 16:11:04 2011
New Revision: 12597
URL: http://svn.gna.org/viewcvs/relax?rev=12597&view=rev
Log:
Merged revisions 12577-12592 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r12577 | bugman | 2011-02-18 18:59:57 +0100 (Fri, 18 Feb 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-7041" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
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r12578 | bugman | 2011-02-19 14:36:23 +0100 (Sat, 19 Feb 2011) | 25 lines
Merged revisions 7043-7044,7046 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
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r7043 | bugman | 2008-07-31 11:29:45 +0200 (Thu, 31 Jul 2008) | 8 lines
Initial support for the bmrb user functions.
The following BNMRB related user functions now exist (the back end does
not yet exist):
bmrb.display()
bmrb.read()
bmrb.write()
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r7044 | bugman | 2008-07-31 11:36:29 +0200 (Thu, 31 Jul 2008) | 3 lines
Activated the bmrb user functions.
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r7046 | bugman | 2008-07-31 11:52:39 +0200 (Thu, 31 Jul 2008) | 6 lines
Added some basic BMRB file format displaying/reading/writing functions.
The STAR format parser and model-free specific code needs to be
implemented before this code will
work.
........
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r12579 | bugman | 2011-02-19 14:39:23 +0100 (Sat, 19 Feb 2011) | 113 lines
Merged revisions 8153,8369-8388 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
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r8153 | bugman | 2008-12-05 20:44:46 +0100 (Fri, 05 Dec 2008) | 3 lines
Import fix!
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r8369 | bugman | 2009-01-11 10:52:13 +0100 (Sun, 11 Jan 2009) | 11 lines
Added a directory for packaging the pystarlib STAR format reader/writer
library with relax.
The pystarlib project by Jurgen F. Doreleijers (jurgenfd att gmail dot
com) is located at
http://code.google.com/p/pystarlib/.
This packaging with relax is temporary until relax can fully use the
library to read and write STAR
files containing relaxation analysis results (model-free for now) for
submission to the BMRB. The
pystarlib library also needs to be packaged with distutils for easy
installation, prior to
reseparation.
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r8370 | bugman | 2009-01-11 10:55:33 +0100 (Sun, 11 Jan 2009) | 6 lines
Added all the pystarlib code.
The original SVN repository path for this code is
http://pystarlib.googlecode.com/svn/trunk/src/STAR
and the code was copied at r15.
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r8371 | bugman | 2009-01-11 12:20:07 +0100 (Sun, 11 Jan 2009) | 3 lines
Created a system test for the writing and reading of a BRMB STAR
formatted file.
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r8372 | bugman | 2009-01-11 12:26:41 +0100 (Sun, 11 Jan 2009) | 3 lines
A few fixes for the BMRB system test.
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r8373 | bugman | 2009-01-11 13:50:12 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a missing import.
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r8374 | bugman | 2009-01-11 13:54:24 +0100 (Sun, 11 Jan 2009) | 3 lines
Some more missing imports.
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r8375 | bugman | 2009-01-11 13:57:26 +0100 (Sun, 11 Jan 2009) | 3 lines
A RelaxError is now raised if the specific_fns BMRB methods do not exist.
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r8376 | bugman | 2009-01-11 14:01:28 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a stub bmrb_write() model-free method.
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r8377 | bugman | 2009-01-11 14:03:58 +0100 (Sun, 11 Jan 2009) | 3 lines
The bmrb_write() method is now in the model-free specific object.
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r8378 | bugman | 2009-01-11 14:05:52 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_write() methods.
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r8379 | bugman | 2009-01-11 14:06:26 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_read() methods.
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r8380 | bugman | 2009-01-11 15:46:03 +0100 (Sun, 11 Jan 2009) | 5 lines
Import fixes for pystarlib, as they were all screwed up.
This allows the unit test framework to function and allows importing of
the code into relax.
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r8381 | bugman | 2009-01-11 15:57:41 +0100 (Sun, 11 Jan 2009) | 5 lines
Removed the BMRB STAR file compression abilities from the user functions.
The pystarlib does not support this.
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r8382 | bugman | 2009-01-11 16:28:13 +0100 (Sun, 11 Jan 2009) | 5 lines
Redesigned the generic BMRB write() function for the pystarlib.File.File
class object.
The open_write_file() function should not be used as pystarlib already
creates the file.
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r8383 | bugman | 2009-01-11 16:30:33 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a printout for the write() function.
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r8384 | bugman | 2009-01-11 16:41:13 +0100 (Sun, 11 Jan 2009) | 5 lines
The pystarlib File object is now initialised and the write() method
called.
This produces a relatively empty file.
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r8385 | bugman | 2009-01-11 17:17:49 +0100 (Sun, 11 Jan 2009) | 5 lines
Fix for the test_rw_bmrb_model_free() system test.
The dir name was being set to the data pipe name!
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r8386 | bugman | 2009-01-11 17:27:34 +0100 (Sun, 11 Jan 2009) | 3 lines
Fixes for the read() function.
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r8387 | bugman | 2009-01-11 17:29:45 +0100 (Sun, 11 Jan 2009) | 3 lines
Fix for the write() function. The directory for placing the file into is
now created.
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r8388 | bugman | 2009-01-11 17:33:47 +0100 (Sun, 11 Jan 2009) | 6 lines
Wrote a basic model-free bmrb_read() method.
This simply parses the STAR formatted file, but does not yet put the
contents into the relax data
store.
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r12580 | bugman | 2011-02-19 14:41:53 +0100 (Sat, 19 Feb 2011) | 52 lines
Merged revisions 8392-8393,8427,8567-8573 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
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r8392 | bugman | 2009-01-11 19:05:40 +0100 (Sun, 11 Jan 2009) | 5 lines
Started to dump the relaxation data into the BMRB file.
Much work is still required and the spin specific values are still not
there.
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r8393 | bugman | 2009-01-11 19:22:44 +0100 (Sun, 11 Jan 2009) | 3 lines
The spectrometer frequency in the BMRB is now a float.
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r8427 | bugman | 2009-01-12 22:20:30 +0100 (Mon, 12 Jan 2009) | 3 lines
All relaxation data is now placed in the BMRB STAR formatted file.
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r8567 | bugman | 2009-01-21 21:02:14 +0100 (Wed, 21 Jan 2009) | 6 lines
Added a directory for the creation of the 'bmrb' package.
This will include translation tables of the various BMRB NMR-STAR format
version, and many BMRB
format related functions.
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r8568 | bugman | 2009-01-21 21:03:14 +0100 (Wed, 21 Jan 2009) | 3 lines
Converted generic_fns.bmrb into the bmrb package initialisation module.
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r8569 | bugman | 2009-01-21 21:03:42 +0100 (Wed, 21 Jan 2009) | 3 lines
Copyright update.
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r8570 | bugman | 2009-01-21 21:04:50 +0100 (Wed, 21 Jan 2009) | 3 lines
Updated the module docstring and added an empty __all__ list.
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r8571 | bugman | 2009-01-21 21:06:37 +0100 (Wed, 21 Jan 2009) | 3 lines
Import fix and copyright update.
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r8572 | bugman | 2009-01-21 21:17:17 +0100 (Wed, 21 Jan 2009) | 5 lines
Renamed the bmrb package to bmrblib.
This is to avoid any future (and current) name clashes.
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r8573 | bugman | 2009-01-21 21:18:35 +0100 (Wed, 21 Jan 2009) | 3 lines
Updates for the renaming to bmrblib.
........
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r12581 | bugman | 2011-02-19 14:47:48 +0100 (Sat, 19 Feb 2011) | 466 lines
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
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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!
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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.
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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.
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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.
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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.
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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.
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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>).
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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.
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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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[... 1749 lines stripped ...]
r12597 - in /branches/relax_disp: ./ data/ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tes...