Author: bugman
Date: Sat Feb 19 15:02:05 2011
New Revision: 12583
URL: http://svn.gna.org/viewcvs/relax?rev=12583&view=rev
Log:
Merged revisions 9708,9710-9746,9748-9792 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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.
........
Added:
1.3/bmrblib/citations/citations.py
- copied unchanged from r9792,
branches/bmrb/bmrblib/citations/citations.py
1.3/bmrblib/kinetics/heteronucl_NOEs_v3_2.py
- copied unchanged from r9792,
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py
1.3/bmrblib/thermodynamics/model_free.py
- copied unchanged from r9792,
branches/bmrb/bmrblib/thermodynamics/model_free.py
1.3/bmrblib/thermodynamics/model_free_v3_1.py
- copied unchanged from r9792,
branches/bmrb/bmrblib/thermodynamics/model_free_v3_1.py
1.3/bmrblib/thermodynamics/model_free_v3_2.py
- copied unchanged from r9792,
branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py
1.3/data/exp_info.py
- copied unchanged from r9792, branches/bmrb/data/exp_info.py
1.3/generic_fns/exp_info.py
- copied unchanged from r9792, branches/bmrb/generic_fns/exp_info.py
Removed:
1.3/bmrblib/thermodynamics/order_parameters.py
1.3/bmrblib/thermodynamics/order_parameters_v3_1.py
1.3/generic_fns/bmrb_saveframes.py
Modified:
1.3/ (props changed)
1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py
1.3/bmrblib/base_classes.py
1.3/bmrblib/citations/__init__.py
1.3/bmrblib/experimental_details/software.py
1.3/bmrblib/kinetics/general_relaxation.py
1.3/bmrblib/kinetics/heteronucl_NOEs.py
1.3/bmrblib/kinetics/relaxation.py
1.3/bmrblib/misc.py
1.3/bmrblib/nmr_star_dict.py
1.3/bmrblib/nmr_star_dict_v3_1.py
1.3/bmrblib/nmr_star_dict_v3_2.py
1.3/bmrblib/thermodynamics/__init__.py
1.3/data/__init__.py
1.3/data/data_classes.py
1.3/data/pipe_container.py
1.3/generic_fns/__init__.py
1.3/generic_fns/bmrb.py
1.3/generic_fns/mol_res_spin.py
1.3/generic_fns/relax_data.py
1.3/prompt/bmrb.py
1.3/prompt/relax_data.py
1.3/prompt/spin.py
1.3/relax_errors.py
1.3/specific_fns/model_free/bmrb.py
1.3/test_suite/system_tests/scripts/bmrb_rw.py
1.3/version.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/NMR_parameters/chem_shift_anisotropy.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/base_classes.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/base_classes.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/citations/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/citations/__init__.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/experimental_details/software.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/experimental_details/software.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/kinetics/general_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/general_relaxation.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/heteronucl_NOEs.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/kinetics/relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/kinetics/relaxation.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/misc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/misc.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/nmr_star_dict.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/nmr_star_dict_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/nmr_star_dict_v3_1.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/nmr_star_dict_v3_2.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/nmr_star_dict_v3_2.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/bmrblib/thermodynamics/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/thermodynamics/__init__.py?rev=12583&r1=12582&r2=12583&view=diff
Removed: 1.3/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/thermodynamics/order_parameters.py?rev=12582&view=auto
Removed: 1.3/bmrblib/thermodynamics/order_parameters_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/bmrblib/thermodynamics/order_parameters_v3_1.py?rev=12582&view=auto
Modified: 1.3/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/__init__.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/data_classes.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/pipe_container.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/__init__.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12583&r1=12582&r2=12583&view=diff
Removed: 1.3/generic_fns/bmrb_saveframes.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb_saveframes.py?rev=12582&view=auto
Modified: 1.3/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12583&r1=12582&r2=12583&view=diff
Modified: 1.3/prompt/relax_data.py
[... 17 lines stripped ...]
r12583 - in /1.3: ./ bmrblib/ bmrblib/NMR_parameters/ bmrblib/citations/ bmrblib/experimental_details/ bmrblib/kinetics/ bmr...