[r9998]
by
bugman
Added the analysis specific API method is_spin_param() to the frame order module.
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2009-11-27 15:00:04
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Tree
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[r9997]
by
bugman
Fixed a bug introduced in r9996.
The mf_minimise module conflicts were not properly resolved. This should now work better.
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2009-11-27 13:57:08
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Tree
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[r9996]
by
bugman
Merged revisions 9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834,9871-9875,9891-9986 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r9696 | semor | 2009-10-09 14:44:40 +0200 (Fri, 09 Oct 2009) | 10 lines
Improved the error handling for AICc model selection.
The code now tells users with too small datasets (n<=k) why AICc model selection does not work in
their situation.
This follows a discussion started at:
https://mail.gna.org/public/relax-devel/2009-10/msg00015.html
(# Message-id: <4ACD6F60.7060102@...>)
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r9700 | bugman | 2009-10-09 18:00:30 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a copyright notice and a function for returning the SVN revision number to the version module.
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r9706 | bugman | 2009-10-09 18:47:13 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a function to get the SVN URL.
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r9709 | bugman | 2009-10-09 20:06:21 +0200 (Fri, 09 Oct 2009) | 3 lines
Comment fix.
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r9747 | bugman | 2009-10-12 16:00:39 +0200 (Mon, 12 Oct 2009) | 3 lines
__linear_ave() is no longer a private function.
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r9794 | bugman | 2009-10-27 10:59:25 +0100 (Tue, 27 Oct 2009) | 7 lines
Added user variable checking to the full_analysis.py script.
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-10/msg00009.html (Message-id:
<E45CDDF4A4E54B34A36BFBA62E6BFF20@...>).
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r9799 | bugman | 2009-10-27 15:24:25 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the frame order grid search.
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r9800 | bugman | 2009-10-27 15:25:08 +0100 (Tue, 27 Oct 2009) | 3 lines
Created the structure.get_pos() user function for extracting atomic positions.
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r9829 | bugman | 2009-10-28 11:47:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added functions for determining the element name and isotope number from an isotope name.
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r9831 | bugman | 2009-10-28 11:51:19 +0100 (Wed, 28 Oct 2009) | 3 lines
Bug fix for the new isotope functions.
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r9834 | bugman | 2009-10-28 13:48:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added checks for insufficient or single field strength relaxation data.
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r9871 | semor | 2009-11-18 15:20:42 +0100 (Wed, 18 Nov 2009) | 6 lines
Added references to the consistency tests code.
In particular, the reference for this newly published paper was added:
Morin & Gagne (2009) JBNMR, 45: 361-372.
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r9872 | semor | 2009-11-18 16:58:50 +0100 (Wed, 18 Nov 2009) | 7 lines
Added references and instructions in the sample script for consistency testing.
This is as proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2009-11/msg00034.html
(Message-id: <7f080ed10911180653w6b59b40dn1e8f715d9b718fd5@...>)
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r9873 | semor | 2009-11-18 17:58:39 +0100 (Wed, 18 Nov 2009) | 5 lines
Added DOI links to the citations and corrected a fused f and i character.
This was proposed by Edward.
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r9874 | semor | 2009-11-18 18:29:02 +0100 (Wed, 18 Nov 2009) | 3 lines
Corrected other strange characters causing failures...
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r9875 | bugman | 2009-11-19 10:37:23 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the 'Branches' subsection of the development chapter into a proper section.
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r9891 | bugman | 2009-11-24 09:24:48 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the dx.map() user function interface.
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r9892 | bugman | 2009-11-24 10:05:30 +0100 (Tue, 24 Nov 2009) | 10 lines
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
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r9893 | bugman | 2009-11-24 10:17:37 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the base class return_conversion_factor() method.
The spin_id arg is now accepted.
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r9894 | bugman | 2009-11-24 10:32:01 +0100 (Tue, 24 Nov 2009) | 6 lines
Created unit tests for the specific_fns API.
This checks the consistency of methods across the API, using method names and arg checks. Only the
frame order theories are currently checked.
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r9895 | bugman | 2009-11-24 10:46:05 +0100 (Tue, 24 Nov 2009) | 3 lines
Renamed specific_fns.base_class.Common_functions to specific_fns.api_base.API_base.
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r9896 | bugman | 2009-11-24 10:55:57 +0100 (Tue, 24 Nov 2009) | 3 lines
The entirety of the specific_fns API is now checked.
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r9897 | bugman | 2009-11-24 10:57:13 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated for the __all__ list for the base_class to api_base rename.
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r9898 | bugman | 2009-11-24 11:07:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of the functions.
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r9899 | bugman | 2009-11-24 11:14:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the back_calc() method from the specific analysis API.
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r9900 | bugman | 2009-11-24 11:20:24 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the copy() method from the specific analysis API.
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r9901 | bugman | 2009-11-24 11:21:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Added a prototype calculate() method to the API.
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r9902 | bugman | 2009-11-24 11:42:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_param_vector() and disassemble_param_vector() from the specific analysis API.
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r9903 | bugman | 2009-11-24 11:45:10 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_scaling_matrix() from the specific analysis API.
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r9904 | bugman | 2009-11-24 11:52:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed back_calc() from the specific analysis API.
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r9905 | bugman | 2009-11-24 11:53:20 +0100 (Tue, 24 Nov 2009) | 3 lines
Completed removal of back_calc() from the specific analysis API.
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r9906 | bugman | 2009-11-24 11:56:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Added create_mc_data() to the specific analysis API.
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r9907 | bugman | 2009-11-24 12:18:58 +0100 (Tue, 24 Nov 2009) | 5 lines
Added data_names() to the specific analysis API.
General docstring clean ups as well.
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r9908 | bugman | 2009-11-24 12:39:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _assemble_param_vector() method.
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r9909 | bugman | 2009-11-24 12:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _disassemble_param_vector() method.
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r9910 | bugman | 2009-11-24 12:56:22 +0100 (Tue, 24 Nov 2009) | 15 lines
A large number of method and documentation variables to the specific analysis API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
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r9911 | bugman | 2009-11-24 12:58:24 +0100 (Tue, 24 Nov 2009) | 10 lines
Converted a number of methods to being private, removing them from the API.
These include:
_grid_search_setup()
_linear_constraints()
_model_setup()
_relax_time()
_select_model()
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r9912 | bugman | 2009-11-24 12:59:22 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the _select_model() method to be private, removing it from the API.
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r9913 | bugman | 2009-11-24 13:05:29 +0100 (Tue, 24 Nov 2009) | 5 lines
Clean up of the create_mc_data() API method across the board.
The spin_id keyword is now accepted by all, and is a keyword.
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r9914 | bugman | 2009-11-24 13:21:18 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring update to return_grace_string().
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r9915 | bugman | 2009-11-24 13:22:09 +0100 (Tue, 24 Nov 2009) | 5 lines
Fixes for the relaxation curve fitting API.
The fixes are for the return_data_name(), return_grace_string(), and return_units() methods.
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r9916 | bugman | 2009-11-24 13:25:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9917 | bugman | 2009-11-24 13:47:33 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring and default arg changes.
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r9918 | bugman | 2009-11-24 13:47:58 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed duplicated epydoc tags.
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r9919 | bugman | 2009-11-24 13:48:37 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire NOE API.
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r9920 | bugman | 2009-11-24 13:49:42 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9921 | bugman | 2009-11-24 14:04:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the check of the default values from the specific analysis API arg checks.
The defaults keyword values can be set to anything by the specific code!
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r9922 | bugman | 2009-11-24 14:52:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the string printout creation in the __check_method_args() method.
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r9923 | bugman | 2009-11-24 15:04:25 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the unused _read() method.
This has been superseded by the spectrum.read_intensities() user function.
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r9924 | bugman | 2009-11-24 15:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Added model_statistics() to the specific analysis API.
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r9925 | bugman | 2009-11-24 15:30:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire N-state model specific API.
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r9926 | bugman | 2009-11-24 15:32:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all self.__*() private methods to self._*() non-API methods.
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r9927 | bugman | 2009-11-24 15:40:14 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9928 | bugman | 2009-11-24 15:50:02 +0100 (Tue, 24 Nov 2009) | 3 lines
Added duplicate_data() to the specific analysis API.
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r9929 | bugman | 2009-11-24 16:46:59 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed some unused methods from the API.
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r9930 | bugman | 2009-11-24 16:48:38 +0100 (Tue, 24 Nov 2009) | 17 lines
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
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r9931 | bugman | 2009-11-24 16:59:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire model-free analysis specific API.
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r9932 | bugman | 2009-11-24 17:05:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all the model-free results methods from private to non-API.
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r9933 | bugman | 2009-11-24 17:08:00 +0100 (Tue, 24 Nov 2009) | 3 lines
Added an empty eliminate_doc variable to the specific analysis API.
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r9934 | bugman | 2009-11-24 17:51:20 +0100 (Tue, 24 Nov 2009) | 5 lines
More fixes for the __format_method() method.
The methods with args and keywords are now properly formatted!
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r9935 | bugman | 2009-11-24 18:02:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the eliminate() and model_statistics() API prototype methods.
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r9936 | bugman | 2009-11-24 18:03:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the N-state model model_statistics() API method.
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r9937 | bugman | 2009-11-24 18:05:40 +0100 (Tue, 24 Nov 2009) | 3 lines
Update for the return_conversion_factor() API prototype method.
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r9938 | bugman | 2009-11-24 18:15:06 +0100 (Tue, 24 Nov 2009) | 3 lines
Shifted many of the model-free specific methods out of the API.
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r9939 | bugman | 2009-11-24 18:35:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the specific analysis base API to use the model_info arg, returned from model_loop().
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r9940 | bugman | 2009-11-24 18:39:15 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated the N-state model model_statistics() method to the model_info arg.
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r9941 | bugman | 2009-11-24 18:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the model-free unit tests. The model_index arg is now called model_info.
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r9942 | bugman | 2009-11-24 18:41:28 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted many of the model-free methods to use model_info rather than model_index.
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r9943 | bugman | 2009-11-24 19:08:56 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the specific analysis base API set_selected_sim() method.
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r9944 | bugman | 2009-11-24 19:18:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the analysis specific base API sim_return_selected() method.
The model_info arg is now being used.
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r9945 | bugman | 2009-11-24 19:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the private __compare_objects() method to the non-API _compare_objects() method.
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r9946 | bugman | 2009-11-24 19:30:09 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of model-free methods, and separation of the private from the API methods.
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r9947 | bugman | 2009-11-24 19:58:18 +0100 (Tue, 24 Nov 2009) | 3 lines
A number of fixes for the model-free analysis specific API methods.
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r9948 | bugman | 2009-11-24 19:58:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Changes to the args for the base API data_init() method.
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r9949 | bugman | 2009-11-24 19:59:32 +0100 (Tue, 24 Nov 2009) | 3 lines
Updates to the methods of the reduced spectral density mapping API.
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r9950 | bugman | 2009-11-25 09:05:00 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the data_init() method for API consistency.
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r9951 | bugman | 2009-11-25 09:15:40 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted many of the J(w) mapping methods to use the model_info arg rather than spin.
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r9952 | bugman | 2009-11-25 09:19:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring updates for returned values.
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r9953 | bugman | 2009-11-25 09:21:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Alphabetical ordering of J(w) mapping methods, and separation of the private from the API methods.
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r9954 | bugman | 2009-11-25 09:26:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fix.
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r9955 | bugman | 2009-11-25 09:31:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the hybrid analysis API to match the base API.
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r9956 | bugman | 2009-11-25 09:38:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of the private and API methods in the hybrid specific analysis.
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r9957 | bugman | 2009-11-25 09:39:48 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted the frame order private methods into non-API methods.
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r9958 | bugman | 2009-11-25 09:44:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of all the non-API frame order specific methods.
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r9959 | bugman | 2009-11-25 09:46:39 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9960 | bugman | 2009-11-25 09:56:56 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the frame order specific analysis API methods to match the base API.
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r9961 | bugman | 2009-11-25 10:02:26 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the frame order user functions.
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r9962 | bugman | 2009-11-25 10:02:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Removal of set_frq() from the consistency testing analysis specific API.
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r9963 | bugman | 2009-11-25 10:07:09 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fixes.
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r9964 | bugman | 2009-11-25 10:17:49 +0100 (Wed, 25 Nov 2009) | 3 lines
More docstring updates.
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r9965 | bugman | 2009-11-25 10:18:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the consistency testing analysis specific API methods to match the base API.
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r9966 | bugman | 2009-11-25 10:43:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Fix for the consistency testing return_units() method for the arg name changes.
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r9967 | bugman | 2009-11-25 10:57:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9968 | bugman | 2009-11-25 10:59:05 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix and reformatting of generic_fns.pcs.read().
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r9969 | bugman | 2009-11-25 12:55:17 +0100 (Wed, 25 Nov 2009) | 5 lines
Decreased the user function docstring size in the relax manual.
This was changed from normal size to \scriptsize to decrease the number of pages in the manual.
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r9970 | bugman | 2009-11-25 13:06:03 +0100 (Wed, 25 Nov 2009) | 5 lines
The user function descriptions in the relax manual are now in columns.
This shrinks the manual even further.
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r9971 | bugman | 2009-11-25 13:11:52 +0100 (Wed, 25 Nov 2009) | 5 lines
Removed the \newpage command from the user function descriptions.
This cuts the manual size by over 100 pages!!!
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r9972 | bugman | 2009-11-25 13:18:28 +0100 (Wed, 25 Nov 2009) | 3 lines
Added '()' to the end of the user functions in the relax manual.
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r9973 | bugman | 2009-11-25 15:41:03 +0100 (Wed, 25 Nov 2009) | 3 lines
Turned all tables from the user functions in the relax manual into floating tables.
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r9974 | bugman | 2009-11-25 15:46:58 +0100 (Wed, 25 Nov 2009) | 5 lines
Clean up of the minimisation docstring.
This no longer causes problems in the relax manual.
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r9975 | bugman | 2009-11-25 15:54:01 +0100 (Wed, 25 Nov 2009) | 3 lines
Switched from the multicols package to just using \twocolumn and \onecolumn.
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r9976 | bugman | 2009-11-25 15:54:36 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the align_tensor.svd() docstring for the relax manual.
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r9977 | bugman | 2009-11-25 16:52:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Added rules to break the user function subsections in the manual apart.
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r9978 | bugman | 2009-11-25 17:18:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Modified the spin ID string documentation to be better presented in the relax manual.
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r9979 | bugman | 2009-11-26 09:09:29 +0100 (Thu, 26 Nov 2009) | 6 lines
User function call examples in the relax manual are now better formatted.
They are allowed to break after '.', '(', and '='. This is for the examples and the Defaults
subsubsection.
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r9980 | bugman | 2009-11-26 10:22:06 +0100 (Thu, 26 Nov 2009) | 3 lines
Allowed for hyphenation in the user function subsection titles.
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r9981 | bugman | 2009-11-26 12:20:26 +0100 (Thu, 26 Nov 2009) | 3 lines
Massive tables in the relax manual are now being split using the longtable package.
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r9982 | bugman | 2009-11-26 12:27:18 +0100 (Thu, 26 Nov 2009) | 3 lines
The tables in the user function chapter now have the same font size as the rest of the text.
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r9983 | bugman | 2009-11-26 12:33:35 +0100 (Thu, 26 Nov 2009) | 3 lines
Better formatting of the user function chapter by using \raggedbottom.
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r9984 | bugman | 2009-11-26 12:50:58 +0100 (Thu, 26 Nov 2009) | 3 lines
Fixed the boolean selection table to be nicer to the automatic manual compilation.
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r9985 | bugman | 2009-11-26 13:16:37 +0100 (Thu, 26 Nov 2009) | 3 lines
The longtables are now properly labelled.
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r9986 | bugman | 2009-11-26 18:36:27 +0100 (Thu, 26 Nov 2009) | 3 lines
Removed the checking of sequence data from generic_fns.value.set().
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2009-11-27 13:53:35
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Tree
|
[r9995]
by
bugman
Modified the program version print out to note that this is the ellipsoidal CS tensor branch.
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2009-11-27 11:31:45
|
Tree
|
[r9994]
by
bugman
Added the rest of the ellipsoidal CS tensor code to the 1.2.10 branch.
This code comes from Pavel Kaderavek <kada att chemi dot muni dot cz> and is located at
https://www.ncbr.chemi.muni.cz/~kada/relax-1.2.10_cst.tar.
The branch is now complete and functional. Conversion to the 1.3 line and code cleanups will be
very painful for this code!
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2009-11-27 11:24:08
|
Tree
|
[r9993]
by
bugman
Merged revisions 9454,9457-9526,9528-9658,9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834,9871-9875,9891-9986 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r9454 | bugman | 2009-09-03 15:23:45 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the non-dangerous Python3k update command.
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r9457 | bugman | 2009-09-03 17:53:41 +0200 (Thu, 03 Sep 2009) | 3 lines
Created a sub-directory for frame order test scripts.
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r9458 | bugman | 2009-09-03 18:18:51 +0200 (Thu, 03 Sep 2009) | 3 lines
Shifted the rigid frame order system test into the sub-directory.
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r9459 | bugman | 2009-09-03 18:31:23 +0200 (Thu, 03 Sep 2009) | 3 lines
Added another rigid frame order system test.
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r9460 | bugman | 2009-09-03 18:32:10 +0200 (Thu, 03 Sep 2009) | 3 lines
Renamed a frame order system test.
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r9461 | bugman | 2009-09-03 19:05:02 +0200 (Thu, 03 Sep 2009) | 3 lines
Specific architecture and optimisation details are now printed if the frame order system tests fail.
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r9462 | bugman | 2009-09-03 19:17:08 +0200 (Thu, 03 Sep 2009) | 3 lines
Fix for the new frame order system test - the results file goes to devnull.
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r9463 | bugman | 2009-09-03 19:25:01 +0200 (Thu, 03 Sep 2009) | 3 lines
The beta angle for the tensor rotations is now folded to be between 0 and pi.
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r9464 | bugman | 2009-09-04 10:24:52 +0200 (Fri, 04 Sep 2009) | 5 lines
Added a function for converting the frame order matrix to the rotational superoperator.
The function is called daeg_to_rotational_superoperator().
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r9465 | bugman | 2009-09-04 11:21:28 +0200 (Fri, 04 Sep 2009) | 5 lines
Fix for the new daeg_to_rotational_superoperator() function.
The frame order matrix shape is now restored.
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r9466 | bugman | 2009-09-04 16:12:31 +0200 (Fri, 04 Sep 2009) | 5 lines
The print_frame_order_2nd_degree() function now accepts the epsilon arg.
This allows zero to be defined differently making the printout nicer.
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r9467 | bugman | 2009-09-07 19:28:57 +0200 (Mon, 07 Sep 2009) | 6 lines
Improved and expanded the output of the print_frame_order_2nd_degree() function.
The print out can now be in integer form, dots can replace zeros, and commas between elements are
now optional. Matrix forms are also converted to array forms.
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r9468 | bugman | 2009-09-07 19:31:49 +0200 (Mon, 07 Sep 2009) | 5 lines
Fix for the __update_model() method.
The theta_axis, phi_axis, and theta_cone params were not being added to the parameter array!
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r9469 | bugman | 2009-09-08 11:14:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Added some unit tests for the R_euler_zyz() function.
This tests some basic axis rotations.
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r9470 | bugman | 2009-09-08 11:26:37 +0200 (Tue, 08 Sep 2009) | 3 lines
Fixes for the R_euler_zyz() unit tests.
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r9471 | bugman | 2009-09-08 11:27:23 +0200 (Tue, 08 Sep 2009) | 5 lines
Fix for the R_euler_zyz() function.
The rotations were being performed in the opposite direction?!?
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r9472 | bugman | 2009-09-08 14:38:05 +0200 (Tue, 08 Sep 2009) | 3 lines
Removed the incorrect part of the R_euler_zyz() docstring.
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r9473 | bugman | 2009-09-08 14:40:37 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for the R_to_euler_zyz() function.
This matches the important bug fix in the R_euler_zyz() function.
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r9474 | bugman | 2009-09-08 14:43:47 +0200 (Tue, 08 Sep 2009) | 5 lines
Fixes for the test_func3() and test_func4() unit tests.
The rotations were backwards because of the R_euler_zyz() fix!
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r9475 | bugman | 2009-09-08 15:11:17 +0200 (Tue, 08 Sep 2009) | 6 lines
Fix to the frame order system tests.
This corresponds to the fixes in R_euler_zyz() where the rotation matrices were in the left-handed
universe and hence the rotation was back to front.
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r9476 | bugman | 2009-09-08 16:40:16 +0200 (Tue, 08 Sep 2009) | 3 lines
Created 3 unit tests of the maths_fns.rotation_matrix.quaternion_to_R() function.
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r9477 | bugman | 2009-09-08 17:07:06 +0200 (Tue, 08 Sep 2009) | 5 lines
Created 3 unit tests of the maths_fns.rotation_matrix.R_axis_angle() function.
These are almost identical to those of quaternion_to_R().
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r9478 | bugman | 2009-09-08 17:42:48 +0200 (Tue, 08 Sep 2009) | 3 lines
Added a unit test for maths_fns.rotation_matrix.R_to_axis_angle() using R = I.
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r9479 | bugman | 2009-09-08 17:43:36 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for R_to_axis_angle().
All vector elements were NaN when the angle is 0. Now the zero vector is not normalised by zero.
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r9480 | bugman | 2009-09-08 17:47:59 +0200 (Tue, 08 Sep 2009) | 3 lines
Added another unit test for maths_fns.rotation_matrix.R_axis_angle().
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r9481 | bugman | 2009-09-08 18:20:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Function renaming and argument order changes in the maths_fns.rotation_matrix module.
The naming scheme is now more logical (as well as the argument order).
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r9482 | bugman | 2009-09-08 18:27:50 +0200 (Tue, 08 Sep 2009) | 3 lines
Alphabetical reordering of functions.
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r9483 | bugman | 2009-09-08 18:52:54 +0200 (Tue, 08 Sep 2009) | 3 lines
Huge simplifications to the unit tests for the maths_fns.rotation_matrix package.
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r9484 | bugman | 2009-09-08 19:17:29 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9485 | bugman | 2009-09-08 19:51:14 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function.
This is accompanied by 2 unit tests.
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r9486 | bugman | 2009-09-08 20:20:34 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.R_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9487 | bugman | 2009-09-08 21:07:41 +0200 (Tue, 08 Sep 2009) | 13 lines
Added a unit test to bounce around all the conversion functions in maths_fns.rotation_matrix.
This bounces through:
1) euler_zyz_to_R().
2) R_to_axis_angle().
3) axis_angle_to_quaternion().
4) quaternion_to_axis_angle().
5) axis_angle_to_R().
6) R_to_quaternion().
7) quaternion_to_R().
8) R_to_euler_zyz().
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r9488 | bugman | 2009-09-09 16:04:40 +0200 (Wed, 09 Sep 2009) | 5 lines
Added a unit test to check if all the maths_fns.kronecker_product.transpose_*() functions revert.
Calling the function twice should return the matrix to the original state.
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r9489 | bugman | 2009-09-10 14:33:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Renamed the data pipes system tests module.
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r9490 | bugman | 2009-09-10 16:51:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Wrote a system test for the writing and re-reading of data pipes.
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r9491 | bugman | 2009-09-10 16:53:06 +0200 (Thu, 10 Sep 2009) | 3 lines
Shifted the valid types private function variable into a module variable.
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r9492 | bugman | 2009-09-10 16:54:55 +0200 (Thu, 10 Sep 2009) | 3 lines
The test_write_read_pipes() system test is now using the VALID_TYPES module variable to get all pipes.
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r9493 | bugman | 2009-09-10 17:01:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Deleted the __init__() class methods as these were empty, and shifted the docstring to that of the class.
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r9494 | bugman | 2009-09-10 17:02:22 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed an empty line.
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r9495 | bugman | 2009-09-10 17:20:21 +0200 (Thu, 10 Sep 2009) | 5 lines
Added a very basic, and completely empty module and class for SRLS analysis.
This is to allow the data pipe to be created.
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r9496 | bugman | 2009-09-10 17:37:16 +0200 (Thu, 10 Sep 2009) | 3 lines
Updated the specific_fns module __all__ list for the SRLS module.
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r9497 | bugman | 2009-09-10 17:38:20 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the test_write_read_pipes() system test to the 'state' test module.
The program state is now being saved as the results file is for just one data pipe.
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r9498 | bugman | 2009-09-10 18:07:22 +0200 (Thu, 10 Sep 2009) | 3 lines
A few fixes for the test_write_read_pipes() system test.
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r9499 | bugman | 2009-09-10 18:32:31 +0200 (Thu, 10 Sep 2009) | 7 lines
Redesign of the relax state loading for adding support for a XML formatted state file.
Half of the load_state() is now in load_pickle(), and a new function load_xml() added.
The determine_format() function will tell if the file is a pickle or XML file, and then
load_pickle() will run the appropriate loading function.
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r9500 | bugman | 2009-09-10 18:36:40 +0200 (Thu, 10 Sep 2009) | 5 lines
Added the pickle flag to save_state().
This defaults to True to prevent relax failures during the XML file implementation.
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r9501 | bugman | 2009-09-10 19:01:25 +0200 (Thu, 10 Sep 2009) | 5 lines
The save_state() function now calls the relax data store to_xml() method.
This method is currently only for one data pipe, and is used by the results writing user function.
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r9502 | bugman | 2009-09-10 19:24:30 +0200 (Thu, 10 Sep 2009) | 6 lines
The relax data store to_xml() method now can add all data pipes to the XML file (or a subset).
The results.write() method now asks to_xml() for just the current pipe to be stored, whereas
state.save() supplies no 'pipes' argument to have all pipes stored.
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r9503 | bugman | 2009-09-10 19:26:22 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the results.write() force arg to the end.
Bool args should be last!
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r9504 | bugman | 2009-09-10 19:37:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed trailing whitespace.
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r9505 | bugman | 2009-09-10 19:56:32 +0200 (Thu, 10 Sep 2009) | 3 lines
Updates to the load_xml() function. This now does something!
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r9506 | bugman | 2009-09-10 20:04:05 +0200 (Thu, 10 Sep 2009) | 3 lines
Created the relax data store is_empty() method.
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r9507 | bugman | 2009-09-11 10:06:05 +0200 (Fri, 11 Sep 2009) | 6 lines
Added the pickle arg to state.save().
This allows the relax state - the contents of the relax data store - to either be saved as XML or as
a pickled object.
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r9508 | bugman | 2009-09-11 10:07:11 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a warning to the state.save() user function about the pickle format compatibility.
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r9509 | bugman | 2009-09-11 10:16:04 +0200 (Fri, 11 Sep 2009) | 6 lines
Absorbed the load_xml() function into load_state().
After shifting the data store check to load_state() for all formats, the function only had one
statement.
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r9510 | bugman | 2009-09-11 10:29:08 +0200 (Fri, 11 Sep 2009) | 3 lines
Docstring clarification of the dir arg.
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r9511 | bugman | 2009-09-11 11:12:30 +0200 (Fri, 11 Sep 2009) | 3 lines
Updated the relax data store from_xml() method for support of the loading of the XML state file.
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r9512 | bugman | 2009-09-11 11:31:44 +0200 (Fri, 11 Sep 2009) | 5 lines
Added the force flag to the state.load() user function.
When True, this causes the relax data store to be reset prior to state loading.
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r9513 | bugman | 2009-09-11 11:36:02 +0200 (Fri, 11 Sep 2009) | 5 lines
Duplicated the test_state() system test into test_state_pickle() and test_state_xml().
This tests both formats.
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r9514 | bugman | 2009-09-11 11:39:53 +0200 (Fri, 11 Sep 2009) | 6 lines
Fixes for load_pickle().
The ds.__reset__() call has been removed because of redundancy and the new ds.is_empty() has been
blacklisted.
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r9515 | bugman | 2009-09-11 11:48:17 +0200 (Fri, 11 Sep 2009) | 3 lines
Changed the default save state to XML.
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r9516 | bugman | 2009-09-11 13:43:34 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a dir arg to a state.save() call in test_state_pickle().
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r9517 | bugman | 2009-09-11 13:52:36 +0200 (Fri, 11 Sep 2009) | 5 lines
Renamed the state.load() and state.save() directory argument from dir_name to dir.
This is to bring it in line with the rest of relax.
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r9518 | bugman | 2009-09-11 14:44:41 +0200 (Fri, 11 Sep 2009) | 3 lines
Fixes for print_frame_order_2nd_degree() for when NaN is encountered.
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r9519 | bugman | 2009-09-11 14:46:04 +0200 (Fri, 11 Sep 2009) | 5 lines
Fix for the print_frame_order_2nd_degree().
The NaN fix was partly incorrect.
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r9520 | bugman | 2009-09-11 15:04:15 +0200 (Fri, 11 Sep 2009) | 3 lines
Made the integer printout 4 char wide.
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r9521 | bugman | 2009-09-11 15:31:42 +0200 (Fri, 11 Sep 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The T23 and not T14 transpose should be performed!
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r9522 | bugman | 2009-09-11 15:59:04 +0200 (Fri, 11 Sep 2009) | 2 lines
Reordered the relax debugging save state so that the format is yyyymmdd_hhmmss rather than yyyyddmm_hhmmss.
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r9523 | bugman | 2009-09-11 17:55:23 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a check for the setting of the domain the tensor corresponds to.
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r9524 | bugman | 2009-09-14 13:59:44 +0200 (Mon, 14 Sep 2009) | 3 lines
Renamed the frame order target function module.
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r9525 | bugman | 2009-09-14 14:07:40 +0200 (Mon, 14 Sep 2009) | 3 lines
Bug fix, the func_iso_cone_elements() method was been replaced with func_iso_cone().
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r9526 | bugman | 2009-09-14 14:23:10 +0200 (Mon, 14 Sep 2009) | 5 lines
Fix for r9525.
The func_iso_cone() was now not being set up.
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r9528 | bugman | 2009-09-18 14:04:52 +0200 (Fri, 18 Sep 2009) | 3 lines
Created the euler_zyz_to_axis_angle() conversion function.
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r9529 | bugman | 2009-09-18 14:28:37 +0200 (Fri, 18 Sep 2009) | 6 lines
Created axis_angle_to_euler_zyz().
The test_euler_zyz_to_euler_zyz() unit test now checks both euler_zyz_to_axis_angle() and
axis_angle_to_euler_zyz().
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r9530 | bugman | 2009-09-18 17:38:27 +0200 (Fri, 18 Sep 2009) | 12 lines
Final 1.3 line redesigns of the relax_io module.
The log() and tee() functions have been renamed to io_streams_log() and io_streams_tee(), and the
old IO.logging_off() class method has been converted to the io_streams_restore() function. The
io_streams_restore() function is also differently designed, using the true original IO streams
(sys.__stdin__, sys.__stdout__, and sys.__stderr__).
The IO.delete() method has been converted to a module function.
The IO class has been eliminated.
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r9531 | bugman | 2009-09-18 18:19:26 +0200 (Fri, 18 Sep 2009) | 6 lines
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This checks the dumping and
reloading of alignment tensors into an XML file.
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r9532 | bugman | 2009-09-18 18:26:40 +0200 (Fri, 18 Sep 2009) | 5 lines
Bug fix for the delete function.
The function was failing if the file was missing!
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r9533 | bugman | 2009-09-18 18:28:05 +0200 (Fri, 18 Sep 2009) | 6 lines
Bug fix for the test suite.
The temporary files were not always deleted if a .bz2 extension was added! Now relax_io.delete() is
being called to fix this.
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r9534 | bugman | 2009-09-18 18:28:56 +0200 (Fri, 18 Sep 2009) | 3 lines
Reactivated the system tests turned off in r9533.
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r9535 | bugman | 2009-09-18 18:32:41 +0200 (Fri, 18 Sep 2009) | 5 lines
Fix for the data_names() method for when no model has been setup.
This allows the frame order data pipe to be written out prior to the model setup.
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r9536 | bugman | 2009-09-18 18:43:02 +0200 (Fri, 18 Sep 2009) | 3 lines
Expansion of the test_to_and_from_xml() system test to check more data structures.
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r9537 | bugman | 2009-09-18 18:47:49 +0200 (Fri, 18 Sep 2009) | 3 lines
The data structures of the AlignTensorList class are now packed into the XML file.
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r9538 | bugman | 2009-09-18 19:11:30 +0200 (Fri, 18 Sep 2009) | 3 lines
Added the blacklist arg to xml_to_object().
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r9539 | bugman | 2009-09-18 19:15:06 +0200 (Fri, 18 Sep 2009) | 6 lines
Reverted r9538. The wrong file was committed!
The command used was:
svn merge -r9538:9537 .
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r9540 | bugman | 2009-09-18 19:15:40 +0200 (Fri, 18 Sep 2009) | 3 lines
Try again: Added the blacklist arg to xml_to_object().
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r9541 | bugman | 2009-09-18 19:18:14 +0200 (Fri, 18 Sep 2009) | 3 lines
Bug fix, the blacklist args now default to [].
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r9542 | bugman | 2009-09-18 19:19:39 +0200 (Fri, 18 Sep 2009) | 3 lines
Fix for the test_to_and_from_xml() check of the 'reduction' data structure.
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r9543 | bugman | 2009-09-18 19:20:15 +0200 (Fri, 18 Sep 2009) | 3 lines
The 'reduction' data structure is now properly created from the XML file.
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r9544 | bugman | 2009-09-21 13:25:14 +0200 (Mon, 21 Sep 2009) | 6 lines
Modified the frame order grid search.
The angle end points are now avoided (as they are the same as the start points) and the beta Euler
angle increments are halved, as the search is half of that of alpha and gamma (0 to pi).
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r9545 | bugman | 2009-09-21 13:53:39 +0200 (Mon, 21 Sep 2009) | 5 lines
Removed the end point of the cone angle from the grid search.
This is unrestricted motion, so is physically not possible.
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r9546 | bugman | 2009-09-21 14:03:55 +0200 (Mon, 21 Sep 2009) | 5 lines
Also halved the number of theta polar angle increments in the frame order grid search.
This is to match the cone axis azimuthal angle phi.
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r9547 | bugman | 2009-09-21 16:20:58 +0200 (Mon, 21 Sep 2009) | 6 lines
Fix for the missing PDB file error.
The extension '.pdb' was being added to the end so if the missing file '1F3Y.pdb' was specified,
the RelaxError would say that '1F3Y.pdb.pdb' was missing.
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r9548 | bugman | 2009-09-21 18:44:14 +0200 (Mon, 21 Sep 2009) | 7 lines
Complete redesign of the grid_search() method.
The grid ops structure is no longer created, rather the grid is directly created to be passed to the
grid search algorithm. The __grid_row() method has been added to create the row of the grid
corresponding to a certain parameter.
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r9549 | bugman | 2009-09-21 19:37:50 +0200 (Mon, 21 Sep 2009) | 3 lines
Implemented the acos grid search for angular parameters of the frame order theories.
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r9550 | bugman | 2009-09-21 19:39:41 +0200 (Mon, 21 Sep 2009) | 3 lines
Fixed the call to the grid search.
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r9551 | bugman | 2009-09-21 20:25:52 +0200 (Mon, 21 Sep 2009) | 5 lines
Fix for the __unpack_opt_results() for the new direct calling of the grid search.
The returned results are different.
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r9552 | bugman | 2009-09-22 11:50:31 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a false, deliberately broken Xplor line to test the parsing of Xplor NOE files.
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r9553 | bugman | 2009-09-22 12:04:37 +0200 (Tue, 22 Sep 2009) | 3 lines
Bug fix for the reading of Xplor NOE data when a line starts with '#'.
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r9554 | bugman | 2009-09-22 13:15:40 +0200 (Tue, 22 Sep 2009) | 5 lines
Fix for the test_opt_rigid_rand_rot() system test.
The changes to the frame order grid search broke this test.
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r9555 | bugman | 2009-09-22 14:28:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a series of checks to the test_curve_fitting() system test.
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r9556 | bugman | 2009-09-22 14:29:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
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r9557 | bugman | 2009-09-22 14:38:58 +0200 (Tue, 22 Sep 2009) | 3 lines
A bit of a clean up of the relaxation curve fitting minimise() method.
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r9558 | bugman | 2009-09-22 14:52:46 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the N-state model grid search setup around the new minfx interface.
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r9559 | bugman | 2009-09-22 15:00:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a comment line.
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r9560 | bugman | 2009-09-22 15:00:25 +0200 (Tue, 22 Sep 2009) | 3 lines
Another clean out of the grid search setup.
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r9561 | bugman | 2009-09-22 15:16:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Removed some trailing whitespace.
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r9562 | bugman | 2009-09-22 18:18:55 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the model-free grid search setup around the new minfx interface.
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r9563 | bugman | 2009-09-22 19:35:05 +0200 (Tue, 22 Sep 2009) | 3 lines
Modified the grid search calls due to changes in minfx.
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r9564 | bugman | 2009-10-05 10:25:33 +0200 (Mon, 05 Oct 2009) | 10 lines
Bug fix: Added the function __deselect_spins() to remove spins with too little data.
This fixes bug #14428 (http://gna.org/bugs/?14428) reported by Pierre-Yves Savard <pierre-yves dott
savard at bcm dot ulaval dot ca>.
The new function is almost identical to that used in the model-free analysis performed by relax in
that spins with no or too little data, or those which would be over-fit are removed from the
analysis.
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r9565 | bugman | 2009-10-05 10:26:24 +0200 (Mon, 05 Oct 2009) | 3 lines
Fix for the system test of Art Palmer's Modelfree4 program for the new __deselect_spins() fn.
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r9566 | bugman | 2009-10-05 11:34:48 +0200 (Mon, 05 Oct 2009) | 3 lines
Added a script for creating Molmol macros to represent the model-free motions.
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r9567 | bugman | 2009-10-05 12:15:51 +0200 (Mon, 05 Oct 2009) | 3 lines
Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
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r9568 | bugman | 2009-10-06 11:22:21 +0200 (Tue, 06 Oct 2009) | 6 lines
Added the spin_id_col arg to the rdc.read() user function.
This allows 2 different formats for spin identification - spin ID string or mol name, res name and
num, and spin name and num.
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r9569 | bugman | 2009-10-06 11:25:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed some empty lines.
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r9570 | bugman | 2009-10-06 11:38:20 +0200 (Tue, 06 Oct 2009) | 9 lines
Changes to the pcs.read() and rdc.read() user function interfaces.
Columns are now numbered from 1 - note this will break many things! The spin_id_col is now accepted
and the spin_id arg is explained.
The docstrings have also been modified all over these user function classes to replace
'identification string' with 'ID string'.
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r9571 | bugman | 2009-10-06 11:39:22 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the call from the prompt to the generic fns.
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r9572 | bugman | 2009-10-06 12:18:35 +0200 (Tue, 06 Oct 2009) | 6 lines
Created the read_spin_data_file() generator function.
This is designed to replace quite a few inconsistent functions throughout the generic function code
base. It reads a columnar formatted file with a spin per line.
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r9573 | bugman | 2009-10-06 12:20:20 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generate_spin_id_data_array() so that column numbering starts at 1.
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r9574 | bugman | 2009-10-06 12:28:13 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generic_fns.rdc.read() to use the new relax_io.read_spin_data_file().
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r9575 | bugman | 2009-10-06 12:32:17 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for the unit tests of generic_fns.mol_res_spin.generate_spin_id_data_array().
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r9576 | bugman | 2009-10-06 12:52:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the calls to rdc.read() and pcs.read() in the system tests.
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r9577 | bugman | 2009-10-06 12:56:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Added a check to see if the file is empty to read_spin_data_file().
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r9578 | bugman | 2009-10-06 13:01:06 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted value.read() to use the new relax_io.read_spin_data_file() function.
This converts the user function to the 1.3 line design as well.
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r9579 | bugman | 2009-10-06 13:19:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Docstring modification better explaining spin_id.
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r9580 | bugman | 2009-10-06 13:20:57 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted spectrum.read_intensities() to use the new relax_io.read_spin_data_file() function.
This is only for the generic formatted file.
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r9581 | bugman | 2009-10-06 13:22:23 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of relax_io.read_spin_data_file().
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r9582 | bugman | 2009-10-06 15:26:28 +0200 (Tue, 06 Oct 2009) | 5 lines
Bug fix for the relax_io.read_spin_data_file() function.
The column number check was incorrect due to the column renumbering.
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r9583 | bugman | 2009-10-06 15:46:25 +0200 (Tue, 06 Oct 2009) | 6 lines
The relax_io.read_spin_data_file() function now calls generic_fns.sequence.validate_sequence().
This is a more advanced check of the sequence information. The validate_sequence() function has
also been modified to handle single data lines.
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r9584 | bugman | 2009-10-06 16:07:58 +0200 (Tue, 06 Oct 2009) | 3 lines
Wrote spin_id_to_data_list() to convert a single spin ID into a list of mol, res, and spin names and numbers.
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r9585 | bugman | 2009-10-06 16:13:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the sequence.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9586 | bugman | 2009-10-06 16:14:54 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the spin_id_to_data_list() function.
The spin ID string was incorrectly named.
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r9587 | bugman | 2009-10-06 16:21:16 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line!
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r9588 | bugman | 2009-10-06 16:22:55 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed some calls to sequence.read() in the unit tests.
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r9589 | bugman | 2009-10-06 17:25:41 +0200 (Tue, 06 Oct 2009) | 5 lines
Rewrote the tokenise() function to allow for the '&' boolean operator for residues and spins.
This allows ':1&:GLY' or '@453&@N' to be parsed.
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r9590 | bugman | 2009-10-06 17:35:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified parse_token() to handle multiple tokens simultaneously.
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r9591 | bugman | 2009-10-06 17:38:48 +0200 (Tue, 06 Oct 2009) | 3 lines
Some fixes for the spin_id_to_data_list() function.
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r9592 | bugman | 2009-10-06 17:45:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for spin_id_to_data_list(), and now it returns a tuple rather than a list.
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r9593 | bugman | 2009-10-06 18:06:03 +0200 (Tue, 06 Oct 2009) | 3 lines
Some more fixes for spin_id_to_data_list().
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r9594 | bugman | 2009-10-06 18:11:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Fix for the read() function. The arguments are now properly sent to generate().
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r9595 | bugman | 2009-10-06 18:19:45 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the test_read() system test.
The residue columns must now be specified.
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r9596 | bugman | 2009-10-06 18:36:04 +0200 (Tue, 06 Oct 2009) | 3 lines
Yet another fix for the new read_spin_data_file() function - hopefully this will be the last!
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r9597 | bugman | 2009-10-06 18:37:01 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of read_spin_data_file().
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r9598 | bugman | 2009-10-06 18:40:24 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the validate_sequence().
The shifted column numbers were not being taken into account.
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r9599 | bugman | 2009-10-06 18:42:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed the test for error values of zero, as this was killing Dasha!
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r9600 | bugman | 2009-10-06 18:43:38 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed all the calls to sequence.read() where the default residue columns were being relied upon.
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r9601 | bugman | 2009-10-06 18:53:57 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9602 | bugman | 2009-10-06 19:07:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Reverted some accidental commenting out of system tests.
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r9603 | bugman | 2009-10-06 19:21:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted select.read() and deselect.read() to use the new relax_io.read_spin_data_file() function.
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r9604 | bugman | 2009-10-06 19:37:39 +0200 (Tue, 06 Oct 2009) | 3 lines
Additions to the select.read() and deselect.read() docstrings.
........
r9605 | bugman | 2009-10-06 19:57:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
........
r9606 | bugman | 2009-10-06 20:07:29 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the relax_data.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9607 | bugman | 2009-10-06 20:13:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9608 | bugman | 2009-10-06 20:22:15 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the pcs.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9609 | bugman | 2009-10-06 20:27:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9610 | bugman | 2009-10-06 20:28:02 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9611 | bugman | 2009-10-06 20:29:46 +0200 (Tue, 06 Oct 2009) | 3 lines
Header realignment.
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r9612 | bugman | 2009-10-07 09:43:42 +0200 (Wed, 07 Oct 2009) | 5 lines
Bug fixes for the RDC and PCS read() functions.
The alignment tensor ID had the same variable name as the spin ID!
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r9613 | bugman | 2009-10-07 09:53:40 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed all the alignment ID args and variables 'id' to 'align_id' in the RDC and PCS user fns.
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r9614 | bugman | 2009-10-07 09:55:26 +0200 (Wed, 07 Oct 2009) | 3 lines
Docstring spelling mistake fix - 'spid_id_col' should be 'spin_id_col'!
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r9615 | bugman | 2009-10-07 10:08:32 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the system tests to use the new 'align_id' args.
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r9616 | bugman | 2009-10-07 10:18:37 +0200 (Wed, 07 Oct 2009) | 6 lines
Removed some unneeded files.
The relaxation delays will be placed into the script itself, and the generic_intensity2.txt file
will replace generic_intensity.txt.
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r9617 | bugman | 2009-10-07 10:19:57 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed generic_intensity2.txt to generic_intensity.txt.
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r9618 | bugman | 2009-10-07 10:28:59 +0200 (Wed, 07 Oct 2009) | 3 lines
Redesigned the test_read_peak_list_generic() system test.
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r9619 | bugman | 2009-10-07 10:29:47 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the test_read_peak_list_generic2() system test.
This was just duplicating test_read_peak_list_generic().
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r9620 | bugman | 2009-10-07 10:30:21 +0200 (Wed, 07 Oct 2009) | 3 lines
Commented out the header.
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r9621 | bugman | 2009-10-07 11:25:42 +0200 (Wed, 07 Oct 2009) | 3 lines
Added the new error class RelaxArgNotNoneError for when an argument should be None.
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r9622 | bugman | 2009-10-07 11:28:35 +0200 (Wed, 07 Oct 2009) | 6 lines
Complete redesign of the generic_fns.spectrum module.
This significantly simplifies the code base (much less jumping between functions) and prepares for
the generically formatted file support.
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r9623 | bugman | 2009-10-07 11:35:45 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the test_read_peak_list_generic() system test.
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r9624 | bugman | 2009-10-07 11:36:44 +0200 (Wed, 07 Oct 2009) | 5 lines
Rewrote the intensity_generic() function.
This is now much simpler (5 lines of code).
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r9625 | bugman | 2009-10-07 11:39:24 +0200 (Wed, 07 Oct 2009) | 3 lines
More fixes for the test_read_peak_list_generic(). It now passes!
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r9626 | bugman | 2009-10-07 12:44:06 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed some unused imports.
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r9627 | bugman | 2009-10-07 14:29:55 +0200 (Wed, 07 Oct 2009) | 6 lines
Wrote the relax_io.write_spin_data_file() function.
This writes spin specific data to a file (can be STDOUT). It will replace the write_header()
and write_body() functions of generic_fns.sequence.
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r9628 | bugman | 2009-10-07 14:31:29 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the write_body(), write_header(), and write_line() functions from generic_fns.sequence.
This should accelerate the switch to relax_io.write_spin_data_file().
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r9629 | bugman | 2009-10-07 14:34:52 +0200 (Wed, 07 Oct 2009) | 3 lines
Import fixes by shifting to relax_io.write_spin_data_file().
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r9630 | bugman | 2009-10-07 14:41:02 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed read_spin_data_file() to read_spin_data() and write_spin_data_file() to write_spin_data().
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r9631 | bugman | 2009-10-07 14:59:07 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed all dependence on write_body() and write_header() from the sequence module.
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r9632 | bugman | 2009-10-07 15:04:47 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted the load_spins() function to use relax_io.write_spin_data().
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r9633 | bugman | 2009-10-07 15:07:56 +0200 (Wed, 07 Oct 2009) | 3 lines
Spacing fixes for write_spin_data().
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r9634 | bugman | 2009-10-07 15:17:25 +0200 (Wed, 07 Oct 2009) | 3 lines
Modified write_spin_data() to dynamically modify the spin ID column widths if the data is too long.
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r9635 | bugman | 2009-10-07 17:49:06 +0200 (Wed, 07 Oct 2009) | 3 lines
Missing import.
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r9636 | bugman | 2009-10-07 17:53:33 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted the file keyword args to read_ and write_spin_data() to normal args.
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r9637 | bugman | 2009-10-07 17:56:40 +0200 (Wed, 07 Oct 2009) | 5 lines
Fixed the write_spin_data() from read().
The file arg must be given, and now as this is set to sys.stdout, STDOUT redirection works again.
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r9638 | bugman | 2009-10-07 18:00:19 +0200 (Wed, 07 Oct 2009) | 5 lines
Fix for the test_write_protein_sequence() unit test.
The output file format is now a little different.
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r9639 | bugman | 2009-10-07 18:16:52 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted value.write() to user relax_io.write_spin_data().
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r9640 | bugman | 2009-10-07 18:18:11 +0200 (Wed, 07 Oct 2009) | 5 lines
Converted the read_spin_data() file arg back to a keyword.
The file_data arg can be used instead!
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r9641 | bugman | 2009-10-07 18:21:07 +0200 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (http://gna.org/bugs/?14464).
The problem fix here (only one of a few) was the new design of the user function classes. This was
breaking the docstring fetching script used to generate the relax manual.
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r9642 | bugman | 2009-10-07 18:24:40 +0200 (Wed, 07 Oct 2009) | 3 lines
Modified the output of the user function docstring parsing.
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r9643 | bugman | 2009-10-07 18:48:19 +0200 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (https://gna.org/bugs/?14464).
Fix for the PDF manual compilation - os.rename() is being used instead of shutil.move(). No idea
why shutil.move() was no longer working?!?
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r9644 | bugman | 2009-10-07 19:32:19 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixed a call to write_spin_data() which should pass in sys.stdout as the file.
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r9645 | bugman | 2009-10-07 19:33:53 +0200 (Wed, 07 Oct 2009) | 3 lines
Prevented __find_bonded_atoms() from connecting protons in the internal PDB reader.
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r9646 | bugman | 2009-10-07 19:46:04 +0200 (Wed, 07 Oct 2009) | 5 lines
Fix for the retrieval of bond vectors for the N-state model.
The object could also be called 'bond_vect' rather than 'xh_vect'.
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r9647 | bugman | 2009-10-07 19:56:59 +0200 (Wed, 07 Oct 2009) | 3 lines
More fixes for the N-state model for the 'xh_vect' and 'bond_vect' mix up.
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r9648 | bugman | 2009-10-07 19:57:27 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9649 | semor | 2009-10-07 20:30:34 +0200 (Wed, 07 Oct 2009) | 7 lines
Modified the sequence.read() entries in order to reflect the new design.
The sequence.read() function now absolutely needs an argument for res_num_col. Hence, this argument
is now shown in the sample script in order to avoid the users lose time figuring out where their
script went bad...
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r9650 | semor | 2009-10-07 20:37:57 +0200 (Wed, 07 Oct 2009) | 8 lines
Modified the relax_data.read() entries in order to reflect the new design.
The relax_data.read() function now absolutely needs arguments for 'res_num_col', 'data_col' and
'error_col'. Hence, this argument is now shown in the sample script in order to avoid the users
lose time figuring out where their script went bad...
........
r9651 | bugman | 2009-10-08 09:24:50 +0200 (Thu, 08 Oct 2009) | 8 lines
Significant improvements to the __find_bonded_atoms() method.
The maximum number of bonds an element can have is now taken into account so that protons are not
thought to be attached to 2 carbons within a 2 Angstrom radius! The atoms closest to the atom of
interest are now connected. Geometry constraints or other advanced techniques are not yet
implemented.
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r9652 | bugman | 2009-10-08 09:45:46 +0200 (Thu, 08 Oct 2009) | 3 lines
Modified the message printed by RelaxInvalidSeqError.
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r9653 | bugman | 2009-10-08 09:46:39 +0200 (Thu, 08 Oct 2009) | 3 lines
read_spin_data() now gives a warning rather than an error if the sequence data in a line is bad.
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r9654 | bugman | 2009-10-08 10:01:18 +0200 (Thu, 08 Oct 2009) | 6 lines
Improvements to the read_spin_data() function.
The data checks now occur during the yield loop. This allows for invalid lines to be skipped while
those with real data are used.
........
r9655 | bugman | 2009-10-08 10:24:34 +0200 (Thu, 08 Oct 2009) | 6 lines
Bug fix for __find_bonded_atoms().
The loop over the maximum number of connect atoms was failing if the number of 'connected' atoms was
less.
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r9656 | bugman | 2009-10-08 10:49:12 +0200 (Thu, 08 Oct 2009) | 3 lines
Removed some debugging print statements.
........
r9657 | bugman | 2009-10-08 12:30:16 +0200 (Thu, 08 Oct 2009) | 3 lines
Created the structure.delete() user function for deleting all structural information from the cdp.
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r9658 | bugman | 2009-10-08 12:42:22 +0200 (Thu, 08 Oct 2009) | 3 lines
Modified the structure.delete() user function to remove all spin specific structural data.
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r9696 | semor | 2009-10-09 14:44:40 +0200 (Fri, 09 Oct 2009) | 10 lines
Improved the error handling for AICc model selection.
The code now tells users with too small datasets (n<=k) why AICc model selection does not work in
their situation.
This follows a discussion started at:
https://mail.gna.org/public/relax-devel/2009-10/msg00015.html
(# Message-id: <4ACD6F60.7060102@...>)
........
r9700 | bugman | 2009-10-09 18:00:30 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a copyright notice and a function for returning the SVN revision number to the version module.
........
r9706 | bugman | 2009-10-09 18:47:13 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a function to get the SVN URL.
........
r9709 | bugman | 2009-10-09 20:06:21 +0200 (Fri, 09 Oct 2009) | 3 lines
Comment fix.
........
r9747 | bugman | 2009-10-12 16:00:39 +0200 (Mon, 12 Oct 2009) | 3 lines
__linear_ave() is no longer a private function.
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r9794 | bugman | 2009-10-27 10:59:25 +0100 (Tue, 27 Oct 2009) | 7 lines
Added user variable checking to the full_analysis.py script.
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-10/msg00009.html (Message-id:
<E45CDDF4A4E54B34A36BFBA62E6BFF20@...>).
........
r9799 | bugman | 2009-10-27 15:24:25 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the frame order grid search.
........
r9800 | bugman | 2009-10-27 15:25:08 +0100 (Tue, 27 Oct 2009) | 3 lines
Created the structure.get_pos() user function for extracting atomic positions.
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r9829 | bugman | 2009-10-28 11:47:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added functions for determining the element name and isotope number from an isotope name.
........
r9831 | bugman | 2009-10-28 11:51:19 +0100 (Wed, 28 Oct 2009) | 3 lines
Bug fix for the new isotope functions.
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r9834 | bugman | 2009-10-28 13:48:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added checks for insufficient or single field strength relaxation data.
........
r9871 | semor | 2009-11-18 15:20:42 +0100 (Wed, 18 Nov 2009) | 6 lines
Added references to the consistency tests code.
In particular, the reference for this newly published paper was added:
Morin & Gagne (2009) JBNMR, 45: 361-372.
........
r9872 | semor | 2009-11-18 16:58:50 +0100 (Wed, 18 Nov 2009) | 7 lines
Added references and instructions in the sample script for consistency testing.
This is as proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2009-11/msg00034.html
(Message-id: <7f080ed10911180653w6b59b40dn1e8f715d9b718fd5@...>)
........
r9873 | semor | 2009-11-18 17:58:39 +0100 (Wed, 18 Nov 2009) | 5 lines
Added DOI links to the citations and corrected a fused f and i character.
This was proposed by Edward.
........
r9874 | semor | 2009-11-18 18:29:02 +0100 (Wed, 18 Nov 2009) | 3 lines
Corrected other strange characters causing failures...
........
r9875 | bugman | 2009-11-19 10:37:23 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the 'Branches' subsection of the development chapter into a proper section.
........
r9891 | bugman | 2009-11-24 09:24:48 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the dx.map() user function interface.
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r9892 | bugman | 2009-11-24 10:05:30 +0100 (Tue, 24 Nov 2009) | 10 lines
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
........
r9893 | bugman | 2009-11-24 10:17:37 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the base class return_conversion_factor() method.
The spin_id arg is now accepted.
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r9894 | bugman | 2009-11-24 10:32:01 +0100 (Tue, 24 Nov 2009) | 6 lines
Created unit tests for the specific_fns API.
This checks the consistency of methods across the API, using method names and arg checks. Only the
frame order theories are currently checked.
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r9895 | bugman | 2009-11-24 10:46:05 +0100 (Tue, 24 Nov 2009) | 3 lines
Renamed specific_fns.base_class.Common_functions to specific_fns.api_base.API_base.
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r9896 | bugman | 2009-11-24 10:55:57 +0100 (Tue, 24 Nov 2009) | 3 lines
The entirety of the specific_fns API is now checked.
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r9897 | bugman | 2009-11-24 10:57:13 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated for the __all__ list for the base_class to api_base rename.
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r9898 | bugman | 2009-11-24 11:07:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of the functions.
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r9899 | bugman | 2009-11-24 11:14:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the back_calc() method from the specific analysis API.
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r9900 | bugman | 2009-11-24 11:20:24 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the copy() method from the specific analysis API.
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r9901 | bugman | 2009-11-24 11:21:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Added a prototype calculate() method to the API.
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r9902 | bugman | 2009-11-24 11:42:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_param_vector() and disassemble_param_vector() from the specific analysis API.
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r9903 | bugman | 2009-11-24 11:45:10 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_scaling_matrix() from the specific analysis API.
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r9904 | bugman | 2009-11-24 11:52:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed back_calc() from the specific analysis API.
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r9905 | bugman | 2009-11-24 11:53:20 +0100 (Tue, 24 Nov 2009) | 3 lines
Completed removal of back_calc() from the specific analysis API.
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r9906 | bugman | 2009-11-24 11:56:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Added create_mc_data() to the specific analysis API.
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r9907 | bugman | 2009-11-24 12:18:58 +0100 (Tue, 24 Nov 2009) | 5 lines
Added data_names() to the specific analysis API.
General docstring clean ups as well.
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r9908 | bugman | 2009-11-24 12:39:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _assemble_param_vector() method.
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r9909 | bugman | 2009-11-24 12:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _disassemble_param_vector() method.
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r9910 | bugman | 2009-11-24 12:56:22 +0100 (Tue, 24 Nov 2009) | 15 lines
A large number of method and documentation variables to the specific analysis API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
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r9911 | bugman | 2009-11-24 12:58:24 +0100 (Tue, 24 Nov 2009) | 10 lines
Converted a number of methods to being private, removing them from the API.
These include:
_grid_search_setup()
_linear_constraints()
_model_setup()
_relax_time()
_select_model()
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r9912 | bugman | 2009-11-24 12:59:22 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the _select_model() method to be private, removing it from the API.
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r9913 | bugman | 2009-11-24 13:05:29 +0100 (Tue, 24 Nov 2009) | 5 lines
Clean up of the create_mc_data() API method across the board.
The spin_id keyword is now accepted by all, and is a keyword.
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r9914 | bugman | 2009-11-24 13:21:18 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring update to return_grace_string().
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r9915 | bugman | 2009-11-24 13:22:09 +0100 (Tue, 24 Nov 2009) | 5 lines
Fixes for the relaxation curve fitting API.
The fixes are for the return_data_name(), return_grace_string(), and return_units() methods.
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r9916 | bugman | 2009-11-24 13:25:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9917 | bugman | 2009-11-24 13:47:33 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring and default arg changes.
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r9918 | bugman | 2009-11-24 13:47:58 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed duplicated epydoc tags.
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r9919 | bugman | 2009-11-24 13:48:37 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire NOE API.
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r9920 | bugman | 2009-11-24 13:49:42 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9921 | bugman | 2009-11-24 14:04:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the check of the default values from the specific analysis API arg checks.
The defaults keyword values can be set to anything by the specific code!
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r9922 | bugman | 2009-11-24 14:52:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the string printout creation in the __check_method_args() method.
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r9923 | bugman | 2009-11-24 15:04:25 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the unused _read() method.
This has been superseded by the spectrum.read_intensities() user function.
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r9924 | bugman | 2009-11-24 15:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Added model_statistics() to the specific analysis API.
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r9925 | bugman | 2009-11-24 15:30:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire N-state model specific API.
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r9926 | bugman | 2009-11-24 15:32:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all self.__*() private methods to self._*() non-API methods.
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r9927 | bugman | 2009-11-24 15:40:14 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
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r9928 | bugman | 2009-11-24 15:50:02 +0100 (Tue, 24 Nov 2009) | 3 lines
Added duplicate_data() to the specific analysis API.
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r9929 | bugman | 2009-11-24 16:46:59 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed some unused methods from the API.
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r9930 | bugman | 2009-11-24 16:48:38 +0100 (Tue, 24 Nov 2009) | 17 lines
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
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r9931 | bugman | 2009-11-24 16:59:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire model-free analysis specific API.
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r9932 | bugman | 2009-11-24 17:05:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all the model-free results methods from private to non-API.
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r9933 | bugman | 2009-11-24 17:08:00 +0100 (Tue, 24 Nov 2009) | 3 lines
Added an empty eliminate_doc variable to the specific analysis API.
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r9934 | bugman | 2009-11-24 17:51:20 +0100 (Tue, 24 Nov 2009) | 5 lines
More fixes for the __format_method() method.
The methods with args and keywords are now properly formatted!
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r9935 | bugman | 2009-11-24 18:02:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the eliminate() and model_statistics() API prototype methods.
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r9936 | bugman | 2009-11-24 18:03:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the N-state model model_statistics() API method.
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r9937 | bugman | 2009-11-24 18:05:40 +0100 (Tue, 24 Nov 2009) | 3 lines
Update for the return_conversion_factor() API prototype method.
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r9938 | bugman | 2009-11-24 18:15:06 +0100 (Tue, 24 Nov 2009) | 3 lines
Shifted many of the model-free specific methods out of the API.
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r9939 | bugman | 2009-11-24 18:35:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the specific analysis base API to use the model_info arg, returned from model_loop().
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r9940 | bugman | 2009-11-24 18:39:15 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated the N-state model model_statistics() method to the model_info arg.
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r9941 | bugman | 2009-11-24 18:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the model-free unit tests. The model_index arg is now called model_info.
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r9942 | bugman | 2009-11-24 18:41:28 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted many of the model-free methods to use model_info rather than model_index.
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r9943 | bugman | 2009-11-24 19:08:56 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the specific analysis base API set_selected_sim() method.
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r9944 | bugman | 2009-11-24 19:18:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the analysis specific base API sim_return_selected() method.
The model_info arg is now being used.
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r9945 | bugman | 2009-11-24 19:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the private __compare_objects() method to the non-API _compare_objects() method.
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r9946 | bugman | 2009-11-24 19:30:09 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of model-free methods, and separation of the private from the API methods.
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r9947 | bugman | 2009-11-24 19:58:18 +0100 (Tue, 24 Nov 2009) | 3 lines
A number of fixes for the model-free analysis specific API methods.
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r9948 | bugman | 2009-11-24 19:58:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Changes to the args for the base API data_init() method.
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r9949 | bugman | 2009-11-24 19:59:32 +0100 (Tue, 24 Nov 2009) | 3 lines
Updates to the methods of the reduced spectral density mapping API.
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r9950 | bugman | 2009-11-25 09:05:00 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the data_init() method for API consistency.
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r9951 | bugman | 2009-11-25 09:15:40 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted many of the J(w) mapping methods to use the model_info arg rather than spin.
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r9952 | bugman | 2009-11-25 09:19:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring updates for returned values.
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r9953 | bugman | 2009-11-25 09:21:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Alphabetical ordering of J(w) mapping methods, and separation of the private from the API methods.
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r9954 | bugman | 2009-11-25 09:26:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fix.
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r9955 | bugman | 2009-11-25 09:31:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the hybrid analysis API to match the base API.
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r9956 | bugman | 2009-11-25 09:38:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of the private and API methods in the hybrid specific analysis.
........
r9957 | bugman | 2009-11-25 09:39:48 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted the frame order private methods into non-API methods.
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r9958 | bugman | 2009-11-25 09:44:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of all the non-API frame order specific methods.
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r9959 | bugman | 2009-11-25 09:46:39 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9960 | bugman | 2009-11-25 09:56:56 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the frame order specific analysis API methods to match the base API.
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r9961 | bugman | 2009-11-25 10:02:26 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the frame order user functions.
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r9962 | bugman | 2009-11-25 10:02:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Removal of set_frq() from the consistency testing analysis specific API.
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r9963 | bugman | 2009-11-25 10:07:09 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fixes.
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r9964 | bugman | 2009-11-25 10:17:49 +0100 (Wed, 25 Nov 2009) | 3 lines
More docstring updates.
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r9965 | bugman | 2009-11-25 10:18:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the consistency testing analysis specific API methods to match the base API.
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r9966 | bugman | 2009-11-25 10:43:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Fix for the consistency testing return_units() method for the arg name changes.
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r9967 | bugman | 2009-11-25 10:57:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9968 | bugman | 2009-11-25 10:59:05 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix and reformatting of generic_fns.pcs.read().
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r9969 | bugman | 2009-11-25 12:55:17 +0100 (Wed, 25 Nov 2009) | 5 lines
Decreased the user function docstring size in the relax manual.
This was changed from normal size to \scriptsize to decrease the number of pages in the manual.
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r9970 | bugman | 2009-11-25 13:06:03 +0100 (Wed, 25 Nov 2009) | 5 lines
The user function descriptions in the relax manual are now in columns.
This shrinks the manual even further.
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r9971 | bugman | 2009-11-25 13:11:52 +0100 (Wed, 25 Nov 2009) | 5 lines
Removed the \newpage command from the user function descriptions.
This cuts the manual size by over 100 pages!!!
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r9972 | bugman | 2009-11-25 13:18:28 +0100 (Wed, 25 Nov 2009) | 3 lines
Added '()' to the end of the user functions in the relax manual.
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r9973 | bugman | 2009-11-25 15:41:03 +0100 (Wed, 25 Nov 2009) | 3 lines
Turned all tables from the user functions in the relax manual into floating tables.
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r9974 | bugman | 2009-11-25 15:46:58 +0100 (Wed, 25 Nov 2009) | 5 lines
Clean up of the minimisation docstring.
This no longer causes problems in the relax manual.
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r9975 | bugman | 2009-11-25 15:54:01 +0100 (Wed, 25 Nov 2009) | 3 lines
Switched from the multicols package to just using \twocolumn and \onecolumn.
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r9976 | bugman | 2009-11-25 15:54:36 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the align_tensor.svd() docstring for the relax manual.
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r9977 | bugman | 2009-11-25 16:52:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Added rules to break the user function subsections in the manual apart.
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r9978 | bugman | 2009-11-25 17:18:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Modified the spin ID string documentation to be better presented in the relax manual.
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r9979 | bugman | 2009-11-26 09:09:29 +0100 (Thu, 26 Nov 2009) | 6 lines
User function call examples in the relax manual are now better formatted.
They are allowed to break after '.', '(', and '='. This is for the examples and the Defaults
subsubsection.
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r9980 | bugman | 2009-11-26 10:22:06 +0100 (Thu, 26 Nov 2009) | 3 lines
Allowed for hyphenation in the user function subsection titles.
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r9981 | bugman | 2009-11-26 12:20:26 +0100 (Thu, 26 Nov 2009) | 3 lines
Massive tables in the relax manual are now being split using the longtable package.
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r9982 | bugman | 2009-11-26 12:27:18 +0100 (Thu, 26 Nov 2009) | 3 lines
The tables in the user function chapter now have the same font size as the rest of the text.
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r9983 | bugman | 2009-11-26 12:33:35 +0100 (Thu, 26 Nov 2009) | 3 lines
Better formatting of the user function chapter by using \raggedbottom.
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r9984 | bugman | 2009-11-26 12:50:58 +0100 (Thu, 26 Nov 2009) | 3 lines
Fixed the boolean selection table to be nicer to the automatic manual compilation.
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r9985 | bugman | 2009-11-26 13:16:37 +0100 (Thu, 26 Nov 2009) | 3 lines
The longtables are now properly labelled.
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r9986 | bugman | 2009-11-26 18:36:27 +0100 (Thu, 26 Nov 2009) | 3 lines
Removed the checking of sequence data from generic_fns.value.set().
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|
2009-11-27 11:11:06
|
Tree
|
[r9992]
by
bugman
Merged revisions 9454,9457-9526,9528-9658,9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834,9871-9875,9891-9986 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r9454 | bugman | 2009-09-03 15:23:45 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the non-dangerous Python3k update command.
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r9457 | bugman | 2009-09-03 17:53:41 +0200 (Thu, 03 Sep 2009) | 3 lines
Created a sub-directory for frame order test scripts.
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r9458 | bugman | 2009-09-03 18:18:51 +0200 (Thu, 03 Sep 2009) | 3 lines
Shifted the rigid frame order system test into the sub-directory.
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r9459 | bugman | 2009-09-03 18:31:23 +0200 (Thu, 03 Sep 2009) | 3 lines
Added another rigid frame order system test.
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r9460 | bugman | 2009-09-03 18:32:10 +0200 (Thu, 03 Sep 2009) | 3 lines
Renamed a frame order system test.
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r9461 | bugman | 2009-09-03 19:05:02 +0200 (Thu, 03 Sep 2009) | 3 lines
Specific architecture and optimisation details are now printed if the frame order system tests fail.
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r9462 | bugman | 2009-09-03 19:17:08 +0200 (Thu, 03 Sep 2009) | 3 lines
Fix for the new frame order system test - the results file goes to devnull.
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r9463 | bugman | 2009-09-03 19:25:01 +0200 (Thu, 03 Sep 2009) | 3 lines
The beta angle for the tensor rotations is now folded to be between 0 and pi.
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r9464 | bugman | 2009-09-04 10:24:52 +0200 (Fri, 04 Sep 2009) | 5 lines
Added a function for converting the frame order matrix to the rotational superoperator.
The function is called daeg_to_rotational_superoperator().
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r9465 | bugman | 2009-09-04 11:21:28 +0200 (Fri, 04 Sep 2009) | 5 lines
Fix for the new daeg_to_rotational_superoperator() function.
The frame order matrix shape is now restored.
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r9466 | bugman | 2009-09-04 16:12:31 +0200 (Fri, 04 Sep 2009) | 5 lines
The print_frame_order_2nd_degree() function now accepts the epsilon arg.
This allows zero to be defined differently making the printout nicer.
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r9467 | bugman | 2009-09-07 19:28:57 +0200 (Mon, 07 Sep 2009) | 6 lines
Improved and expanded the output of the print_frame_order_2nd_degree() function.
The print out can now be in integer form, dots can replace zeros, and commas between elements are
now optional. Matrix forms are also converted to array forms.
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r9468 | bugman | 2009-09-07 19:31:49 +0200 (Mon, 07 Sep 2009) | 5 lines
Fix for the __update_model() method.
The theta_axis, phi_axis, and theta_cone params were not being added to the parameter array!
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r9469 | bugman | 2009-09-08 11:14:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Added some unit tests for the R_euler_zyz() function.
This tests some basic axis rotations.
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r9470 | bugman | 2009-09-08 11:26:37 +0200 (Tue, 08 Sep 2009) | 3 lines
Fixes for the R_euler_zyz() unit tests.
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r9471 | bugman | 2009-09-08 11:27:23 +0200 (Tue, 08 Sep 2009) | 5 lines
Fix for the R_euler_zyz() function.
The rotations were being performed in the opposite direction?!?
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r9472 | bugman | 2009-09-08 14:38:05 +0200 (Tue, 08 Sep 2009) | 3 lines
Removed the incorrect part of the R_euler_zyz() docstring.
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r9473 | bugman | 2009-09-08 14:40:37 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for the R_to_euler_zyz() function.
This matches the important bug fix in the R_euler_zyz() function.
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r9474 | bugman | 2009-09-08 14:43:47 +0200 (Tue, 08 Sep 2009) | 5 lines
Fixes for the test_func3() and test_func4() unit tests.
The rotations were backwards because of the R_euler_zyz() fix!
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r9475 | bugman | 2009-09-08 15:11:17 +0200 (Tue, 08 Sep 2009) | 6 lines
Fix to the frame order system tests.
This corresponds to the fixes in R_euler_zyz() where the rotation matrices were in the left-handed
universe and hence the rotation was back to front.
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r9476 | bugman | 2009-09-08 16:40:16 +0200 (Tue, 08 Sep 2009) | 3 lines
Created 3 unit tests of the maths_fns.rotation_matrix.quaternion_to_R() function.
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r9477 | bugman | 2009-09-08 17:07:06 +0200 (Tue, 08 Sep 2009) | 5 lines
Created 3 unit tests of the maths_fns.rotation_matrix.R_axis_angle() function.
These are almost identical to those of quaternion_to_R().
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r9478 | bugman | 2009-09-08 17:42:48 +0200 (Tue, 08 Sep 2009) | 3 lines
Added a unit test for maths_fns.rotation_matrix.R_to_axis_angle() using R = I.
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r9479 | bugman | 2009-09-08 17:43:36 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for R_to_axis_angle().
All vector elements were NaN when the angle is 0. Now the zero vector is not normalised by zero.
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r9480 | bugman | 2009-09-08 17:47:59 +0200 (Tue, 08 Sep 2009) | 3 lines
Added another unit test for maths_fns.rotation_matrix.R_axis_angle().
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r9481 | bugman | 2009-09-08 18:20:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Function renaming and argument order changes in the maths_fns.rotation_matrix module.
The naming scheme is now more logical (as well as the argument order).
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r9482 | bugman | 2009-09-08 18:27:50 +0200 (Tue, 08 Sep 2009) | 3 lines
Alphabetical reordering of functions.
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r9483 | bugman | 2009-09-08 18:52:54 +0200 (Tue, 08 Sep 2009) | 3 lines
Huge simplifications to the unit tests for the maths_fns.rotation_matrix package.
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r9484 | bugman | 2009-09-08 19:17:29 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9485 | bugman | 2009-09-08 19:51:14 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function.
This is accompanied by 2 unit tests.
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r9486 | bugman | 2009-09-08 20:20:34 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.R_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9487 | bugman | 2009-09-08 21:07:41 +0200 (Tue, 08 Sep 2009) | 13 lines
Added a unit test to bounce around all the conversion functions in maths_fns.rotation_matrix.
This bounces through:
1) euler_zyz_to_R().
2) R_to_axis_angle().
3) axis_angle_to_quaternion().
4) quaternion_to_axis_angle().
5) axis_angle_to_R().
6) R_to_quaternion().
7) quaternion_to_R().
8) R_to_euler_zyz().
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r9488 | bugman | 2009-09-09 16:04:40 +0200 (Wed, 09 Sep 2009) | 5 lines
Added a unit test to check if all the maths_fns.kronecker_product.transpose_*() functions revert.
Calling the function twice should return the matrix to the original state.
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r9489 | bugman | 2009-09-10 14:33:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Renamed the data pipes system tests module.
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r9490 | bugman | 2009-09-10 16:51:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Wrote a system test for the writing and re-reading of data pipes.
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r9491 | bugman | 2009-09-10 16:53:06 +0200 (Thu, 10 Sep 2009) | 3 lines
Shifted the valid types private function variable into a module variable.
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r9492 | bugman | 2009-09-10 16:54:55 +0200 (Thu, 10 Sep 2009) | 3 lines
The test_write_read_pipes() system test is now using the VALID_TYPES module variable to get all pipes.
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r9493 | bugman | 2009-09-10 17:01:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Deleted the __init__() class methods as these were empty, and shifted the docstring to that of the class.
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r9494 | bugman | 2009-09-10 17:02:22 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed an empty line.
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r9495 | bugman | 2009-09-10 17:20:21 +0200 (Thu, 10 Sep 2009) | 5 lines
Added a very basic, and completely empty module and class for SRLS analysis.
This is to allow the data pipe to be created.
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r9496 | bugman | 2009-09-10 17:37:16 +0200 (Thu, 10 Sep 2009) | 3 lines
Updated the specific_fns module __all__ list for the SRLS module.
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r9497 | bugman | 2009-09-10 17:38:20 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the test_write_read_pipes() system test to the 'state' test module.
The program state is now being saved as the results file is for just one data pipe.
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r9498 | bugman | 2009-09-10 18:07:22 +0200 (Thu, 10 Sep 2009) | 3 lines
A few fixes for the test_write_read_pipes() system test.
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r9499 | bugman | 2009-09-10 18:32:31 +0200 (Thu, 10 Sep 2009) | 7 lines
Redesign of the relax state loading for adding support for a XML formatted state file.
Half of the load_state() is now in load_pickle(), and a new function load_xml() added.
The determine_format() function will tell if the file is a pickle or XML file, and then
load_pickle() will run the appropriate loading function.
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r9500 | bugman | 2009-09-10 18:36:40 +0200 (Thu, 10 Sep 2009) | 5 lines
Added the pickle flag to save_state().
This defaults to True to prevent relax failures during the XML file implementation.
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r9501 | bugman | 2009-09-10 19:01:25 +0200 (Thu, 10 Sep 2009) | 5 lines
The save_state() function now calls the relax data store to_xml() method.
This method is currently only for one data pipe, and is used by the results writing user function.
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r9502 | bugman | 2009-09-10 19:24:30 +0200 (Thu, 10 Sep 2009) | 6 lines
The relax data store to_xml() method now can add all data pipes to the XML file (or a subset).
The results.write() method now asks to_xml() for just the current pipe to be stored, whereas
state.save() supplies no 'pipes' argument to have all pipes stored.
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r9503 | bugman | 2009-09-10 19:26:22 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the results.write() force arg to the end.
Bool args should be last!
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r9504 | bugman | 2009-09-10 19:37:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed trailing whitespace.
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r9505 | bugman | 2009-09-10 19:56:32 +0200 (Thu, 10 Sep 2009) | 3 lines
Updates to the load_xml() function. This now does something!
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r9506 | bugman | 2009-09-10 20:04:05 +0200 (Thu, 10 Sep 2009) | 3 lines
Created the relax data store is_empty() method.
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r9507 | bugman | 2009-09-11 10:06:05 +0200 (Fri, 11 Sep 2009) | 6 lines
Added the pickle arg to state.save().
This allows the relax state - the contents of the relax data store - to either be saved as XML or as
a pickled object.
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r9508 | bugman | 2009-09-11 10:07:11 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a warning to the state.save() user function about the pickle format compatibility.
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r9509 | bugman | 2009-09-11 10:16:04 +0200 (Fri, 11 Sep 2009) | 6 lines
Absorbed the load_xml() function into load_state().
After shifting the data store check to load_state() for all formats, the function only had one
statement.
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r9510 | bugman | 2009-09-11 10:29:08 +0200 (Fri, 11 Sep 2009) | 3 lines
Docstring clarification of the dir arg.
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r9511 | bugman | 2009-09-11 11:12:30 +0200 (Fri, 11 Sep 2009) | 3 lines
Updated the relax data store from_xml() method for support of the loading of the XML state file.
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r9512 | bugman | 2009-09-11 11:31:44 +0200 (Fri, 11 Sep 2009) | 5 lines
Added the force flag to the state.load() user function.
When True, this causes the relax data store to be reset prior to state loading.
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r9513 | bugman | 2009-09-11 11:36:02 +0200 (Fri, 11 Sep 2009) | 5 lines
Duplicated the test_state() system test into test_state_pickle() and test_state_xml().
This tests both formats.
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r9514 | bugman | 2009-09-11 11:39:53 +0200 (Fri, 11 Sep 2009) | 6 lines
Fixes for load_pickle().
The ds.__reset__() call has been removed because of redundancy and the new ds.is_empty() has been
blacklisted.
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r9515 | bugman | 2009-09-11 11:48:17 +0200 (Fri, 11 Sep 2009) | 3 lines
Changed the default save state to XML.
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r9516 | bugman | 2009-09-11 13:43:34 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a dir arg to a state.save() call in test_state_pickle().
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r9517 | bugman | 2009-09-11 13:52:36 +0200 (Fri, 11 Sep 2009) | 5 lines
Renamed the state.load() and state.save() directory argument from dir_name to dir.
This is to bring it in line with the rest of relax.
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r9518 | bugman | 2009-09-11 14:44:41 +0200 (Fri, 11 Sep 2009) | 3 lines
Fixes for print_frame_order_2nd_degree() for when NaN is encountered.
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r9519 | bugman | 2009-09-11 14:46:04 +0200 (Fri, 11 Sep 2009) | 5 lines
Fix for the print_frame_order_2nd_degree().
The NaN fix was partly incorrect.
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r9520 | bugman | 2009-09-11 15:04:15 +0200 (Fri, 11 Sep 2009) | 3 lines
Made the integer printout 4 char wide.
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r9521 | bugman | 2009-09-11 15:31:42 +0200 (Fri, 11 Sep 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The T23 and not T14 transpose should be performed!
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r9522 | bugman | 2009-09-11 15:59:04 +0200 (Fri, 11 Sep 2009) | 2 lines
Reordered the relax debugging save state so that the format is yyyymmdd_hhmmss rather than yyyyddmm_hhmmss.
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r9523 | bugman | 2009-09-11 17:55:23 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a check for the setting of the domain the tensor corresponds to.
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r9524 | bugman | 2009-09-14 13:59:44 +0200 (Mon, 14 Sep 2009) | 3 lines
Renamed the frame order target function module.
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r9525 | bugman | 2009-09-14 14:07:40 +0200 (Mon, 14 Sep 2009) | 3 lines
Bug fix, the func_iso_cone_elements() method was been replaced with func_iso_cone().
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r9526 | bugman | 2009-09-14 14:23:10 +0200 (Mon, 14 Sep 2009) | 5 lines
Fix for r9525.
The func_iso_cone() was now not being set up.
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r9528 | bugman | 2009-09-18 14:04:52 +0200 (Fri, 18 Sep 2009) | 3 lines
Created the euler_zyz_to_axis_angle() conversion function.
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r9529 | bugman | 2009-09-18 14:28:37 +0200 (Fri, 18 Sep 2009) | 6 lines
Created axis_angle_to_euler_zyz().
The test_euler_zyz_to_euler_zyz() unit test now checks both euler_zyz_to_axis_angle() and
axis_angle_to_euler_zyz().
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r9530 | bugman | 2009-09-18 17:38:27 +0200 (Fri, 18 Sep 2009) | 12 lines
Final 1.3 line redesigns of the relax_io module.
The log() and tee() functions have been renamed to io_streams_log() and io_streams_tee(), and the
old IO.logging_off() class method has been converted to the io_streams_restore() function. The
io_streams_restore() function is also differently designed, using the true original IO streams
(sys.__stdin__, sys.__stdout__, and sys.__stderr__).
The IO.delete() method has been converted to a module function.
The IO class has been eliminated.
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r9531 | bugman | 2009-09-18 18:19:26 +0200 (Fri, 18 Sep 2009) | 6 lines
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This checks the dumping and
reloading of alignment tensors into an XML file.
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r9532 | bugman | 2009-09-18 18:26:40 +0200 (Fri, 18 Sep 2009) | 5 lines
Bug fix for the delete function.
The function was failing if the file was missing!
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r9533 | bugman | 2009-09-18 18:28:05 +0200 (Fri, 18 Sep 2009) | 6 lines
Bug fix for the test suite.
The temporary files were not always deleted if a .bz2 extension was added! Now relax_io.delete() is
being called to fix this.
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r9534 | bugman | 2009-09-18 18:28:56 +0200 (Fri, 18 Sep 2009) | 3 lines
Reactivated the system tests turned off in r9533.
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r9535 | bugman | 2009-09-18 18:32:41 +0200 (Fri, 18 Sep 2009) | 5 lines
Fix for the data_names() method for when no model has been setup.
This allows the frame order data pipe to be written out prior to the model setup.
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r9536 | bugman | 2009-09-18 18:43:02 +0200 (Fri, 18 Sep 2009) | 3 lines
Expansion of the test_to_and_from_xml() system test to check more data structures.
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r9537 | bugman | 2009-09-18 18:47:49 +0200 (Fri, 18 Sep 2009) | 3 lines
The data structures of the AlignTensorList class are now packed into the XML file.
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r9538 | bugman | 2009-09-18 19:11:30 +0200 (Fri, 18 Sep 2009) | 3 lines
Added the blacklist arg to xml_to_object().
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r9539 | bugman | 2009-09-18 19:15:06 +0200 (Fri, 18 Sep 2009) | 6 lines
Reverted r9538. The wrong file was committed!
The command used was:
svn merge -r9538:9537 .
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r9540 | bugman | 2009-09-18 19:15:40 +0200 (Fri, 18 Sep 2009) | 3 lines
Try again: Added the blacklist arg to xml_to_object().
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r9541 | bugman | 2009-09-18 19:18:14 +0200 (Fri, 18 Sep 2009) | 3 lines
Bug fix, the blacklist args now default to [].
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r9542 | bugman | 2009-09-18 19:19:39 +0200 (Fri, 18 Sep 2009) | 3 lines
Fix for the test_to_and_from_xml() check of the 'reduction' data structure.
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r9543 | bugman | 2009-09-18 19:20:15 +0200 (Fri, 18 Sep 2009) | 3 lines
The 'reduction' data structure is now properly created from the XML file.
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r9544 | bugman | 2009-09-21 13:25:14 +0200 (Mon, 21 Sep 2009) | 6 lines
Modified the frame order grid search.
The angle end points are now avoided (as they are the same as the start points) and the beta Euler
angle increments are halved, as the search is half of that of alpha and gamma (0 to pi).
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r9545 | bugman | 2009-09-21 13:53:39 +0200 (Mon, 21 Sep 2009) | 5 lines
Removed the end point of the cone angle from the grid search.
This is unrestricted motion, so is physically not possible.
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r9546 | bugman | 2009-09-21 14:03:55 +0200 (Mon, 21 Sep 2009) | 5 lines
Also halved the number of theta polar angle increments in the frame order grid search.
This is to match the cone axis azimuthal angle phi.
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r9547 | bugman | 2009-09-21 16:20:58 +0200 (Mon, 21 Sep 2009) | 6 lines
Fix for the missing PDB file error.
The extension '.pdb' was being added to the end so if the missing file '1F3Y.pdb' was specified,
the RelaxError would say that '1F3Y.pdb.pdb' was missing.
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r9548 | bugman | 2009-09-21 18:44:14 +0200 (Mon, 21 Sep 2009) | 7 lines
Complete redesign of the grid_search() method.
The grid ops structure is no longer created, rather the grid is directly created to be passed to the
grid search algorithm. The __grid_row() method has been added to create the row of the grid
corresponding to a certain parameter.
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r9549 | bugman | 2009-09-21 19:37:50 +0200 (Mon, 21 Sep 2009) | 3 lines
Implemented the acos grid search for angular parameters of the frame order theories.
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r9550 | bugman | 2009-09-21 19:39:41 +0200 (Mon, 21 Sep 2009) | 3 lines
Fixed the call to the grid search.
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r9551 | bugman | 2009-09-21 20:25:52 +0200 (Mon, 21 Sep 2009) | 5 lines
Fix for the __unpack_opt_results() for the new direct calling of the grid search.
The returned results are different.
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r9552 | bugman | 2009-09-22 11:50:31 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a false, deliberately broken Xplor line to test the parsing of Xplor NOE files.
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r9553 | bugman | 2009-09-22 12:04:37 +0200 (Tue, 22 Sep 2009) | 3 lines
Bug fix for the reading of Xplor NOE data when a line starts with '#'.
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r9554 | bugman | 2009-09-22 13:15:40 +0200 (Tue, 22 Sep 2009) | 5 lines
Fix for the test_opt_rigid_rand_rot() system test.
The changes to the frame order grid search broke this test.
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r9555 | bugman | 2009-09-22 14:28:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a series of checks to the test_curve_fitting() system test.
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r9556 | bugman | 2009-09-22 14:29:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
........
r9557 | bugman | 2009-09-22 14:38:58 +0200 (Tue, 22 Sep 2009) | 3 lines
A bit of a clean up of the relaxation curve fitting minimise() method.
........
r9558 | bugman | 2009-09-22 14:52:46 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the N-state model grid search setup around the new minfx interface.
........
r9559 | bugman | 2009-09-22 15:00:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a comment line.
........
r9560 | bugman | 2009-09-22 15:00:25 +0200 (Tue, 22 Sep 2009) | 3 lines
Another clean out of the grid search setup.
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r9561 | bugman | 2009-09-22 15:16:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Removed some trailing whitespace.
........
r9562 | bugman | 2009-09-22 18:18:55 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the model-free grid search setup around the new minfx interface.
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r9563 | bugman | 2009-09-22 19:35:05 +0200 (Tue, 22 Sep 2009) | 3 lines
Modified the grid search calls due to changes in minfx.
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r9564 | bugman | 2009-10-05 10:25:33 +0200 (Mon, 05 Oct 2009) | 10 lines
Bug fix: Added the function __deselect_spins() to remove spins with too little data.
This fixes bug #14428 (http://gna.org/bugs/?14428) reported by Pierre-Yves Savard <pierre-yves dott
savard at bcm dot ulaval dot ca>.
The new function is almost identical to that used in the model-free analysis performed by relax in
that spins with no or too little data, or those which would be over-fit are removed from the
analysis.
........
r9565 | bugman | 2009-10-05 10:26:24 +0200 (Mon, 05 Oct 2009) | 3 lines
Fix for the system test of Art Palmer's Modelfree4 program for the new __deselect_spins() fn.
........
r9566 | bugman | 2009-10-05 11:34:48 +0200 (Mon, 05 Oct 2009) | 3 lines
Added a script for creating Molmol macros to represent the model-free motions.
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r9567 | bugman | 2009-10-05 12:15:51 +0200 (Mon, 05 Oct 2009) | 3 lines
Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
........
r9568 | bugman | 2009-10-06 11:22:21 +0200 (Tue, 06 Oct 2009) | 6 lines
Added the spin_id_col arg to the rdc.read() user function.
This allows 2 different formats for spin identification - spin ID string or mol name, res name and
num, and spin name and num.
........
r9569 | bugman | 2009-10-06 11:25:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed some empty lines.
........
r9570 | bugman | 2009-10-06 11:38:20 +0200 (Tue, 06 Oct 2009) | 9 lines
Changes to the pcs.read() and rdc.read() user function interfaces.
Columns are now numbered from 1 - note this will break many things! The spin_id_col is now accepted
and the spin_id arg is explained.
The docstrings have also been modified all over these user function classes to replace
'identification string' with 'ID string'.
........
r9571 | bugman | 2009-10-06 11:39:22 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the call from the prompt to the generic fns.
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r9572 | bugman | 2009-10-06 12:18:35 +0200 (Tue, 06 Oct 2009) | 6 lines
Created the read_spin_data_file() generator function.
This is designed to replace quite a few inconsistent functions throughout the generic function code
base. It reads a columnar formatted file with a spin per line.
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r9573 | bugman | 2009-10-06 12:20:20 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generate_spin_id_data_array() so that column numbering starts at 1.
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r9574 | bugman | 2009-10-06 12:28:13 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generic_fns.rdc.read() to use the new relax_io.read_spin_data_file().
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r9575 | bugman | 2009-10-06 12:32:17 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for the unit tests of generic_fns.mol_res_spin.generate_spin_id_data_array().
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r9576 | bugman | 2009-10-06 12:52:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the calls to rdc.read() and pcs.read() in the system tests.
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r9577 | bugman | 2009-10-06 12:56:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Added a check to see if the file is empty to read_spin_data_file().
........
r9578 | bugman | 2009-10-06 13:01:06 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted value.read() to use the new relax_io.read_spin_data_file() function.
This converts the user function to the 1.3 line design as well.
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r9579 | bugman | 2009-10-06 13:19:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Docstring modification better explaining spin_id.
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r9580 | bugman | 2009-10-06 13:20:57 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted spectrum.read_intensities() to use the new relax_io.read_spin_data_file() function.
This is only for the generic formatted file.
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r9581 | bugman | 2009-10-06 13:22:23 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of relax_io.read_spin_data_file().
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r9582 | bugman | 2009-10-06 15:26:28 +0200 (Tue, 06 Oct 2009) | 5 lines
Bug fix for the relax_io.read_spin_data_file() function.
The column number check was incorrect due to the column renumbering.
........
r9583 | bugman | 2009-10-06 15:46:25 +0200 (Tue, 06 Oct 2009) | 6 lines
The relax_io.read_spin_data_file() function now calls generic_fns.sequence.validate_sequence().
This is a more advanced check of the sequence information. The validate_sequence() function has
also been modified to handle single data lines.
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r9584 | bugman | 2009-10-06 16:07:58 +0200 (Tue, 06 Oct 2009) | 3 lines
Wrote spin_id_to_data_list() to convert a single spin ID into a list of mol, res, and spin names and numbers.
........
r9585 | bugman | 2009-10-06 16:13:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the sequence.read() user fn to use the new relax_io.read_spin_data_file() function.
........
r9586 | bugman | 2009-10-06 16:14:54 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the spin_id_to_data_list() function.
The spin ID string was incorrectly named.
........
r9587 | bugman | 2009-10-06 16:21:16 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line!
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r9588 | bugman | 2009-10-06 16:22:55 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed some calls to sequence.read() in the unit tests.
........
r9589 | bugman | 2009-10-06 17:25:41 +0200 (Tue, 06 Oct 2009) | 5 lines
Rewrote the tokenise() function to allow for the '&' boolean operator for residues and spins.
This allows ':1&:GLY' or '@453&@N' to be parsed.
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r9590 | bugman | 2009-10-06 17:35:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified parse_token() to handle multiple tokens simultaneously.
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r9591 | bugman | 2009-10-06 17:38:48 +0200 (Tue, 06 Oct 2009) | 3 lines
Some fixes for the spin_id_to_data_list() function.
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r9592 | bugman | 2009-10-06 17:45:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for spin_id_to_data_list(), and now it returns a tuple rather than a list.
........
r9593 | bugman | 2009-10-06 18:06:03 +0200 (Tue, 06 Oct 2009) | 3 lines
Some more fixes for spin_id_to_data_list().
........
r9594 | bugman | 2009-10-06 18:11:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Fix for the read() function. The arguments are now properly sent to generate().
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r9595 | bugman | 2009-10-06 18:19:45 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the test_read() system test.
The residue columns must now be specified.
........
r9596 | bugman | 2009-10-06 18:36:04 +0200 (Tue, 06 Oct 2009) | 3 lines
Yet another fix for the new read_spin_data_file() function - hopefully this will be the last!
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r9597 | bugman | 2009-10-06 18:37:01 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of read_spin_data_file().
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r9598 | bugman | 2009-10-06 18:40:24 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the validate_sequence().
The shifted column numbers were not being taken into account.
........
r9599 | bugman | 2009-10-06 18:42:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed the test for error values of zero, as this was killing Dasha!
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r9600 | bugman | 2009-10-06 18:43:38 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed all the calls to sequence.read() where the default residue columns were being relied upon.
........
r9601 | bugman | 2009-10-06 18:53:57 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9602 | bugman | 2009-10-06 19:07:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Reverted some accidental commenting out of system tests.
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r9603 | bugman | 2009-10-06 19:21:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted select.read() and deselect.read() to use the new relax_io.read_spin_data_file() function.
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r9604 | bugman | 2009-10-06 19:37:39 +0200 (Tue, 06 Oct 2009) | 3 lines
Additions to the select.read() and deselect.read() docstrings.
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r9605 | bugman | 2009-10-06 19:57:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9606 | bugman | 2009-10-06 20:07:29 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the relax_data.read() user fn to use the new relax_io.read_spin_data_file() function.
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r9607 | bugman | 2009-10-06 20:13:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9608 | bugman | 2009-10-06 20:22:15 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the pcs.read() user fn to use the new relax_io.read_spin_data_file() function.
........
r9609 | bugman | 2009-10-06 20:27:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
........
r9610 | bugman | 2009-10-06 20:28:02 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
........
r9611 | bugman | 2009-10-06 20:29:46 +0200 (Tue, 06 Oct 2009) | 3 lines
Header realignment.
........
r9612 | bugman | 2009-10-07 09:43:42 +0200 (Wed, 07 Oct 2009) | 5 lines
Bug fixes for the RDC and PCS read() functions.
The alignment tensor ID had the same variable name as the spin ID!
........
r9613 | bugman | 2009-10-07 09:53:40 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed all the alignment ID args and variables 'id' to 'align_id' in the RDC and PCS user fns.
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r9614 | bugman | 2009-10-07 09:55:26 +0200 (Wed, 07 Oct 2009) | 3 lines
Docstring spelling mistake fix - 'spid_id_col' should be 'spin_id_col'!
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r9615 | bugman | 2009-10-07 10:08:32 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the system tests to use the new 'align_id' args.
........
r9616 | bugman | 2009-10-07 10:18:37 +0200 (Wed, 07 Oct 2009) | 6 lines
Removed some unneeded files.
The relaxation delays will be placed into the script itself, and the generic_intensity2.txt file
will replace generic_intensity.txt.
........
r9617 | bugman | 2009-10-07 10:19:57 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed generic_intensity2.txt to generic_intensity.txt.
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r9618 | bugman | 2009-10-07 10:28:59 +0200 (Wed, 07 Oct 2009) | 3 lines
Redesigned the test_read_peak_list_generic() system test.
........
r9619 | bugman | 2009-10-07 10:29:47 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the test_read_peak_list_generic2() system test.
This was just duplicating test_read_peak_list_generic().
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r9620 | bugman | 2009-10-07 10:30:21 +0200 (Wed, 07 Oct 2009) | 3 lines
Commented out the header.
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r9621 | bugman | 2009-10-07 11:25:42 +0200 (Wed, 07 Oct 2009) | 3 lines
Added the new error class RelaxArgNotNoneError for when an argument should be None.
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r9622 | bugman | 2009-10-07 11:28:35 +0200 (Wed, 07 Oct 2009) | 6 lines
Complete redesign of the generic_fns.spectrum module.
This significantly simplifies the code base (much less jumping between functions) and prepares for
the generically formatted file support.
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r9623 | bugman | 2009-10-07 11:35:45 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the test_read_peak_list_generic() system test.
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r9624 | bugman | 2009-10-07 11:36:44 +0200 (Wed, 07 Oct 2009) | 5 lines
Rewrote the intensity_generic() function.
This is now much simpler (5 lines of code).
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r9625 | bugman | 2009-10-07 11:39:24 +0200 (Wed, 07 Oct 2009) | 3 lines
More fixes for the test_read_peak_list_generic(). It now passes!
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r9626 | bugman | 2009-10-07 12:44:06 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed some unused imports.
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r9627 | bugman | 2009-10-07 14:29:55 +0200 (Wed, 07 Oct 2009) | 6 lines
Wrote the relax_io.write_spin_data_file() function.
This writes spin specific data to a file (can be STDOUT). It will replace the write_header()
and write_body() functions of generic_fns.sequence.
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r9628 | bugman | 2009-10-07 14:31:29 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the write_body(), write_header(), and write_line() functions from generic_fns.sequence.
This should accelerate the switch to relax_io.write_spin_data_file().
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r9629 | bugman | 2009-10-07 14:34:52 +0200 (Wed, 07 Oct 2009) | 3 lines
Import fixes by shifting to relax_io.write_spin_data_file().
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r9630 | bugman | 2009-10-07 14:41:02 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed read_spin_data_file() to read_spin_data() and write_spin_data_file() to write_spin_data().
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r9631 | bugman | 2009-10-07 14:59:07 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed all dependence on write_body() and write_header() from the sequence module.
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r9632 | bugman | 2009-10-07 15:04:47 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted the load_spins() function to use relax_io.write_spin_data().
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r9633 | bugman | 2009-10-07 15:07:56 +0200 (Wed, 07 Oct 2009) | 3 lines
Spacing fixes for write_spin_data().
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r9634 | bugman | 2009-10-07 15:17:25 +0200 (Wed, 07 Oct 2009) | 3 lines
Modified write_spin_data() to dynamically modify the spin ID column widths if the data is too long.
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r9635 | bugman | 2009-10-07 17:49:06 +0200 (Wed, 07 Oct 2009) | 3 lines
Missing import.
........
r9636 | bugman | 2009-10-07 17:53:33 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted the file keyword args to read_ and write_spin_data() to normal args.
........
r9637 | bugman | 2009-10-07 17:56:40 +0200 (Wed, 07 Oct 2009) | 5 lines
Fixed the write_spin_data() from read().
The file arg must be given, and now as this is set to sys.stdout, STDOUT redirection works again.
........
r9638 | bugman | 2009-10-07 18:00:19 +0200 (Wed, 07 Oct 2009) | 5 lines
Fix for the test_write_protein_sequence() unit test.
The output file format is now a little different.
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r9639 | bugman | 2009-10-07 18:16:52 +0200 (Wed, 07 Oct 2009) | 3 lines
Converted value.write() to user relax_io.write_spin_data().
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r9640 | bugman | 2009-10-07 18:18:11 +0200 (Wed, 07 Oct 2009) | 5 lines
Converted the read_spin_data() file arg back to a keyword.
The file_data arg can be used instead!
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r9641 | bugman | 2009-10-07 18:21:07 +0200 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (http://gna.org/bugs/?14464).
The problem fix here (only one of a few) was the new design of the user function classes. This was
breaking the docstring fetching script used to generate the relax manual.
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r9642 | bugman | 2009-10-07 18:24:40 +0200 (Wed, 07 Oct 2009) | 3 lines
Modified the output of the user function docstring parsing.
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r9643 | bugman | 2009-10-07 18:48:19 +0200 (Wed, 07 Oct 2009) | 6 lines
Partial bug fix for bug #14464 (https://gna.org/bugs/?14464).
Fix for the PDF manual compilation - os.rename() is being used instead of shutil.move(). No idea
why shutil.move() was no longer working?!?
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r9644 | bugman | 2009-10-07 19:32:19 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixed a call to write_spin_data() which should pass in sys.stdout as the file.
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r9645 | bugman | 2009-10-07 19:33:53 +0200 (Wed, 07 Oct 2009) | 3 lines
Prevented __find_bonded_atoms() from connecting protons in the internal PDB reader.
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r9646 | bugman | 2009-10-07 19:46:04 +0200 (Wed, 07 Oct 2009) | 5 lines
Fix for the retrieval of bond vectors for the N-state model.
The object could also be called 'bond_vect' rather than 'xh_vect'.
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r9647 | bugman | 2009-10-07 19:56:59 +0200 (Wed, 07 Oct 2009) | 3 lines
More fixes for the N-state model for the 'xh_vect' and 'bond_vect' mix up.
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r9648 | bugman | 2009-10-07 19:57:27 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed a debugging print statement.
........
r9649 | semor | 2009-10-07 20:30:34 +0200 (Wed, 07 Oct 2009) | 7 lines
Modified the sequence.read() entries in order to reflect the new design.
The sequence.read() function now absolutely needs an argument for res_num_col. Hence, this argument
is now shown in the sample script in order to avoid the users lose time figuring out where their
script went bad...
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r9650 | semor | 2009-10-07 20:37:57 +0200 (Wed, 07 Oct 2009) | 8 lines
Modified the relax_data.read() entries in order to reflect the new design.
The relax_data.read() function now absolutely needs arguments for 'res_num_col', 'data_col' and
'error_col'. Hence, this argument is now shown in the sample script in order to avoid the users
lose time figuring out where their script went bad...
........
r9651 | bugman | 2009-10-08 09:24:50 +0200 (Thu, 08 Oct 2009) | 8 lines
Significant improvements to the __find_bonded_atoms() method.
The maximum number of bonds an element can have is now taken into account so that protons are not
thought to be attached to 2 carbons within a 2 Angstrom radius! The atoms closest to the atom of
interest are now connected. Geometry constraints or other advanced techniques are not yet
implemented.
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r9652 | bugman | 2009-10-08 09:45:46 +0200 (Thu, 08 Oct 2009) | 3 lines
Modified the message printed by RelaxInvalidSeqError.
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r9653 | bugman | 2009-10-08 09:46:39 +0200 (Thu, 08 Oct 2009) | 3 lines
read_spin_data() now gives a warning rather than an error if the sequence data in a line is bad.
........
r9654 | bugman | 2009-10-08 10:01:18 +0200 (Thu, 08 Oct 2009) | 6 lines
Improvements to the read_spin_data() function.
The data checks now occur during the yield loop. This allows for invalid lines to be skipped while
those with real data are used.
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r9655 | bugman | 2009-10-08 10:24:34 +0200 (Thu, 08 Oct 2009) | 6 lines
Bug fix for __find_bonded_atoms().
The loop over the maximum number of connect atoms was failing if the number of 'connected' atoms was
less.
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r9656 | bugman | 2009-10-08 10:49:12 +0200 (Thu, 08 Oct 2009) | 3 lines
Removed some debugging print statements.
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r9657 | bugman | 2009-10-08 12:30:16 +0200 (Thu, 08 Oct 2009) | 3 lines
Created the structure.delete() user function for deleting all structural information from the cdp.
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r9658 | bugman | 2009-10-08 12:42:22 +0200 (Thu, 08 Oct 2009) | 3 lines
Modified the structure.delete() user function to remove all spin specific structural data.
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r9696 | semor | 2009-10-09 14:44:40 +0200 (Fri, 09 Oct 2009) | 10 lines
Improved the error handling for AICc model selection.
The code now tells users with too small datasets (n<=k) why AICc model selection does not work in
their situation.
This follows a discussion started at:
https://mail.gna.org/public/relax-devel/2009-10/msg00015.html
(# Message-id: <4ACD6F60.7060102@...>)
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r9700 | bugman | 2009-10-09 18:00:30 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a copyright notice and a function for returning the SVN revision number to the version module.
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r9706 | bugman | 2009-10-09 18:47:13 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a function to get the SVN URL.
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r9709 | bugman | 2009-10-09 20:06:21 +0200 (Fri, 09 Oct 2009) | 3 lines
Comment fix.
........
r9747 | bugman | 2009-10-12 16:00:39 +0200 (Mon, 12 Oct 2009) | 3 lines
__linear_ave() is no longer a private function.
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r9794 | bugman | 2009-10-27 10:59:25 +0100 (Tue, 27 Oct 2009) | 7 lines
Added user variable checking to the full_analysis.py script.
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-10/msg00009.html (Message-id:
<E45CDDF4A4E54B34A36BFBA62E6BFF20@...>).
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r9799 | bugman | 2009-10-27 15:24:25 +0100 (Tue, 27 Oct 2009) | 3 lines
Fix for the frame order grid search.
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r9800 | bugman | 2009-10-27 15:25:08 +0100 (Tue, 27 Oct 2009) | 3 lines
Created the structure.get_pos() user function for extracting atomic positions.
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r9829 | bugman | 2009-10-28 11:47:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added functions for determining the element name and isotope number from an isotope name.
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r9831 | bugman | 2009-10-28 11:51:19 +0100 (Wed, 28 Oct 2009) | 3 lines
Bug fix for the new isotope functions.
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r9834 | bugman | 2009-10-28 13:48:59 +0100 (Wed, 28 Oct 2009) | 3 lines
Added checks for insufficient or single field strength relaxation data.
........
r9871 | semor | 2009-11-18 15:20:42 +0100 (Wed, 18 Nov 2009) | 6 lines
Added references to the consistency tests code.
In particular, the reference for this newly published paper was added:
Morin & Gagne (2009) JBNMR, 45: 361-372.
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r9872 | semor | 2009-11-18 16:58:50 +0100 (Wed, 18 Nov 2009) | 7 lines
Added references and instructions in the sample script for consistency testing.
This is as proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2009-11/msg00034.html
(Message-id: <7f080ed10911180653w6b59b40dn1e8f715d9b718fd5@...>)
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r9873 | semor | 2009-11-18 17:58:39 +0100 (Wed, 18 Nov 2009) | 5 lines
Added DOI links to the citations and corrected a fused f and i character.
This was proposed by Edward.
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r9874 | semor | 2009-11-18 18:29:02 +0100 (Wed, 18 Nov 2009) | 3 lines
Corrected other strange characters causing failures...
........
r9875 | bugman | 2009-11-19 10:37:23 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the 'Branches' subsection of the development chapter into a proper section.
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r9891 | bugman | 2009-11-24 09:24:48 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the dx.map() user function interface.
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r9892 | bugman | 2009-11-24 10:05:30 +0100 (Tue, 24 Nov 2009) | 10 lines
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
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r9893 | bugman | 2009-11-24 10:17:37 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the base class return_conversion_factor() method.
The spin_id arg is now accepted.
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r9894 | bugman | 2009-11-24 10:32:01 +0100 (Tue, 24 Nov 2009) | 6 lines
Created unit tests for the specific_fns API.
This checks the consistency of methods across the API, using method names and arg checks. Only the
frame order theories are currently checked.
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r9895 | bugman | 2009-11-24 10:46:05 +0100 (Tue, 24 Nov 2009) | 3 lines
Renamed specific_fns.base_class.Common_functions to specific_fns.api_base.API_base.
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r9896 | bugman | 2009-11-24 10:55:57 +0100 (Tue, 24 Nov 2009) | 3 lines
The entirety of the specific_fns API is now checked.
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r9897 | bugman | 2009-11-24 10:57:13 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated for the __all__ list for the base_class to api_base rename.
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r9898 | bugman | 2009-11-24 11:07:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of the functions.
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r9899 | bugman | 2009-11-24 11:14:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the back_calc() method from the specific analysis API.
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r9900 | bugman | 2009-11-24 11:20:24 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the copy() method from the specific analysis API.
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r9901 | bugman | 2009-11-24 11:21:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Added a prototype calculate() method to the API.
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r9902 | bugman | 2009-11-24 11:42:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_param_vector() and disassemble_param_vector() from the specific analysis API.
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r9903 | bugman | 2009-11-24 11:45:10 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_scaling_matrix() from the specific analysis API.
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r9904 | bugman | 2009-11-24 11:52:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed back_calc() from the specific analysis API.
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r9905 | bugman | 2009-11-24 11:53:20 +0100 (Tue, 24 Nov 2009) | 3 lines
Completed removal of back_calc() from the specific analysis API.
........
r9906 | bugman | 2009-11-24 11:56:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Added create_mc_data() to the specific analysis API.
........
r9907 | bugman | 2009-11-24 12:18:58 +0100 (Tue, 24 Nov 2009) | 5 lines
Added data_names() to the specific analysis API.
General docstring clean ups as well.
........
r9908 | bugman | 2009-11-24 12:39:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _assemble_param_vector() method.
........
r9909 | bugman | 2009-11-24 12:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _disassemble_param_vector() method.
........
r9910 | bugman | 2009-11-24 12:56:22 +0100 (Tue, 24 Nov 2009) | 15 lines
A large number of method and documentation variables to the specific analysis API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
........
r9911 | bugman | 2009-11-24 12:58:24 +0100 (Tue, 24 Nov 2009) | 10 lines
Converted a number of methods to being private, removing them from the API.
These include:
_grid_search_setup()
_linear_constraints()
_model_setup()
_relax_time()
_select_model()
........
r9912 | bugman | 2009-11-24 12:59:22 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the _select_model() method to be private, removing it from the API.
........
r9913 | bugman | 2009-11-24 13:05:29 +0100 (Tue, 24 Nov 2009) | 5 lines
Clean up of the create_mc_data() API method across the board.
The spin_id keyword is now accepted by all, and is a keyword.
........
r9914 | bugman | 2009-11-24 13:21:18 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring update to return_grace_string().
........
r9915 | bugman | 2009-11-24 13:22:09 +0100 (Tue, 24 Nov 2009) | 5 lines
Fixes for the relaxation curve fitting API.
The fixes are for the return_data_name(), return_grace_string(), and return_units() methods.
........
r9916 | bugman | 2009-11-24 13:25:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9917 | bugman | 2009-11-24 13:47:33 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring and default arg changes.
........
r9918 | bugman | 2009-11-24 13:47:58 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed duplicated epydoc tags.
........
r9919 | bugman | 2009-11-24 13:48:37 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire NOE API.
........
r9920 | bugman | 2009-11-24 13:49:42 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9921 | bugman | 2009-11-24 14:04:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the check of the default values from the specific analysis API arg checks.
The defaults keyword values can be set to anything by the specific code!
........
r9922 | bugman | 2009-11-24 14:52:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the string printout creation in the __check_method_args() method.
........
r9923 | bugman | 2009-11-24 15:04:25 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the unused _read() method.
This has been superseded by the spectrum.read_intensities() user function.
........
r9924 | bugman | 2009-11-24 15:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Added model_statistics() to the specific analysis API.
........
r9925 | bugman | 2009-11-24 15:30:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire N-state model specific API.
........
r9926 | bugman | 2009-11-24 15:32:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all self.__*() private methods to self._*() non-API methods.
........
r9927 | bugman | 2009-11-24 15:40:14 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9928 | bugman | 2009-11-24 15:50:02 +0100 (Tue, 24 Nov 2009) | 3 lines
Added duplicate_data() to the specific analysis API.
........
r9929 | bugman | 2009-11-24 16:46:59 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed some unused methods from the API.
........
r9930 | bugman | 2009-11-24 16:48:38 +0100 (Tue, 24 Nov 2009) | 17 lines
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
........
r9931 | bugman | 2009-11-24 16:59:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire model-free analysis specific API.
........
r9932 | bugman | 2009-11-24 17:05:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all the model-free results methods from private to non-API.
........
r9933 | bugman | 2009-11-24 17:08:00 +0100 (Tue, 24 Nov 2009) | 3 lines
Added an empty eliminate_doc variable to the specific analysis API.
........
r9934 | bugman | 2009-11-24 17:51:20 +0100 (Tue, 24 Nov 2009) | 5 lines
More fixes for the __format_method() method.
The methods with args and keywords are now properly formatted!
........
r9935 | bugman | 2009-11-24 18:02:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the eliminate() and model_statistics() API prototype methods.
........
r9936 | bugman | 2009-11-24 18:03:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the N-state model model_statistics() API method.
........
r9937 | bugman | 2009-11-24 18:05:40 +0100 (Tue, 24 Nov 2009) | 3 lines
Update for the return_conversion_factor() API prototype method.
........
r9938 | bugman | 2009-11-24 18:15:06 +0100 (Tue, 24 Nov 2009) | 3 lines
Shifted many of the model-free specific methods out of the API.
........
r9939 | bugman | 2009-11-24 18:35:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the specific analysis base API to use the model_info arg, returned from model_loop().
........
r9940 | bugman | 2009-11-24 18:39:15 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated the N-state model model_statistics() method to the model_info arg.
........
r9941 | bugman | 2009-11-24 18:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the model-free unit tests. The model_index arg is now called model_info.
........
r9942 | bugman | 2009-11-24 18:41:28 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted many of the model-free methods to use model_info rather than model_index.
........
r9943 | bugman | 2009-11-24 19:08:56 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the specific analysis base API set_selected_sim() method.
........
r9944 | bugman | 2009-11-24 19:18:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the analysis specific base API sim_return_selected() method.
The model_info arg is now being used.
........
r9945 | bugman | 2009-11-24 19:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the private __compare_objects() method to the non-API _compare_objects() method.
........
r9946 | bugman | 2009-11-24 19:30:09 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of model-free methods, and separation of the private from the API methods.
........
r9947 | bugman | 2009-11-24 19:58:18 +0100 (Tue, 24 Nov 2009) | 3 lines
A number of fixes for the model-free analysis specific API methods.
........
r9948 | bugman | 2009-11-24 19:58:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Changes to the args for the base API data_init() method.
........
r9949 | bugman | 2009-11-24 19:59:32 +0100 (Tue, 24 Nov 2009) | 3 lines
Updates to the methods of the reduced spectral density mapping API.
........
r9950 | bugman | 2009-11-25 09:05:00 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the data_init() method for API consistency.
........
r9951 | bugman | 2009-11-25 09:15:40 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted many of the J(w) mapping methods to use the model_info arg rather than spin.
........
r9952 | bugman | 2009-11-25 09:19:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring updates for returned values.
........
r9953 | bugman | 2009-11-25 09:21:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Alphabetical ordering of J(w) mapping methods, and separation of the private from the API methods.
........
r9954 | bugman | 2009-11-25 09:26:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fix.
........
r9955 | bugman | 2009-11-25 09:31:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the hybrid analysis API to match the base API.
........
r9956 | bugman | 2009-11-25 09:38:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of the private and API methods in the hybrid specific analysis.
........
r9957 | bugman | 2009-11-25 09:39:48 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted the frame order private methods into non-API methods.
........
r9958 | bugman | 2009-11-25 09:44:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of all the non-API frame order specific methods.
........
r9959 | bugman | 2009-11-25 09:46:39 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
........
r9960 | bugman | 2009-11-25 09:56:56 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the frame order specific analysis API methods to match the base API.
........
r9961 | bugman | 2009-11-25 10:02:26 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the frame order user functions.
........
r9962 | bugman | 2009-11-25 10:02:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Removal of set_frq() from the consistency testing analysis specific API.
........
r9963 | bugman | 2009-11-25 10:07:09 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fixes.
........
r9964 | bugman | 2009-11-25 10:17:49 +0100 (Wed, 25 Nov 2009) | 3 lines
More docstring updates.
........
r9965 | bugman | 2009-11-25 10:18:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the consistency testing analysis specific API methods to match the base API.
........
r9966 | bugman | 2009-11-25 10:43:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Fix for the consistency testing return_units() method for the arg name changes.
........
r9967 | bugman | 2009-11-25 10:57:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
........
r9968 | bugman | 2009-11-25 10:59:05 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix and reformatting of generic_fns.pcs.read().
........
r9969 | bugman | 2009-11-25 12:55:17 +0100 (Wed, 25 Nov 2009) | 5 lines
Decreased the user function docstring size in the relax manual.
This was changed from normal size to \scriptsize to decrease the number of pages in the manual.
........
r9970 | bugman | 2009-11-25 13:06:03 +0100 (Wed, 25 Nov 2009) | 5 lines
The user function descriptions in the relax manual are now in columns.
This shrinks the manual even further.
........
r9971 | bugman | 2009-11-25 13:11:52 +0100 (Wed, 25 Nov 2009) | 5 lines
Removed the \newpage command from the user function descriptions.
This cuts the manual size by over 100 pages!!!
........
r9972 | bugman | 2009-11-25 13:18:28 +0100 (Wed, 25 Nov 2009) | 3 lines
Added '()' to the end of the user functions in the relax manual.
........
r9973 | bugman | 2009-11-25 15:41:03 +0100 (Wed, 25 Nov 2009) | 3 lines
Turned all tables from the user functions in the relax manual into floating tables.
........
r9974 | bugman | 2009-11-25 15:46:58 +0100 (Wed, 25 Nov 2009) | 5 lines
Clean up of the minimisation docstring.
This no longer causes problems in the relax manual.
........
r9975 | bugman | 2009-11-25 15:54:01 +0100 (Wed, 25 Nov 2009) | 3 lines
Switched from the multicols package to just using \twocolumn and \onecolumn.
........
r9976 | bugman | 2009-11-25 15:54:36 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the align_tensor.svd() docstring for the relax manual.
........
r9977 | bugman | 2009-11-25 16:52:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Added rules to break the user function subsections in the manual apart.
........
r9978 | bugman | 2009-11-25 17:18:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Modified the spin ID string documentation to be better presented in the relax manual.
........
r9979 | bugman | 2009-11-26 09:09:29 +0100 (Thu, 26 Nov 2009) | 6 lines
User function call examples in the relax manual are now better formatted.
They are allowed to break after '.', '(', and '='. This is for the examples and the Defaults
subsubsection.
........
r9980 | bugman | 2009-11-26 10:22:06 +0100 (Thu, 26 Nov 2009) | 3 lines
Allowed for hyphenation in the user function subsection titles.
........
r9981 | bugman | 2009-11-26 12:20:26 +0100 (Thu, 26 Nov 2009) | 3 lines
Massive tables in the relax manual are now being split using the longtable package.
........
r9982 | bugman | 2009-11-26 12:27:18 +0100 (Thu, 26 Nov 2009) | 3 lines
The tables in the user function chapter now have the same font size as the rest of the text.
........
r9983 | bugman | 2009-11-26 12:33:35 +0100 (Thu, 26 Nov 2009) | 3 lines
Better formatting of the user function chapter by using \raggedbottom.
........
r9984 | bugman | 2009-11-26 12:50:58 +0100 (Thu, 26 Nov 2009) | 3 lines
Fixed the boolean selection table to be nicer to the automatic manual compilation.
........
r9985 | bugman | 2009-11-26 13:16:37 +0100 (Thu, 26 Nov 2009) | 3 lines
The longtables are now properly labelled.
........
r9986 | bugman | 2009-11-26 18:36:27 +0100 (Thu, 26 Nov 2009) | 3 lines
Removed the checking of sequence data from generic_fns.value.set().
........
|
2009-11-27 10:14:20
|
Tree
|
[r9991]
by
bugman
Merged revisions 9891-9986 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
........
r9891 | bugman | 2009-11-24 09:24:48 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the dx.map() user function interface.
........
r9892 | bugman | 2009-11-24 10:05:30 +0100 (Tue, 24 Nov 2009) | 10 lines
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
........
r9893 | bugman | 2009-11-24 10:17:37 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the base class return_conversion_factor() method.
The spin_id arg is now accepted.
........
r9894 | bugman | 2009-11-24 10:32:01 +0100 (Tue, 24 Nov 2009) | 6 lines
Created unit tests for the specific_fns API.
This checks the consistency of methods across the API, using method names and arg checks. Only the
frame order theories are currently checked.
........
r9895 | bugman | 2009-11-24 10:46:05 +0100 (Tue, 24 Nov 2009) | 3 lines
Renamed specific_fns.base_class.Common_functions to specific_fns.api_base.API_base.
........
r9896 | bugman | 2009-11-24 10:55:57 +0100 (Tue, 24 Nov 2009) | 3 lines
The entirety of the specific_fns API is now checked.
........
r9897 | bugman | 2009-11-24 10:57:13 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated for the __all__ list for the base_class to api_base rename.
........
r9898 | bugman | 2009-11-24 11:07:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of the functions.
........
r9899 | bugman | 2009-11-24 11:14:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the back_calc() method from the specific analysis API.
........
r9900 | bugman | 2009-11-24 11:20:24 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the copy() method from the specific analysis API.
........
r9901 | bugman | 2009-11-24 11:21:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Added a prototype calculate() method to the API.
........
r9902 | bugman | 2009-11-24 11:42:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_param_vector() and disassemble_param_vector() from the specific analysis API.
........
r9903 | bugman | 2009-11-24 11:45:10 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_scaling_matrix() from the specific analysis API.
........
r9904 | bugman | 2009-11-24 11:52:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed back_calc() from the specific analysis API.
........
r9905 | bugman | 2009-11-24 11:53:20 +0100 (Tue, 24 Nov 2009) | 3 lines
Completed removal of back_calc() from the specific analysis API.
........
r9906 | bugman | 2009-11-24 11:56:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Added create_mc_data() to the specific analysis API.
........
r9907 | bugman | 2009-11-24 12:18:58 +0100 (Tue, 24 Nov 2009) | 5 lines
Added data_names() to the specific analysis API.
General docstring clean ups as well.
........
r9908 | bugman | 2009-11-24 12:39:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _assemble_param_vector() method.
........
r9909 | bugman | 2009-11-24 12:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _disassemble_param_vector() method.
........
r9910 | bugman | 2009-11-24 12:56:22 +0100 (Tue, 24 Nov 2009) | 15 lines
A large number of method and documentation variables to the specific analysis API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
........
r9911 | bugman | 2009-11-24 12:58:24 +0100 (Tue, 24 Nov 2009) | 10 lines
Converted a number of methods to being private, removing them from the API.
These include:
_grid_search_setup()
_linear_constraints()
_model_setup()
_relax_time()
_select_model()
........
r9912 | bugman | 2009-11-24 12:59:22 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the _select_model() method to be private, removing it from the API.
........
r9913 | bugman | 2009-11-24 13:05:29 +0100 (Tue, 24 Nov 2009) | 5 lines
Clean up of the create_mc_data() API method across the board.
The spin_id keyword is now accepted by all, and is a keyword.
........
r9914 | bugman | 2009-11-24 13:21:18 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring update to return_grace_string().
........
r9915 | bugman | 2009-11-24 13:22:09 +0100 (Tue, 24 Nov 2009) | 5 lines
Fixes for the relaxation curve fitting API.
The fixes are for the return_data_name(), return_grace_string(), and return_units() methods.
........
r9916 | bugman | 2009-11-24 13:25:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9917 | bugman | 2009-11-24 13:47:33 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring and default arg changes.
........
r9918 | bugman | 2009-11-24 13:47:58 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed duplicated epydoc tags.
........
r9919 | bugman | 2009-11-24 13:48:37 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire NOE API.
........
r9920 | bugman | 2009-11-24 13:49:42 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9921 | bugman | 2009-11-24 14:04:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the check of the default values from the specific analysis API arg checks.
The defaults keyword values can be set to anything by the specific code!
........
r9922 | bugman | 2009-11-24 14:52:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the string printout creation in the __check_method_args() method.
........
r9923 | bugman | 2009-11-24 15:04:25 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the unused _read() method.
This has been superseded by the spectrum.read_intensities() user function.
........
r9924 | bugman | 2009-11-24 15:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Added model_statistics() to the specific analysis API.
........
r9925 | bugman | 2009-11-24 15:30:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire N-state model specific API.
........
r9926 | bugman | 2009-11-24 15:32:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all self.__*() private methods to self._*() non-API methods.
........
r9927 | bugman | 2009-11-24 15:40:14 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the API methods.
........
r9928 | bugman | 2009-11-24 15:50:02 +0100 (Tue, 24 Nov 2009) | 3 lines
Added duplicate_data() to the specific analysis API.
........
r9929 | bugman | 2009-11-24 16:46:59 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed some unused methods from the API.
........
r9930 | bugman | 2009-11-24 16:48:38 +0100 (Tue, 24 Nov 2009) | 17 lines
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
........
r9931 | bugman | 2009-11-24 16:59:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire model-free analysis specific API.
........
r9932 | bugman | 2009-11-24 17:05:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all the model-free results methods from private to non-API.
........
r9933 | bugman | 2009-11-24 17:08:00 +0100 (Tue, 24 Nov 2009) | 3 lines
Added an empty eliminate_doc variable to the specific analysis API.
........
r9934 | bugman | 2009-11-24 17:51:20 +0100 (Tue, 24 Nov 2009) | 5 lines
More fixes for the __format_method() method.
The methods with args and keywords are now properly formatted!
........
r9935 | bugman | 2009-11-24 18:02:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the eliminate() and model_statistics() API prototype methods.
........
r9936 | bugman | 2009-11-24 18:03:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the N-state model model_statistics() API method.
........
r9937 | bugman | 2009-11-24 18:05:40 +0100 (Tue, 24 Nov 2009) | 3 lines
Update for the return_conversion_factor() API prototype method.
........
r9938 | bugman | 2009-11-24 18:15:06 +0100 (Tue, 24 Nov 2009) | 3 lines
Shifted many of the model-free specific methods out of the API.
........
r9939 | bugman | 2009-11-24 18:35:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the specific analysis base API to use the model_info arg, returned from model_loop().
........
r9940 | bugman | 2009-11-24 18:39:15 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated the N-state model model_statistics() method to the model_info arg.
........
r9941 | bugman | 2009-11-24 18:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the model-free unit tests. The model_index arg is now called model_info.
........
r9942 | bugman | 2009-11-24 18:41:28 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted many of the model-free methods to use model_info rather than model_index.
........
r9943 | bugman | 2009-11-24 19:08:56 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the specific analysis base API set_selected_sim() method.
........
r9944 | bugman | 2009-11-24 19:18:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the analysis specific base API sim_return_selected() method.
The model_info arg is now being used.
........
r9945 | bugman | 2009-11-24 19:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the private __compare_objects() method to the non-API _compare_objects() method.
........
r9946 | bugman | 2009-11-24 19:30:09 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of model-free methods, and separation of the private from the API methods.
........
r9947 | bugman | 2009-11-24 19:58:18 +0100 (Tue, 24 Nov 2009) | 3 lines
A number of fixes for the model-free analysis specific API methods.
........
r9948 | bugman | 2009-11-24 19:58:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Changes to the args for the base API data_init() method.
........
r9949 | bugman | 2009-11-24 19:59:32 +0100 (Tue, 24 Nov 2009) | 3 lines
Updates to the methods of the reduced spectral density mapping API.
........
r9950 | bugman | 2009-11-25 09:05:00 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the data_init() method for API consistency.
........
r9951 | bugman | 2009-11-25 09:15:40 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted many of the J(w) mapping methods to use the model_info arg rather than spin.
........
r9952 | bugman | 2009-11-25 09:19:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring updates for returned values.
........
r9953 | bugman | 2009-11-25 09:21:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Alphabetical ordering of J(w) mapping methods, and separation of the private from the API methods.
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r9954 | bugman | 2009-11-25 09:26:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fix.
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r9955 | bugman | 2009-11-25 09:31:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the hybrid analysis API to match the base API.
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r9956 | bugman | 2009-11-25 09:38:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of the private and API methods in the hybrid specific analysis.
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r9957 | bugman | 2009-11-25 09:39:48 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted the frame order private methods into non-API methods.
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r9958 | bugman | 2009-11-25 09:44:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of all the non-API frame order specific methods.
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r9959 | bugman | 2009-11-25 09:46:39 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9960 | bugman | 2009-11-25 09:56:56 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the frame order specific analysis API methods to match the base API.
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r9961 | bugman | 2009-11-25 10:02:26 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the frame order user functions.
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r9962 | bugman | 2009-11-25 10:02:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Removal of set_frq() from the consistency testing analysis specific API.
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r9963 | bugman | 2009-11-25 10:07:09 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fixes.
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r9964 | bugman | 2009-11-25 10:17:49 +0100 (Wed, 25 Nov 2009) | 3 lines
More docstring updates.
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r9965 | bugman | 2009-11-25 10:18:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the consistency testing analysis specific API methods to match the base API.
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r9966 | bugman | 2009-11-25 10:43:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Fix for the consistency testing return_units() method for the arg name changes.
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r9967 | bugman | 2009-11-25 10:57:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9968 | bugman | 2009-11-25 10:59:05 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix and reformatting of generic_fns.pcs.read().
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r9969 | bugman | 2009-11-25 12:55:17 +0100 (Wed, 25 Nov 2009) | 5 lines
Decreased the user function docstring size in the relax manual.
This was changed from normal size to \scriptsize to decrease the number of pages in the manual.
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r9970 | bugman | 2009-11-25 13:06:03 +0100 (Wed, 25 Nov 2009) | 5 lines
The user function descriptions in the relax manual are now in columns.
This shrinks the manual even further.
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r9971 | bugman | 2009-11-25 13:11:52 +0100 (Wed, 25 Nov 2009) | 5 lines
Removed the \newpage command from the user function descriptions.
This cuts the manual size by over 100 pages!!!
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r9972 | bugman | 2009-11-25 13:18:28 +0100 (Wed, 25 Nov 2009) | 3 lines
Added '()' to the end of the user functions in the relax manual.
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r9973 | bugman | 2009-11-25 15:41:03 +0100 (Wed, 25 Nov 2009) | 3 lines
Turned all tables from the user functions in the relax manual into floating tables.
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r9974 | bugman | 2009-11-25 15:46:58 +0100 (Wed, 25 Nov 2009) | 5 lines
Clean up of the minimisation docstring.
This no longer causes problems in the relax manual.
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r9975 | bugman | 2009-11-25 15:54:01 +0100 (Wed, 25 Nov 2009) | 3 lines
Switched from the multicols package to just using \twocolumn and \onecolumn.
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r9976 | bugman | 2009-11-25 15:54:36 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the align_tensor.svd() docstring for the relax manual.
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r9977 | bugman | 2009-11-25 16:52:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Added rules to break the user function subsections in the manual apart.
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r9978 | bugman | 2009-11-25 17:18:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Modified the spin ID string documentation to be better presented in the relax manual.
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r9979 | bugman | 2009-11-26 09:09:29 +0100 (Thu, 26 Nov 2009) | 6 lines
User function call examples in the relax manual are now better formatted.
They are allowed to break after '.', '(', and '='. This is for the examples and the Defaults
subsubsection.
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r9980 | bugman | 2009-11-26 10:22:06 +0100 (Thu, 26 Nov 2009) | 3 lines
Allowed for hyphenation in the user function subsection titles.
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r9981 | bugman | 2009-11-26 12:20:26 +0100 (Thu, 26 Nov 2009) | 3 lines
Massive tables in the relax manual are now being split using the longtable package.
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r9982 | bugman | 2009-11-26 12:27:18 +0100 (Thu, 26 Nov 2009) | 3 lines
The tables in the user function chapter now have the same font size as the rest of the text.
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r9983 | bugman | 2009-11-26 12:33:35 +0100 (Thu, 26 Nov 2009) | 3 lines
Better formatting of the user function chapter by using \raggedbottom.
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r9984 | bugman | 2009-11-26 12:50:58 +0100 (Thu, 26 Nov 2009) | 3 lines
Fixed the boolean selection table to be nicer to the automatic manual compilation.
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r9985 | bugman | 2009-11-26 13:16:37 +0100 (Thu, 26 Nov 2009) | 3 lines
The longtables are now properly labelled.
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r9986 | bugman | 2009-11-26 18:36:27 +0100 (Thu, 26 Nov 2009) | 3 lines
Removed the checking of sequence data from generic_fns.value.set().
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2009-11-27 09:51:22
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Tree
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[r9990]
by
bugman
Added bmrb_read() and bmrb_write() to the analysis specific base API.
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2009-11-27 09:50:50
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Tree
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[r9989]
by
bugman
relax now launches when the wx python module is not installed.
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2009-11-27 09:46:40
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Tree
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