Author: bugman
Date: Thu Sep 25 18:39:08 2008
New Revision: 7312
URL: http://svn.gna.org/viewcvs/relax?rev=7312&view=rev
Log:
Merged revisions 7236-7302,7304-7305,7308-7310 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r7236 | bugman | 2008-09-24 14:47:48 +0200 (Wed, 24 Sep 2008) | 5 lines
Created the specific base class method model_loop().
This defaults to one model per spin system, and can be used by most
analysis types.
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r7237 | bugman | 2008-09-24 14:49:48 +0200 (Wed, 24 Sep 2008) | 3 lines
Activated the model_loop() generator method.
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r7238 | bugman | 2008-09-24 16:10:56 +0200 (Wed, 24 Sep 2008) | 3 lines
Changed model_loop() to return the spin container.
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r7239 | bugman | 2008-09-24 16:18:13 +0200 (Wed, 24 Sep 2008) | 3 lines
Created the sim_return_chi2() base class method.
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r7240 | bugman | 2008-09-24 16:19:59 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the sim_return_selected() base class method to accept the spin
container.
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r7241 | bugman | 2008-09-24 16:22:23 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the sim_return_param() base class method to accept the spin
container.
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r7242 | bugman | 2008-09-24 16:26:40 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the set_error() base class method to accept the spin container.
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r7243 | bugman | 2008-09-24 16:33:09 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the Grace class methods into module functions.
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r7244 | bugman | 2008-09-24 16:41:32 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the determine_graph_type() function to the new relax design.
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r7245 | bugman | 2008-09-24 16:59:13 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the get_data() function to the new relax design.
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r7246 | bugman | 2008-09-24 17:01:41 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the view() function to the new design.
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r7247 | bugman | 2008-09-24 17:23:34 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the 4 write_*() functions to the new design.
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r7248 | bugman | 2008-09-24 17:36:02 +0200 (Wed, 24 Sep 2008) | 3 lines
The pipe argument is now optional for RelaxNoSimError.
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r7249 | bugman | 2008-09-24 17:43:04 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the Grace write() function to the new design.
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r7250 | bugman | 2008-09-24 17:54:52 +0200 (Wed, 24 Sep 2008) | 3 lines
Updated the grace.write() user function interface to the new design.
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r7251 | bugman | 2008-09-24 17:56:02 +0200 (Wed, 24 Sep 2008) | 3 lines
A few small fixes for the write() function.
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r7252 | bugman | 2008-09-24 18:00:27 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the grace.write() user function interface.
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r7253 | bugman | 2008-09-24 18:02:10 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed a remaining instance of 'self' from the write() function.
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r7254 | bugman | 2008-09-24 18:03:32 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the call to get_data().
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r7255 | bugman | 2008-09-24 18:06:31 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the calls to x_return_value() and y_return_value().
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r7256 | bugman | 2008-09-24 18:33:07 +0200 (Wed, 24 Sep 2008) | 3 lines
Shifted the focus of the Grace module from residues to spins.
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r7257 | bugman | 2008-09-24 18:33:45 +0200 (Wed, 24 Sep 2008) | 3 lines
Fatal indentation fix.
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r7258 | bugman | 2008-09-24 18:43:16 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the determine_seq_type() function.
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r7259 | bugman | 2008-09-24 18:46:03 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the count_molecules() and count_residues() functions.
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r7260 | bugman | 2008-09-24 18:47:54 +0200 (Wed, 24 Sep 2008) | 3 lines
Merged the count_selected_spins() function into count_spins().
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r7261 | bugman | 2008-09-24 18:49:04 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed the call to count_selected_spins().
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r7262 | bugman | 2008-09-24 18:51:20 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the test_count_spins() unit test.
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r7263 | bugman | 2008-09-24 18:52:16 +0200 (Wed, 24 Sep 2008) | 3 lines
Another fix for the test_count_spins() unit test.
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r7264 | bugman | 2008-09-24 19:00:08 +0200 (Wed, 24 Sep 2008) | 3 lines
An important fix for the model-free minimisation code for the merged
count_spins() function.
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r7265 | bugman | 2008-09-24 19:02:47 +0200 (Wed, 24 Sep 2008) | 3 lines
Propagation of the spin_id variable.
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r7266 | bugman | 2008-09-24 19:15:52 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the select_all_sims() function to use the model_loop().
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r7267 | bugman | 2008-09-24 19:17:29 +0200 (Wed, 24 Sep 2008) | 3 lines
Updated the set_selected_sim() method.
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r7268 | bugman | 2008-09-24 19:18:50 +0200 (Wed, 24 Sep 2008) | 3 lines
Shifted set_selected_sim() to the base class.
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r7269 | bugman | 2008-09-24 19:20:07 +0200 (Wed, 24 Sep 2008) | 3 lines
Docstring and comment fixes for select_all_sims().
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r7270 | bugman | 2008-09-24 19:28:49 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the model-free model_loop() generator method.
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r7271 | bugman | 2008-09-24 19:32:51 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed some dud arguments to the model_loop() generator.
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r7272 | bugman | 2008-09-24 19:49:02 +0200 (Wed, 24 Sep 2008) | 3 lines
Deleted the set_selected_sim() methods, as the base class method is
sufficient.
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r7273 | bugman | 2008-09-24 19:50:08 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed some unused imports of return_spin_from_index().
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r7274 | bugman | 2008-09-24 19:55:23 +0200 (Wed, 24 Sep 2008) | 3 lines
Fix for the model-free model_loop() generator function.
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r7275 | bugman | 2008-09-24 19:56:41 +0200 (Wed, 24 Sep 2008) | 3 lines
Another fix for the model_loop() generator.
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r7276 | bugman | 2008-09-24 20:16:55 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the identification of multiple data sets in the write() function.
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r7277 | bugman | 2008-09-24 20:18:15 +0200 (Wed, 24 Sep 2008) | 3 lines
Passed the missing 'data' data structure into write_header().
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r7278 | bugman | 2008-09-24 20:27:38 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the data_names() methods to the new design.
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r7279 | bugman | 2008-09-24 20:36:59 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the call to generate_vector_dist().
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r7280 | bugman | 2008-09-24 20:54:46 +0200 (Wed, 24 Sep 2008) | 3 lines
The structural object is now initialised with an empty Structure_container
appended.
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r7281 | bugman | 2008-09-24 20:55:08 +0200 (Wed, 24 Sep 2008) | 3 lines
The Structure_container no longer needs to be initialised.
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r7282 | bugman | 2008-09-24 21:07:12 +0200 (Wed, 24 Sep 2008) | 7 lines
Reverted r7280 and r7281 as this fix was flawed.
The command used was:
svn merge -r7281:7279 .
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r7283 | bugman | 2008-09-24 21:20:07 +0200 (Wed, 24 Sep 2008) | 3 lines
The Structure_container is appended in the create_diff_tensor_pdb()
function.
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r7284 | bugman | 2008-09-24 21:22:03 +0200 (Wed, 24 Sep 2008) | 3 lines
The centre of mass atom is now set to the first.
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r7285 | bugman | 2008-09-24 21:45:20 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the setting of j_min in generate_vector_dist() when the maximum angle
is not given.
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r7286 | bugman | 2008-09-24 21:54:17 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixes for the generate_vector_residues() function when the neg flag is True.
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r7287 | bugman | 2008-09-24 21:57:31 +0200 (Wed, 24 Sep 2008) | 3 lines
Fix for the sim_return_param() method.
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r7288 | bugman | 2008-09-24 21:59:11 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the arg order for set_error().
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r7289 | bugman | 2008-09-24 23:20:14 +0200 (Wed, 24 Sep 2008) | 3 lines
Created the test_Selection_contains_spin8() unit test.
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r7290 | bugman | 2008-09-24 23:24:02 +0200 (Wed, 24 Sep 2008) | 5 lines
Fix for the contains_spin() class method.
This is a hack which might cause failures!
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r7291 | bugman | 2008-09-24 23:31:34 +0200 (Wed, 24 Sep 2008) | 6 lines
Reverted the hack of r7290.
The command used was:
svn merge -r7290:7289 .
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r7292 | bugman | 2008-09-25 15:32:17 +0200 (Thu, 25 Sep 2008) | 6 lines
Reverted r7289 as this unit test was bad.
The command used was:
svn merge -r7289:7288 .
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r7293 | bugman | 2008-09-25 15:48:24 +0200 (Thu, 25 Sep 2008) | 3 lines
Added a simple system test for the calculation of unit XH bond vectors.
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r7294 | bugman | 2008-09-25 15:57:07 +0200 (Thu, 25 Sep 2008) | 3 lines
Activated the unit vector system test.
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r7295 | bugman | 2008-09-25 16:39:11 +0200 (Thu, 25 Sep 2008) | 3 lines
Fixes for the unit vector system test.
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r7296 | bugman | 2008-09-25 16:42:37 +0200 (Thu, 25 Sep 2008) | 3 lines
Added another system test for the calculation of unit XH vectors, but with
spin numbers removed.
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r7297 | bugman | 2008-09-25 16:45:26 +0200 (Thu, 25 Sep 2008) | 3 lines
Allowed the number arg in the spin.number() user function to be None.
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r7298 | bugman | 2008-09-25 16:50:22 +0200 (Thu, 25 Sep 2008) | 3 lines
Allowed the spin number to be reset to None.
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r7299 | bugman | 2008-09-25 16:55:03 +0200 (Thu, 25 Sep 2008) | 3 lines
Added some more checks in the unit vector system tests.
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r7300 | bugman | 2008-09-25 16:59:26 +0200 (Thu, 25 Sep 2008) | 3 lines
Added 2 more unit vector system tests, this time using the internal PDB
reader.
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r7301 | bugman | 2008-09-25 17:01:30 +0200 (Thu, 25 Sep 2008) | 3 lines
Fixed the number arg unit test of spin.number().
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r7302 | bugman | 2008-09-25 17:52:15 +0200 (Thu, 25 Sep 2008) | 7 lines
Added support to the internal PDB structural object for determining
connected atoms.
This is for when no CONECT records exist. The method __find_bonded_atom()
has been renamed to
__bonded_atom(), and the new method __find_bonded_atoms() has been written.
This new method
connects all atoms located a certain distance from each other.
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r7304 | bugman | 2008-09-25 18:04:14 +0200 (Thu, 25 Sep 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-6740" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/rdc_analysis
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r7305 | bugman | 2008-09-25 18:09:31 +0200 (Thu, 25 Sep 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/rdc_analysis
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r7308 | bugman | 2008-09-25 18:19:56 +0200 (Thu, 25 Sep 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-6740" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/rdc_analysis
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r7309 | bugman | 2008-09-25 18:30:20 +0200 (Thu, 25 Sep 2008) | 1124 lines
Merged revisions
6837,6839,6841-6857,6859-6878,6880,6882-6938,6941-6945,6952,6957-6992,7021,7029,7076-7077,7080-7093,7106-7121,7130-7146,7148-7189,7191-7208,7226-7227,7230-7231,7307
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/rdc_analysis
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r6837 | bugman | 2008-07-08 16:23:35 +0200 (Tue, 08 Jul 2008) | 3 lines
Created the framework for a user function class for handling RDCs (by
copying the relax_data code).
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r6839 | bugman | 2008-07-08 20:30:14 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed a test for the model setup in the set_non_spin_params() method.
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r6841 | bugman | 2008-07-08 21:02:19 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index
flag is True.
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r6842 | bugman | 2008-07-08 21:03:21 +0200 (Tue, 08 Jul 2008) | 5 lines
Added a number of new parameters to the return_data_name() method.
This include the bond length, and heteronucleus and proton types.
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r6843 | bugman | 2008-07-08 21:12:31 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index
flag is True.
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r6844 | bugman | 2008-07-08 21:17:05 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed some debugging code.
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r6845 | bugman | 2008-07-08 21:24:29 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the rdc.read() user function from the relax_data.read() code.
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r6846 | bugman | 2008-07-08 21:25:41 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'ri_label' to 'id'.
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r6847 | bugman | 2008-07-08 21:26:26 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'relax_data' to 'rdc'.
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r6848 | bugman | 2008-07-08 21:36:00 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all of the rdc user functions from the relax_data code.
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r6849 | bugman | 2008-07-08 21:37:46 +0200 (Tue, 08 Jul 2008) | 3 lines
Created a generic_fns rdc module by copying the relax_data module.
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r6850 | bugman | 2008-07-08 21:54:07 +0200 (Tue, 08 Jul 2008) | 3 lines
Created 2 new error classes, RelaxNoRDCError and RelaxRDCError.
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r6851 | bugman | 2008-07-08 22:03:09 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the read() function from the relax_data code.
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r6852 | bugman | 2008-07-08 22:20:28 +0200 (Tue, 08 Jul 2008) | 3 lines
Made the error column optional in the loading of RDCs.
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r6853 | bugman | 2008-07-08 22:25:44 +0200 (Tue, 08 Jul 2008) | 3 lines
Fixes for the read() function to allow the error column to be missing.
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r6854 | bugman | 2008-07-09 10:59:43 +0200 (Wed, 09 Jul 2008) | 8 lines
Split up the n_state_model.model() user function.
The new user functions are:
n_state_model.number_of_states()
n_state_model.ref_domain()
n_state_model.setup_model()
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r6855 | bugman | 2008-07-09 11:02:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the unit tests broken by the split up of n_state_model.model().
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r6856 | bugman | 2008-07-09 11:04:15 +0200 (Wed, 09 Jul 2008) | 3 lines
Wrote the model arg unit test for the n_state_model.setup_model() user
function.
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r6857 | bugman | 2008-07-09 11:06:51 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the N-state model system test.
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r6859 | bugman | 2008-07-09 11:18:53 +0200 (Wed, 09 Jul 2008) | 3 lines
Split up the model_setup() method into number_of_states(), ref_domain(),
and setup_model().
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r6860 | bugman | 2008-07-09 11:20:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the new error class RelaxNoModelError.
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r6861 | bugman | 2008-07-09 11:21:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the n_state_model.select_model() user function.
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r6862 | bugman | 2008-07-09 11:23:36 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring and print out fixes for the n_state_model.select_model() user
function.
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r6863 | bugman | 2008-07-09 11:26:09 +0200 (Wed, 09 Jul 2008) | 5 lines
Renamed the n_state_model.setup_model() user function to
n_state_model.select_model().
This is to match the convention of the other analyses.
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r6864 | bugman | 2008-07-09 11:26:58 +0200 (Wed, 09 Jul 2008) | 3 lines
System test fix for the renaming of n_state_model.setup_model().
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r6865 | bugman | 2008-07-09 11:29:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Added some error checking for the validity of the selected model type.
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r6866 | bugman | 2008-07-09 11:41:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the model checking in the minimise() method.
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r6867 | bugman | 2008-07-09 11:51:05 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the setup_model() method so that the model parameters can be set
up by numerous methods.
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r6868 | bugman | 2008-07-09 11:52:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the model arg of the n_state_model.select_model() user function.
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r6869 | bugman | 2008-07-09 13:29:21 +0200 (Wed, 09 Jul 2008) | 3 lines
Spun out some of the minimisation code into the minimise_setup_tensors()
method.
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r6870 | bugman | 2008-07-09 13:33:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Renamed setup_model() to the private __update_model() method.
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r6871 | bugman | 2008-07-09 13:34:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Made a call to __update_model() from select_model().
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r6872 | bugman | 2008-07-09 13:37:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Made the __update_model() method less fatal.
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r6873 | bugman | 2008-07-09 13:38:55 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the call to __update_model() from number_of_states().
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r6874 | bugman | 2008-07-09 13:39:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Added a call to __update_model() from ref_domain().
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r6875 | bugman | 2008-07-09 13:40:26 +0200 (Wed, 09 Jul 2008) | 3 lines
Added an alias to the current data pipe in minimise_setup_tensors().
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r6876 | bugman | 2008-07-09 13:43:57 +0200 (Wed, 09 Jul 2008) | 3 lines
Passed the param_vector into minimise_setup_tensors() and fixed the
variable of the returned data.
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r6877 | bugman | 2008-07-09 13:53:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the __update_model() to prevent the model data being
overwritten or too many params added.
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r6878 | bugman | 2008-07-09 14:40:41 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the minimise_setup_rdcs() method.
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r6880 | bugman | 2008-07-09 15:05:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified minimise_setup_rdcs() to throw a warning if RDCs exist but XH
bond vectors are missing.
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r6882 | bugman | 2008-07-09 15:11:47 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for minimise_setup_rdcs(). The spin id is now generated for the
warning.
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r6883 | bugman | 2008-07-09 15:18:36 +0200 (Wed, 09 Jul 2008) | 3 lines
The N_state_opt class now accepts the model, rdcs, and xh_vect arguments.
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r6884 | bugman | 2008-07-09 15:35:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified the N_state_opt class to handle both alignment tensor and RDC
optimisation.
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r6885 | bugman | 2008-07-09 15:40:54 +0200 (Wed, 09 Jul 2008) | 6 lines
Changed the N_state_opt functions to be model dependent.
The func_rdcs() method is now func_population(), and the func_tensors()
method is now
func_2domain().
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r6886 | bugman | 2008-07-09 15:42:16 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the N_state_opt class set up for the tensor optimisation.
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r6887 | bugman | 2008-07-09 15:49:39 +0200 (Wed, 09 Jul 2008) | 3 lines
[... 1114 lines stripped ...]
r7312 - in /branches/bmrb: ./ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_fns/ specific_fns/model_...