Merged revisions 12577-12592 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
................
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@.../svn/relax/branches/bmrb
................
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@.../svn/relax/branches/bmrb
........
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()
........
r7044 | bugman | 2008-07-31 11:36:29 +0200 (Thu, 31 Jul 2008) | 3 lines
Activated the bmrb user functions.
........
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.
........
................
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@.../svn/relax/branches/bmrb
........
r8153 | bugman | 2008-12-05 20:44:46 +0100 (Fri, 05 Dec 2008) | 3 lines
Import fix!
........
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.
........
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.
........
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.
........
r8372 | bugman | 2009-01-11 12:26:41 +0100 (Sun, 11 Jan 2009) | 3 lines
A few fixes for the BMRB system test.
........
r8373 | bugman | 2009-01-11 13:50:12 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a missing import.
........
r8374 | bugman | 2009-01-11 13:54:24 +0100 (Sun, 11 Jan 2009) | 3 lines
Some more missing imports.
........
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.
........
r8376 | bugman | 2009-01-11 14:01:28 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a stub bmrb_write() model-free method.
........
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.
........
r8378 | bugman | 2009-01-11 14:05:52 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_write() methods.
........
r8379 | bugman | 2009-01-11 14:06:26 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_read() methods.
........
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.
........
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.
........
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.
........
r8383 | bugman | 2009-01-11 16:30:33 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a printout for the write() function.
........
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.
........
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!
........
r8386 | bugman | 2009-01-11 17:27:34 +0100 (Sun, 11 Jan 2009) | 3 lines
Fixes for the read() function.
........
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.
........
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.
........
................
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@.../svn/relax/branches/bmrb
........
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.
........
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.
........
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.
........
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.
........
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.
........
r8569 | bugman | 2009-01-21 21:03:42 +0100 (Wed, 21 Jan 2009) | 3 lines
Copyright update.
........
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.
........
r8571 | bugman | 2009-01-21 21:06:37 +0100 (Wed, 21 Jan 2009) | 3 lines
Import fix and copyright update.
........
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.
........
r8573 | bugman | 2009-01-21 21:18:35 +0100 (Wed, 21 Jan 2009) | 3 lines
Updates for the renaming to bmrblib.
........
................
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@.../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.
........
r8836 | bugman | 2009-02-22 00:05:49 +0100 (Sun, 22 Feb 2009) | 3 lines
Fixed the call to pystarlib.File().
........
r8837 | bugman | 2009-02-22 00:16:19 +0100 (Sun, 22 Feb 2009) | 3 lines
Small temporary fix for the file writing.
........
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.
........
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.
........
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.
........
r8844 | bugman | 2009-02-22 13:29:20 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the unused HeteronuclT1Software tag category class.
........
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.
........
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.
........
r8848 | bugman | 2009-02-22 14:00:14 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the heteronucl_NOEs and heteronucl_T2_relaxation saveframes.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r8864 | bugman | 2009-02-22 23:28:23 +0100 (Sun, 22 Feb 2009) | 3 lines
Updated the __all__ list.
........
r8865 | bugman | 2009-02-22 23:33:38 +0100 (Sun, 22 Feb 2009) | 3 lines
Added directories for all the NMR-STAR dictionary supergroups.
........
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.
........
r8867 | bugman | 2009-02-22 23:43:13 +0100 (Sun, 22 Feb 2009) | 3 lines
Bug fix for the __all__ list.
........
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.
........
r8869 | bugman | 2009-02-23 11:52:25 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the entity saveframe category.
........
r8870 | bugman | 2009-02-23 14:01:18 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the v3.1 entity saveframe category.
........
r8871 | bugman | 2009-02-23 14:10:02 +0100 (Mon, 23 Feb 2009) | 3 lines
Fixed some miss named variables (this has no effect).
........
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.
........
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.
........
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.
........
r8876 | bugman | 2009-02-26 14:58:28 +0100 (Thu, 26 Feb 2009) | 3 lines
Bug fix.
........
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!
........
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.
........
r8881 | bugman | 2009-02-27 14:35:07 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed the useless ri_inc variable.
........
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@...>).
........
r8884 | bugman | 2009-02-27 15:16:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule name is now correctly passed in.
........
r8885 | bugman | 2009-02-27 15:56:25 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed some remnant args.
........
r8886 | bugman | 2009-02-27 16:04:17 +0100 (Fri, 27 Feb 2009) | 3 lines
The _Entity.ID is now created.
........
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().
........
r8888 | bugman | 2009-02-27 17:20:49 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule type is now determined.
........
r8889 | bugman | 2009-02-27 17:25:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The residue numbers are being stored in self now.
........
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.
........
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.
........
r8892 | bugman | 2009-02-27 18:02:22 +0100 (Fri, 27 Feb 2009) | 3 lines
The EntityCompIndex saveframe is now being created.
........
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().
........
r8905 | bugman | 2009-03-05 11:34:04 +0100 (Thu, 05 Mar 2009) | 3 lines
The data pipe is no longer needed.
........
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().
........
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.
........
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.
........
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.
........
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.
........
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!
........
r8921 | bugman | 2009-03-06 15:42:34 +0100 (Fri, 06 Mar 2009) | 3 lines
Docstring fix.
........
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.
........
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.
........
r8930 | bugman | 2009-03-08 22:43:32 +0100 (Sun, 08 Mar 2009) | 3 lines
Added a call to pack_data() from bmrb_read().
........
r8934 | bugman | 2009-03-08 23:38:36 +0100 (Sun, 08 Mar 2009) | 3 lines
Simplified the bmrb_read() function.
........
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().
........
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!
........
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).
........
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.
........
r8941 | bugman | 2009-03-09 13:50:40 +0100 (Mon, 09 Mar 2009) | 3 lines
Added the saveframe category for model-free data.
........
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).
........
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.
........
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.
........
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!
........
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.
........
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.
........
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.
........
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.
........
r8951 | bugman | 2009-03-10 14:19:36 +0100 (Tue, 10 Mar 2009) | 3 lines
Fixed the reading of relaxation data.
........
r8952 | bugman | 2009-03-10 14:27:37 +0100 (Tue, 10 Mar 2009) | 3 lines
Made the model-free saveframe category name version specific.
........
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).
........
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.
........
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.
........
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!
........
r8961 | bugman | 2009-03-10 19:28:32 +0100 (Tue, 10 Mar 2009) | 3 lines
Created the CSA parts of the BMRB API.
........
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.
........
r8964 | bugman | 2009-03-11 14:03:55 +0100 (Wed, 11 Mar 2009) | 3 lines
Docstring addition - CSA must be in ppm.
........
r8965 | bugman | 2009-03-11 15:12:01 +0100 (Wed, 11 Mar 2009) | 3 lines
The CSA is now sent in as ppm values.
........
r8966 | bugman | 2009-03-11 15:16:12 +0100 (Wed, 11 Mar 2009) | 3 lines
Docstring and comment removal of 'NOE'.
........
r8967 | bugman | 2009-03-11 15:22:06 +0100 (Wed, 11 Mar 2009) | 3 lines
Added the ID counter for the Order_param saveframe.
........
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().
........
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@...>).
........
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@...>).
........
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.
........
................
r12582 | bugman | 2011-02-19 14:52:26 +0100 (Sat, 19 Feb 2011) | 248 lines
Merged revisions 9274,9442,9445,9455,9661-9695,9697-9699,9701-9703,9705 via svnmerge from
svn+ssh://bugman@.../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.
........
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.
........
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.
........
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'!)
........
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'.
........
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().
........
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.
........
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.
........
r9680 | bugman | 2009-10-09 12:01:55 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
........
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!
........
r9682 | bugman | 2009-10-09 12:12:16 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
........
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.
........
r9684 | bugman | 2009-10-09 12:44:10 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
........
r9685 | bugman | 2009-10-09 12:44:59 +0200 (Fri, 09 Oct 2009) | 3 lines
Redesigned pack_data() to handle sequence generation.
........
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).
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9697 | bugman | 2009-10-09 15:48:19 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
........
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.
........
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.
........
r9701 | bugman | 2009-10-09 18:15:15 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the translate() method to handle not doing anything.
........
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.
........
r9703 | bugman | 2009-10-09 18:38:35 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the missing Task tag to the Software saveframe.
........
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.
........
................
r12583 | bugman | 2011-02-19 15:02:05 +0100 (Sat, 19 Feb 2011) | 373 lines
Merged revisions 9708,9710-9746,9748-9792 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb
........
r9708 | bugman | 2009-10-09 18:49:25 +0200 (Fri, 09 Oct 2009) | 3 lines
The SVN repository URL is now sent into the Software saveframe.
........
r9710 | bugman | 2009-10-09 20:22:55 +0200 (Fri, 09 Oct 2009) | 3 lines
The program state is now being saved in the BMRB system test.
........
r9711 | bugman | 2009-10-09 20:24:11 +0200 (Fri, 09 Oct 2009) | 5 lines
Created a data container for storing experimental details.
This will be used extensively for the BMRB file generation.
........
r9712 | bugman | 2009-10-09 20:25:00 +0200 (Fri, 09 Oct 2009) | 5 lines
Created the user function bmrb.software_select().
This currently doesn't do anything.
........
r9713 | bugman | 2009-10-09 20:41:30 +0200 (Fri, 09 Oct 2009) | 5 lines
Created the ContainerList base class object.
This is just a generic list type with XML methods, used to hold basic elements.
........
r9714 | bugman | 2009-10-09 20:46:25 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the system test to force save the program state.
........
r9715 | bugman | 2009-10-09 20:52:52 +0200 (Fri, 09 Oct 2009) | 3 lines
The bmrb.software_select() user function is now more functional.
........
r9716 | bugman | 2009-10-09 21:19:02 +0200 (Fri, 09 Oct 2009) | 3 lines
Expanded the experimental information data container to include all the software info.
........
r9717 | bugman | 2009-10-09 21:20:49 +0200 (Fri, 09 Oct 2009) | 6 lines
Many fixes to the Element and ContainerList to_xml() methods.
The objects within these are now properly converted to XML with the to_xml() method beign called
if it exists.
........
r9718 | bugman | 2009-10-09 21:39:14 +0200 (Fri, 09 Oct 2009) | 3 lines
More info is now being placed into the software containers of the experimental info container.
........
r9719 | bugman | 2009-10-09 21:44:46 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the software task to the software containers.
........
r9720 | bugman | 2009-10-11 15:29:05 +0200 (Sun, 11 Oct 2009) | 3 lines
Updated the __all__ package lists.
........
r9721 | bugman | 2009-10-11 15:41:56 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the bmrb.software() user function for manually specifying the software used.
........
r9722 | bugman | 2009-10-11 15:59:38 +0200 (Sun, 11 Oct 2009) | 3 lines
Shifted the software() and software_select() functions into their own module, 'generic_fns.exp_info'.
........
r9723 | bugman | 2009-10-11 16:04:48 +0200 (Sun, 11 Oct 2009) | 3 lines
Removed the kludgy bmrb_saveframes module and shifted the code into exp_info.
........
r9724 | bugman | 2009-10-11 16:07:31 +0200 (Sun, 11 Oct 2009) | 3 lines
Import fix from the previous module deletion.
........
r9725 | bugman | 2009-10-11 16:35:55 +0200 (Sun, 11 Oct 2009) | 3 lines
All attributes (even those of None) are being stored.
........
r9726 | bugman | 2009-10-11 16:39:43 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the bmrb_write_software() function for dumping the software info into the BMRB file.
........
r9727 | bugman | 2009-10-11 16:59:52 +0200 (Sun, 11 Oct 2009) | 5 lines
TagTable.create_tag_table() now handles single element data.
This allows the single element data to be submitted simultaneously with list data.
........
r9728 | bugman | 2009-10-11 17:05:37 +0200 (Sun, 11 Oct 2009) | 5 lines
Non-list data can now be used by TagTable.create_tag_table().
The method converts to lists on the fly.
........
r9729 | bugman | 2009-10-11 17:06:25 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the software add() method.
........
r9730 | bugman | 2009-10-11 17:14:09 +0200 (Sun, 11 Oct 2009) | 5 lines
Created version.version_full() from the code in generic_fns.exp_info.
The get_revision() and get_url() functions have had the 'get_' part removed.
........
r9731 | bugman | 2009-10-11 17:23:37 +0200 (Sun, 11 Oct 2009) | 3 lines
Shifted the program info into module variables.
........
r9732 | bugman | 2009-10-11 17:26:10 +0200 (Sun, 11 Oct 2009) | 3 lines
Added relax to the BMRB file.
........
r9733 | bugman | 2009-10-11 17:27:43 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the version_full() function due to 'url = url()'!!
........
r9734 | bugman | 2009-10-11 18:45:46 +0200 (Sun, 11 Oct 2009) | 3 lines
Modified bmrb_write_software() to handle if no other software packages are specified.
........
r9735 | bugman | 2009-10-11 18:47:08 +0200 (Sun, 11 Oct 2009) | 3 lines
Changed the default version to 3.2 in the stand alone operation of the BMRB system test.
........
r9736 | bugman | 2009-10-11 18:51:55 +0200 (Sun, 11 Oct 2009) | 3 lines
bmrb_write_software() now throws a RelaxError if no software has been specified.
........
r9737 | bugman | 2009-10-11 19:31:19 +0200 (Sun, 11 Oct 2009) | 3 lines
The element (or atom type) info is being sent into bmrblib.
........
r9738 | bugman | 2009-10-11 19:40:06 +0200 (Sun, 11 Oct 2009) | 3 lines
The element type is now being recorded in the CSA and model-free saveframes.
........
r9739 | bugman | 2009-10-11 19:42:51 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the bmrb_write() method for the new element storage.
........
r9740 | bugman | 2009-10-11 19:58:14 +0200 (Sun, 11 Oct 2009) | 5 lines
Added a call to the non-existent bmrb.citation() user function.
This will be used to design the UI.
........
r9741 | bugman | 2009-10-11 20:06:57 +0200 (Sun, 11 Oct 2009) | 3 lines
Removed the web address part of the DOI number.
........
r9742 | bugman | 2009-10-11 22:50:14 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the add_citation() method for adding citations to the experimental info container.
........
r9743 | bugman | 2009-10-11 22:53:10 +0200 (Sun, 11 Oct 2009) | 3 lines
Simplified the software container setup by absorbing Software and SoftwareList into software_setup().
........
r9744 | bugman | 2009-10-12 00:30:47 +0200 (Mon, 12 Oct 2009) | 3 lines
Created the bmrb.citation() user function.
........
r9745 | bugman | 2009-10-12 00:40:00 +0200 (Mon, 12 Oct 2009) | 3 lines
A number of fixes for the XML storage of the experimental info container.
........
r9746 | bugman | 2009-10-12 11:56:41 +0200 (Mon, 12 Oct 2009) | 3 lines
Fixes for the generic_fns package __all__ list.
........
r9748 | bugman | 2009-10-13 14:11:27 +0200 (Tue, 13 Oct 2009) | 6 lines
Large renamings of the Order_parameters saveframe to Model_free.
The modules still need to be renamed. Everything will be called model_free unless v3.1 or earlier
saveframes are created, then order_parameters will be used.
........
r9749 | bugman | 2009-10-13 14:12:11 +0200 (Tue, 13 Oct 2009) | 3 lines
Renamed the modules from order_parameters* to model_free*.
........
r9750 | bugman | 2009-10-13 14:22:31 +0200 (Tue, 13 Oct 2009) | 3 lines
Set up the NMR-STAR v3.2 model_free saveframe.
........
r9751 | bugman | 2009-10-13 14:32:31 +0200 (Tue, 13 Oct 2009) | 3 lines
The v3.2 model_free saveframe is now correctly created.
........
r9752 | bugman | 2009-10-13 14:35:29 +0200 (Tue, 13 Oct 2009) | 5 lines
Fix for the v3.1 order_parameters saveframe.
SfCategory was set to "model_free", not "order_parameters".
........
r9753 | bugman | 2009-10-13 16:35:05 +0200 (Tue, 13 Oct 2009) | 3 lines
Comment fixes.
........
r9754 | bugman | 2009-10-13 17:21:42 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified translate() so that only strings or lists of strings can ever be returned!
........
r9755 | bugman | 2009-10-13 17:39:17 +0200 (Tue, 13 Oct 2009) | 3 lines
Citations are now being placed into the BMRB submission file.
........
r9756 | bugman | 2009-10-13 18:24:23 +0200 (Tue, 13 Oct 2009) | 3 lines
The relax citations are now placed into the BMRB file.
........
r9757 | bugman | 2009-10-13 18:26:38 +0200 (Tue, 13 Oct 2009) | 3 lines
Removed a debugging print statement.
........
r9758 | bugman | 2009-10-13 19:07:23 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified add_citation() to return the citation ID number.
........
r9759 | bugman | 2009-10-13 19:21:22 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified the BMRB system test to catch the citation ID number and pass it into bmrb.software().
........
r9760 | bugman | 2009-10-13 19:22:24 +0200 (Tue, 13 Oct 2009) | 3 lines
Fix for the BMRB system test. The arg to bmrb.software() should be cite_ids.
........
r9761 | bugman | 2009-10-13 19:32:05 +0200 (Tue, 13 Oct 2009) | 3 lines
Created the is_int_list() function for argument checking.
........
r9762 | bugman | 2009-10-13 19:33:29 +0200 (Tue, 13 Oct 2009) | 3 lines
Created the RelaxNoneListIntError class.
........
r9763 | bugman | 2009-10-13 20:00:34 +0200 (Tue, 13 Oct 2009) | 5 lines
The BMRB SoftwareCitation tag category is now being created.
This points back to the relevant Citation saveframe.
........
r9764 | bugman | 2009-10-13 20:21:14 +0200 (Tue, 13 Oct 2009) | 3 lines
Fixes for the software citations.
........
r9765 | bugman | 2009-10-14 14:46:19 +0200 (Wed, 14 Oct 2009) | 3 lines
Modified the BMRB system test to have citation ID strings, rather than numbers.
........
r9766 | bugman | 2009-10-14 14:52:55 +0200 (Wed, 14 Oct 2009) | 3 lines
Citation ID strings are now handled by the bmrb.citation() user function.
........
r9767 | bugman | 2009-10-14 14:54:03 +0200 (Wed, 14 Oct 2009) | 3 lines
Fix for the bmrb.software() printout (it was saying bmrb.software_select(...))!
........
r9768 | bugman | 2009-10-14 15:27:17 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the get_cite_id_num() method to convert the citation ID string to a citation ID number.
........
r9769 | bugman | 2009-10-14 15:27:54 +0200 (Wed, 14 Oct 2009) | 3 lines
The BMRB file now uses the citation ID numbers properly.
........
r9770 | bugman | 2009-10-14 15:39:29 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the TempCalibrationMethod and TempControlMethod tags to the General Relaxation saveframe.
........
r9771 | bugman | 2009-10-14 15:40:22 +0200 (Wed, 14 Oct 2009) | 3 lines
Changed the label class variable.
........
r9772 | bugman | 2009-10-14 15:51:32 +0200 (Wed, 14 Oct 2009) | 3 lines
Added calls to the relax_data.temp_calibration() and relax_data.temp_control() user functions.
........
r9773 | bugman | 2009-10-14 15:55:39 +0200 (Wed, 14 Oct 2009) | 3 lines
Fix for the call to relax_data.temp_*() in the BMRB system test.
........
r9774 | bugman | 2009-10-14 17:57:26 +0200 (Wed, 14 Oct 2009) | 3 lines
The temperature control and calibration methods are now being placed into the BMRB file.
........
r9775 | bugman | 2009-10-14 18:22:54 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the, as of yet unused, SampleConditionListID tag to the General_relaxation saveframe.
........
r9776 | bugman | 2009-10-14 18:28:40 +0200 (Wed, 14 Oct 2009) | 8 lines
Updated or added the Relaxation_* tags of General_relaxation saveframe.
These include:
Relaxation_coherence_type
Relaxation_type_common_name
Relaxation_val_units
........
r9777 | bugman | 2009-10-14 18:30:36 +0200 (Wed, 14 Oct 2009) | 5 lines
Changed the R1 and R2 common names.
These now match those described at https://mail.gna.org/public/relax-devel/2009-03/msg00037.html.
........
r9778 | bugman | 2009-10-14 18:31:28 +0200 (Wed, 14 Oct 2009) | 3 lines
Changed RelaxationValUnits to match https://mail.gna.org/public/relax-devel/2009-03/msg00037.html.
........
r9779 | bugman | 2009-10-14 19:09:27 +0200 (Wed, 14 Oct 2009) | 3 lines
Expanded the General_relaxation saveframe to accept almost all info into bmrblib.
........
r9780 | bugman | 2009-10-25 22:10:56 +0100 (Sun, 25 Oct 2009) | 3 lines
Expanded the Modelfree saveframe to include much more information.
........
r9781 | bugman | 2009-10-25 22:18:27 +0100 (Sun, 25 Oct 2009) | 3 lines
Expanded the add() method docstring to cover all args.
........
r9782 | bugman | 2009-10-25 22:22:09 +0100 (Sun, 25 Oct 2009) | 3 lines
The software citation IDs are now handled, and all the new model-free info supplied.
........
r9783 | bugman | 2009-10-26 15:26:13 +0100 (Mon, 26 Oct 2009) | 3 lines
The HeteronuclNOE saveframe now only has the temp control and calibration tags for v3.2.
........
r9784 | bugman | 2009-10-26 17:17:15 +0100 (Mon, 26 Oct 2009) | 5 lines
Reintroduced the temp_calibration and temp_control args to Relaxation.add().
These are not used and are provided as dummy args for compatibility between different BMRB formats.
........
r9785 | bugman | 2009-10-26 17:23:24 +0100 (Mon, 26 Oct 2009) | 3 lines
Made the temp calibration v3.2 specific for the heteronuclear NOE saveframe.
........
r9786 | bugman | 2009-10-26 17:28:34 +0100 (Mon, 26 Oct 2009) | 3 lines
Bug fix for the model free saveframe for v3.0 and v3.1 (previously called the OrderParameter saveframe).
........
r9787 | bugman | 2009-10-26 18:18:08 +0100 (Mon, 26 Oct 2009) | 6 lines
Atom info changes in the model-free saveframe.
The 'Atom_ID' tag is now changed to 'Obs_atom_ID' for v3.2. The Obs_atom_type and
Obs_atom_isotope_number tags have been added to the saveframe.
........
r9788 | bugman | 2009-10-26 18:19:18 +0100 (Mon, 26 Oct 2009) | 3 lines
relax now places the isotope number into the BMRB file.
........
r9789 | bugman | 2009-10-26 18:36:35 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a check to see if the element type has been specified.
........
r9790 | bugman | 2009-10-26 18:40:40 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a missing RelaxError import.
........
r9791 | bugman | 2009-10-26 18:46:04 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a call to the non-existent spin.element() user function.
........
r9792 | bugman | 2009-10-26 19:08:38 +0100 (Mon, 26 Oct 2009) | 3 lines
Implemented the spin.element() user function.
........
................
r12584 | bugman | 2011-02-19 15:08:38 +0100 (Sat, 19 Feb 2011) | 340 lines
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@.../svn/relax/branches/bmrb
........
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.
........
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.
........
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.
........
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.
........
r9801 | bugman | 2009-10-27 15:29:50 +0100 (Tue, 27 Oct 2009) | 3 lines
The translate function now handles numpy arrays.
........
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.
........
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.
........
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.
........
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!!!
........
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.
........
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.
........
r9808 | bugman | 2009-10-27 16:20:35 +0100 (Tue, 27 Oct 2009) | 3 lines
Added a catch for Rex error values of None.
........
r9809 | bugman | 2009-10-27 16:34:45 +0100 (Tue, 27 Oct 2009) | 3 lines
Expansion of the chemical shift anisotropy saveframe.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9821 | bugman | 2009-10-27 23:20:02 +0100 (Tue, 27 Oct 2009) | 3 lines
Added the SfFramecode tag to the general relaxation saveframe.
........
r9822 | bugman | 2009-10-27 23:20:29 +0100 (Tue, 27 Oct 2009) | 3 lines
Variable renaming.
........
r9823 | bugman | 2009-10-27 23:22:45 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the previous variable change.
........
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.
........
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).
........
r9826 | bugman | 2009-10-28 11:05:19 +0100 (Wed, 28 Oct 2009) | 3 lines
Fix for the _General_Relaxation_list.Sf_category tag.
........
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.
........
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.
........
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.
........
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.
........
r9836 | bugman | 2009-10-28 18:20:02 +0100 (Wed, 28 Oct 2009) | 3 lines
Shifted a line of code to the correct place.
........
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.
........
r9838 | bugman | 2009-10-29 11:23:53 +0100 (Thu, 29 Oct 2009) | 3 lines
Added support for the method saveframe.
........
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.
........
r9840 | bugman | 2009-10-29 11:59:17 +0100 (Thu, 29 Oct 2009) | 3 lines
Created the bmrb.thiol_state() user function.
........
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.
........
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.
........
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.
........
r9844 | bugman | 2009-10-29 14:42:57 +0100 (Thu, 29 Oct 2009) | 3 lines
The method saveframes are now accessible from the API.
........
r9845 | bugman | 2009-10-29 14:43:56 +0100 (Thu, 29 Oct 2009) | 3 lines
Missing import fix.
........
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.
........
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.
........
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.
........
r9849 | bugman | 2009-10-29 14:55:05 +0100 (Thu, 29 Oct 2009) | 3 lines
The script name was being overwritten.
........
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.
........
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.
........
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.
........
r9853 | bugman | 2009-10-29 16:23:02 +0100 (Thu, 29 Oct 2009) | 3 lines
Changed the method saveframe category name.
........
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 .
-----
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.
-----
........
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.
........
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.
........
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.
........
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.
........
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'.
........
r9860 | bugman | 2009-10-29 18:25:57 +0100 (Thu, 29 Oct 2009) | 3 lines
Fixes for the BMRB system test.
........
r9861 | bugman | 2009-10-29 19:12:15 +0100 (Thu, 29 Oct 2009) | 3 lines
Suppressed a retarded warning message in pystarlib.
........
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.
........
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.
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
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/).
........
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).
........
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.
........
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.
........
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.
........
r11264 | bugman | 2010-06-29 23:16:35 +0200 (Tue, 29 Jun 2010) | 3 lines
Started to create the diffusion tensor saveframe.
........
................
r12585 | bugman | 2011-02-19 15:12:38 +0100 (Sat, 19 Feb 2011) | 122 lines
Merged revisions 11633,11638-11660 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb
........
r11633 | bugman | 2010-10-06 18:55:05 +0200 (Wed, 06 Oct 2010) | 5 lines
Bug fix for the BMRB system tests.
The file paths were incorrect.
........
r11638 | bugman | 2010-10-15 17:53:49 +0200 (Fri, 15 Oct 2010) | 5 lines
Fixes for the BMRB system tests.
These tests were non-functional!
........
r11639 | bugman | 2010-10-15 18:05:22 +0200 (Fri, 15 Oct 2010) | 3 lines
Fixes for the file paths to sync with the 1.3 line.
........
r11640 | bugman | 2010-10-15 18:05:59 +0200 (Fri, 15 Oct 2010) | 3 lines
Fix for all the BMRB related user functions - exec_info is now a private variable.
........
r11641 | bugman | 2010-10-19 15:33:49 +0200 (Tue, 19 Oct 2010) | 3 lines
Added checks and the RelaxNoModuleInstallError relax error to make sure that bmrblib is installed.
........
r11642 | bugman | 2010-10-19 20:05:32 +0200 (Tue, 19 Oct 2010) | 6 lines
The diffusion tensor saveframe is now being created in the BMRB submission file.
This saveframe is not complete and contains no tensor information, as bmrblib does not support this
yet.
........
r11643 | bugman | 2010-10-20 20:04:43 +0200 (Wed, 20 Oct 2010) | 5 lines
Removed the v3.2 BMRB imports as these no longer exist.
There is no 3.2 version!
........
r11644 | bugman | 2010-10-21 00:17:29 +0200 (Thu, 21 Oct 2010) | 3 lines
Removed the BMRB NMR-STAR v3.2 system test and started to add data checks for the old and new pipes.
........
r11645 | bugman | 2010-10-21 20:08:53 +0200 (Thu, 21 Oct 2010) | 6 lines
Advancements for the diffusion tensor support in the BMRB file.
All of the tensor data is now being written out, and a very incomplete bmrb_read() function has been
added.
........
r11646 | bugman | 2010-10-21 22:35:20 +0200 (Thu, 21 Oct 2010) | 3 lines
The diffusion tensor bmrb_read() function is now complete and the tensor is being created.
........
r11647 | bugman | 2010-10-21 23:42:05 +0200 (Thu, 21 Oct 2010) | 3 lines
The prolate diffusion tensors are now correctly created from the BMRB files.
........
r11648 | bugman | 2010-10-22 00:42:54 +0200 (Fri, 22 Oct 2010) | 3 lines
The reading of entity information from the BMRB file is fixed.
........
r11649 | bugman | 2010-10-22 01:30:29 +0200 (Fri, 22 Oct 2010) | 5 lines
Fixes for the citations BMRB writing.
The author structure is now split up before sending to the saveframe class.
........
r11650 | bugman | 2010-10-22 11:33:46 +0200 (Fri, 22 Oct 2010) | 3 lines
The spectrometer frequency is now converted to MHz before being sent to BMRBlib.
........
r11651 | bugman | 2010-10-22 15:18:18 +0200 (Fri, 22 Oct 2010) | 3 lines
The saveframe description for the relax scripts now says that they are relax scripts.
........
r11652 | bugman | 2010-10-22 17:59:25 +0200 (Fri, 22 Oct 2010) | 3 lines
The relaxation data reading is functional again, matching the new design of bmrblib.
........
r11653 | bugman | 2010-10-22 19:21:54 +0200 (Fri, 22 Oct 2010) | 3 lines
The restoration of the data from BMRB files into data pipes is now fully tested in the system tests.
........
r11654 | bugman | 2010-10-22 19:53:19 +0200 (Fri, 22 Oct 2010) | 3 lines
Caught when no diffusion tensor data is yielded by the bmrblib loop() method.
........
r11655 | bugman | 2010-10-22 22:11:38 +0200 (Fri, 22 Oct 2010) | 3 lines
A few system and unit test fixes broken by recent rearrangements of the diffusion tensor code.
........
r11656 | bugman | 2010-10-22 23:10:00 +0200 (Fri, 22 Oct 2010) | 6 lines
Fix for the test_read() unit test of generic_fns.relax_data.read().
The relaxation data structures are now handled differently in this branch and all data structures
have the same from for all spins, even if data is missing.
........
r11657 | bugman | 2010-10-25 09:56:03 +0200 (Mon, 25 Oct 2010) | 3 lines
Restored the reversal of the rotation matrix when determining Euler angles for a tensor in the PDB frame.
........
r11658 | bugman | 2010-10-25 10:04:58 +0200 (Mon, 25 Oct 2010) | 5 lines
Shifted the core of the model-free _select_model() method into _model_map().
This allows other parts of the code to translate model names to model-free equations and parameters.
........
r11659 | bugman | 2010-10-25 10:07:51 +0200 (Mon, 25 Oct 2010) | 5 lines
Removed the model-free and CSA info from the blacklisted spin variables.
This is to test the implementation of model-free and CSA BMRB saveframe reading.
........
r11660 | bugman | 2010-10-25 10:08:53 +0200 (Mon, 25 Oct 2010) | 3 lines
Implemented the reading of model-free and CSA BMRB saveframes from NMR-STAR files.
........
................
r12586 | bugman | 2011-02-19 15:17:02 +0100 (Sat, 19 Feb 2011) | 327 lines
Merged revisions 11691-11693,11699,11921,12076-12079,12419,12461-12513,12515-12516,12521-12530 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb
........
r11691 | bugman | 2010-11-22 18:17:49 +0100 (Mon, 22 Nov 2010) | 3 lines
The spheroid theta and phi angles are now taken from the BMRB input file.
........
r11692 | bugman | 2010-11-22 19:12:19 +0100 (Mon, 22 Nov 2010) | 5 lines
The version 3.0 BMRB system test now skips the local_tm and diffusion data.
The old NMR-STAR definition cannot support this data.
........
r11693 | bugman | 2010-11-22 19:21:45 +0100 (Mon, 22 Nov 2010) | 3 lines
Comment expansion in the BMRB system tests.
........
r11699 | bugman | 2010-11-27 23:57:58 +0100 (Sat, 27 Nov 2010) | 3 lines
The NMR spectrometer and relaxation experiment saveframes are now created.
........
r11921 | bugman | 2010-12-20 17:17:50 +0100 (Mon, 20 Dec 2010) | 6 lines
Fix for the molecule.type() user function due to the addition of the type arg to molecule.create().
The molecule.type() user function now uses a different naming of molecules. These are translated
to BMRB names when creating BRMB deposition files.
........
r12076 | bugman | 2010-12-31 15:08:13 +0100 (Fri, 31 Dec 2010) | 3 lines
The BMRB system test now checks for the bond length in the spin containers.
........
r12077 | bugman | 2010-12-31 15:09:33 +0100 (Fri, 31 Dec 2010) | 3 lines
The bond length is now placed in the temporary tag Model_free.Val_bond_length in the BMRB file.
........
r12078 | bugman | 2010-12-31 15:16:57 +0100 (Fri, 31 Dec 2010) | 3 lines
The bond length is now read from the BMRB files created by relax.
........
r12079 | bugman | 2010-12-31 15:26:27 +0100 (Fri, 31 Dec 2010) | 3 lines
The bond length is not in the NMR-STAR v3.0 file!
........
r12419 | bugman | 2011-01-21 14:46:36 +0100 (Fri, 21 Jan 2011) | 3 lines
ContainerList has been replaced by RelaxListType in the latest svnmerge.py update.
........
r12461 | bugman | 2011-01-31 14:50:05 +0100 (Mon, 31 Jan 2011) | 3 lines
Spin names are not used in the spin ID strings as the AtomName tag is not compulsory.
........
r12462 | bugman | 2011-01-31 14:51:21 +0100 (Mon, 31 Jan 2011) | 5 lines
Removed the molecule name generation from the entity data, as the entity data is not always there.
This fixes a crash when reading BMRB files with no entity saveframe.
........
r12463 | bugman | 2011-01-31 15:07:25 +0100 (Mon, 31 Jan 2011) | 5 lines
The number of spins is now constructed from the 's2' var if 'data_ids' does not exist.
This allows v2.1 model-free saveframes to be read.
........
r12464 | bugman | 2011-01-31 15:19:03 +0100 (Mon, 31 Jan 2011) | 6 lines
Reverted r12461 as this was the wrong way to do this.
The command used was:
svn merge -r12461:12460 .
........
r12465 | bugman | 2011-01-31 15:38:28 +0100 (Mon, 31 Jan 2011) | 5 lines
Shifted the sequence generation code into the BMRB specific generate_sequence() function.
This is to allow for strangeness in the BMRB entries :S
........
r12466 | bugman | 2011-01-31 15:46:36 +0100 (Mon, 31 Jan 2011) | 3 lines
The reading of BMRB model-free saveframes will now generate sequence data if needed.
........
r12467 | bugman | 2011-01-31 15:48:09 +0100 (Mon, 31 Jan 2011) | 3 lines
Removed a debugging print out from generate_sequence().
........
r12468 | bugman | 2011-01-31 16:06:26 +0100 (Mon, 31 Jan 2011) | 3 lines
Better handling of missing data in the BMRB model-free saveframes.
........
r12469 | bugman | 2011-01-31 16:31:56 +0100 (Mon, 31 Jan 2011) | 3 lines
The relaxation data pack_data() function can now handle missing errors.
........
r12470 | bugman | 2011-01-31 16:33:17 +0100 (Mon, 31 Jan 2011) | 3 lines
Some missing imports.
........
r12471 | bugman | 2011-01-31 16:36:54 +0100 (Mon, 31 Jan 2011) | 3 lines
The model-free model is only created if there is one in the BMRB file now.
........
r12472 | bugman | 2011-01-31 16:48:53 +0100 (Mon, 31 Jan 2011) | 5 lines
Added a catch for broken sequence information in the BMRB file.
This will result in no spin being found.
........
r12473 | bugman | 2011-01-31 17:02:11 +0100 (Mon, 31 Jan 2011) | 3 lines
Fixes for the BMRB system tests - the install path is now in the status object and not __main__.
........
r12474 | bugman | 2011-01-31 18:06:50 +0100 (Mon, 31 Jan 2011) | 5 lines
Fixes for the experimental info data structures.
The element_name and element_desc are now simply name and desc in the Element container.
........
r12475 | bugman | 2011-01-31 18:44:11 +0100 (Mon, 31 Jan 2011) | 3 lines
Fix for the model-free _model_setup() which was not merged from the main 1.3 line.
........
r12476 | bugman | 2011-01-31 19:39:54 +0100 (Mon, 31 Jan 2011) | 3 lines
The BMRB generate_sequence() function can now handle if no molecule name is given.
........
r12477 | bugman | 2011-01-31 19:52:37 +0100 (Mon, 31 Jan 2011) | 3 lines
The BMRB generate_sequence() function can now handle args of None.
........
r12478 | bugman | 2011-01-31 19:57:00 +0100 (Mon, 31 Jan 2011) | 3 lines
Model-free saveframes without any data are now skipped.
........
r12479 | bugman | 2011-02-01 10:50:44 +0100 (Tue, 01 Feb 2011) | 3 lines
Fixed a RelaxError in _model_map() so that a model-free model of None will raise the correct error.
........
r12480 | bugman | 2011-02-01 10:53:32 +0100 (Tue, 01 Feb 2011) | 3 lines
Fixed the print out of a RelaxError and Warning for the model-free model from the BMRB file.
........
r12481 | bugman | 2011-02-01 11:01:22 +0100 (Tue, 01 Feb 2011) | 3 lines
Added a catch to _bmrb_model_map() for Modelfree4 model names in the BMRB files.
........
r12482 | bugman | 2011-02-01 14:20:22 +0100 (Tue, 01 Feb 2011) | 3 lines
Expanded the conversion of Modelfree4 model numbers to include all of the relax model numbers as well.
........
r12483 | bugman | 2011-02-01 14:43:41 +0100 (Tue, 01 Feb 2011) | 3 lines
The Python round() function is now used to create the MHz frequency label for the relaxation data.
........
r12484 | bugman | 2011-02-01 15:51:49 +0100 (Tue, 01 Feb 2011) | 5 lines
The molecule number from EntityID is now being used to fill in the model-free data.
This is necessary for multiple molecule entries in BMRB files.
........
r12485 | bugman | 2011-02-01 16:26:23 +0100 (Tue, 01 Feb 2011) | 3 lines
The isotope number is now being guessed from the atom name if not given in the BMRB file.
........
r12486 | bugman | 2011-02-01 16:41:04 +0100 (Tue, 01 Feb 2011) | 3 lines
Better handling of the EntityID tag in the model-free saveframe.
........
r12487 | bugman | 2011-02-01 16:42:33 +0100 (Tue, 01 Feb 2011) | 3 lines
The relaxation frequency label is now rounded to the nearest factor of 10.
........
r12488 | bugman | 2011-02-01 17:00:01 +0100 (Tue, 01 Feb 2011) | 3 lines
The correlation times are now being scaled based on the TauEValUnits tag value.
........
r12489 | bugman | 2011-02-01 17:33:03 +0100 (Tue, 01 Feb 2011) | 3 lines
The relax model-free model name in the BMRB file can now be handled.
........
r12490 | bugman | 2011-02-01 17:37:35 +0100 (Tue, 01 Feb 2011) | 3 lines
The correlation time errors are now scaled as well.
........
r12491 | bugman | 2011-02-01 20:03:23 +0100 (Tue, 01 Feb 2011) | 3 lines
Shifted some of the code out of specific_fns/model_free/bmrb.py for use in generic_fns/relax_data.py.
........
r12492 | bugman | 2011-02-01 20:04:57 +0100 (Tue, 01 Feb 2011) | 3 lines
Fixes for the new generic_fns.bmrb functions molecule_names() and num_spins().
........
r12493 | bugman | 2011-02-01 20:07:46 +0100 (Tue, 01 Feb 2011) | 3 lines
specific_fns.model_free.bmrb now uses the generic_fns.bmrb functions derived from itself.
........
r12494 | bugman | 2011-02-01 20:10:30 +0100 (Tue, 01 Feb 2011) | 3 lines
Shifted the spin ID generation code into generic_fns.bmrb.generate_sequence().
........
r12495 | bugman | 2011-02-01 20:11:36 +0100 (Tue, 01 Feb 2011) | 3 lines
Fix for molecule_names(), the list is now being returned.
........
r12496 | bugman | 2011-02-01 20:24:54 +0100 (Tue, 01 Feb 2011) | 3 lines
The Rex value read from the BMRB file is now scaled to the correct value.
........
r12497 | bugman | 2011-02-01 20:29:43 +0100 (Tue, 01 Feb 2011) | 3 lines
A fix for BMRB files with no relaxation data - Rex cannot be scaled to the correct value!!!
........
r12498 | bugman | 2011-02-01 20:44:06 +0100 (Tue, 01 Feb 2011) | 3 lines
Missing spaces in the BMRB model-free model name are now accepted.
........
r12499 | bugman | 2011-02-01 20:59:41 +0100 (Tue, 01 Feb 2011) | 3 lines
Atom names can now be missing from the model-free saveframes.
........
r12500 | bugman | 2011-02-01 21:10:47 +0100 (Tue, 01 Feb 2011) | 3 lines
Added 'S2, te, S2f' as a BMRB 'm5' model-free model.
........
r12501 | bugman | 2011-02-01 21:34:55 +0100 (Tue, 01 Feb 2011) | 3 lines
Brackets are now removed from the molecule name - this kills the spin IDs.
........
r12502 | bugman | 2011-02-01 21:37:39 +0100 (Tue, 01 Feb 2011) | 3 lines
Atom types of '.' in the model-free saveframes can now be handled.
........
r12503 | bugman | 2011-02-02 13:26:24 +0100 (Wed, 02 Feb 2011) | 3 lines
The default version of 3.1 in all the BMRB user functions has been turned off.
........
r12504 | bugman | 2011-02-02 13:27:46 +0100 (Wed, 02 Feb 2011) | 3 lines
The BMRB user function version args can now be None to allow Bmrblib decide on the default version.
........
r12505 | bugman | 2011-02-02 13:43:13 +0100 (Wed, 02 Feb 2011) | 3 lines
The model-free bmrb module is now using the new bmrblib create_nmr_star() interface.
........
r12506 | bugman | 2011-02-02 16:47:02 +0100 (Wed, 02 Feb 2011) | 3 lines
Created the BMRB list_sample_conditions() function to return a list of sample condition names.
........
r12507 | bugman | 2011-02-02 16:53:10 +0100 (Wed, 02 Feb 2011) | 3 lines
The model-free bmrb_read() now accepts a sample conditions arg and checks that only one is loaded.
........
r12508 | bugman | 2011-02-02 17:01:31 +0100 (Wed, 02 Feb 2011) | 3 lines
The bmrb.read() user function now accepts the sample_conditions arg.
........
r12509 | bugman | 2011-02-02 18:25:45 +0100 (Wed, 02 Feb 2011) | 3 lines
The back-end of the bmrb.read() user function is now recognising the sample_conditions arg.
........
r12510 | bugman | 2011-02-02 19:19:53 +0100 (Wed, 02 Feb 2011) | 5 lines
The sample_conditions arg to bmrb.read() is now set to None.
This is to allow single condition files to be always read.
........
r12511 | bugman | 2011-02-03 13:03:58 +0100 (Thu, 03 Feb 2011) | 3 lines
Fix for generic_fns.mol_res_spin.bmrb_read() for when no molecule name is present.
........
r12512 | bugman | 2011-02-03 13:30:10 +0100 (Thu, 03 Feb 2011) | 3 lines
Square brackets and commas are now also removed from the BMRB molecule name.
........
r12513 | bugman | 2011-02-03 20:34:33 +0100 (Thu, 03 Feb 2011) | 3 lines
Fix for the Rex scaling - the factor was incorrect!
........
r12515 | bugman | 2011-02-07 15:05:54 +0100 (Mon, 07 Feb 2011) | 3 lines
The sample conditions label is now being used to select the correct BMRB saveframes to read.
........
r12516 | bugman | 2011-02-07 15:17:28 +0100 (Mon, 07 Feb 2011) | 3 lines
Fix for the sample label matching - this is only performed if the sample label is given.
........
r12521 | bugman | 2011-02-14 19:43:21 +0100 (Mon, 14 Feb 2011) | 3 lines
Removed a debugging print out.
........
r12522 | bugman | 2011-02-15 08:55:04 +0100 (Tue, 15 Feb 2011) | 3 lines
The relaxation values and errors from the BMRB file are being converted from ms to s now.
........
r12523 | bugman | 2011-02-15 09:00:39 +0100 (Tue, 15 Feb 2011) | 3 lines
Fixes for pack_data() to allow the errors to be a numpy array.
........
r12524 | bugman | 2011-02-15 09:13:40 +0100 (Tue, 15 Feb 2011) | 3 lines
The values are now properly scaled and values and errors are inverted to go from Tx to Rx values.
........
r12525 | bugman | 2011-02-15 11:48:51 +0100 (Tue, 15 Feb 2011) | 3 lines
Better handling of missing data in the BMRB relaxation saveframes.
........
r12526 | bugman | 2011-02-15 11:57:37 +0100 (Tue, 15 Feb 2011) | 3 lines
Fix for the num_spins() BMRB function - the keys are not always present.
........
r12527 | bugman | 2011-02-15 14:48:21 +0100 (Tue, 15 Feb 2011) | 3 lines
All te model-free parameters in BMRB files which should be ts are now being converted.
........
r12528 | bugman | 2011-02-15 18:11:21 +0100 (Tue, 15 Feb 2011) | 3 lines
Simplification of the BMRB num_spins() function.
........
r12529 | bugman | 2011-02-16 15:38:49 +0100 (Wed, 16 Feb 2011) | 3 lines
Missing model-free parameter error tags in BMRB files can now be handled.
........
r12530 | bugman | 2011-02-16 15:40:29 +0100 (Wed, 16 Feb 2011) | 3 lines
Updated the BMRB specific_fns bmrb_read() method to include the sample conditions.
........
................
r12587 | bugman | 2011-02-19 15:18:05 +0100 (Sat, 19 Feb 2011) | 23 lines
Merged revisions 12532-12534,12576 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb
........
r12532 | bugman | 2011-02-17 10:21:43 +0100 (Thu, 17 Feb 2011) | 3 lines
Fix for the _bmrb_model_map() method - the bad models must come first in the list!
........
r12533 | bugman | 2011-02-17 10:23:31 +0100 (Thu, 17 Feb 2011) | 3 lines
The error tags from the Order_parameters saveframe are only used if they exist.
........
r12534 | bugman | 2011-02-17 10:41:36 +0100 (Thu, 17 Feb 2011) | 5 lines
The Modelfree software problem of calling ts te is now handled correctly.
The te parameter is now converted to ts, and the te parameter and error in relax are set to None.
........
r12576 | bugman | 2011-02-18 18:29:53 +0100 (Fri, 18 Feb 2011) | 3 lines
Fix for the PDC system tests - the generic_fns.relax_data.pack_data() args are different in the branch.
........
................
r12588 | bugman | 2011-02-19 15:26:46 +0100 (Sat, 19 Feb 2011) | 6 lines
Fix for the badly merged data.data_classes module.
Due to the age of the branch, this was quite heavily damaged. However the file in the bmrb branch
is identical to that of the 1.3 line, prior to merging of the branch back in.
................
r12589 | bugman | 2011-02-19 15:39:47 +0100 (Sat, 19 Feb 2011) | 5 lines
Fix for the diffusion tensor module.
This was also destroyed in the merger of the bmrb branch.
................
r12590 | bugman | 2011-02-19 15:48:30 +0100 (Sat, 19 Feb 2011) | 3 lines
The BMRB system tests are now skipped if the bmrblib cannot be found.
................
r12591 | bugman | 2011-02-19 15:50:33 +0100 (Sat, 19 Feb 2011) | 3 lines
Removed the Numeric module from the --info print out as it is completely unused now.
................
r12592 | bugman | 2011-02-19 15:52:43 +0100 (Sat, 19 Feb 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/bmrb
................
