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Commit Date  
[r26349] by bugman

Added a printout of the frame order model in the target function setup function.

This is printed out when the minimise.calculate, minimise.grid_search, or minimise.execute user
function are called, and is for better feedback, especially in the auto-analysis where the
repetitive optimisations can be confusing.

2014-10-22 13:22:03 Tree
[r26348] by bugman

Implemented the spin_selection Boolean argument for the interatom.define user function.

This has been added to the frontend with a description, and to the backend. When set, it allows the
spin selections to define the interatomic data container selection.

2014-10-22 12:52:21 Tree
[r26347] by bugman

Modified the N_state_model.test_CaM_IQ_tensor_fit system/GUI test for implementing a new feature.

The 'spin_selection' argument has been added to the interatom.define user function. This will be
used to carry the spin selections over into the interatomic data containers.

2014-10-22 12:37:25 Tree
[r26346] by bugman

Updated the N_state_model.test_CaM_IQ_tensor_fit system test so it operates correctly as a GUI test.

All user functions are now executed through the special self._execute_uf() method to allow either
the prompt interpreter or the GUI to execute the user function.

2014-10-22 12:34:35 Tree
[r26345] by bugman

The verbosity argument for the N-state model optimisation is now propagated for more printouts.

The argument for the calculate() and minimise() API methods is now sent into
specific_analyses.n_state_model.optimisation.target_fn_setup(), and from there into the
pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data() functions. That way the
number of RDCs and PCSs used in the N-state model is reported back to the user for better feedback.

2014-10-22 12:26:17 Tree
[r26344] by bugman

Added printouts to pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data().

These functions now accept the verbosity argument which if greater than 0 will activate printouts of
how many RDCs or PCSs have been assembled for each alignment. This will be useful for user feedback
as the spin verses interatomic data container selections can be difficult to understand.

2014-10-22 12:22:11 Tree
[r26343] by bugman

Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

This test is however still far too slow.

2014-10-22 12:01:58 Tree
[r26342] by bugman

Added spacing after the minimise.grid_search user function setup printouts.

This is for better spacing for the next messages from the specific analysis.

2014-10-22 12:00:50 Tree
[r26341] by bugman

Lists of lists containing rows of None are now better supported by the lib.xml functions.

The object_to_xml() function will now convert the float parts to IEEE-754 byte arrays, and the None
parts will be stored as None in the <ieee_754_byte_array> list node. The matching xml_to_object()
method has also been modified to read in this new node format. This affects the results.write and
state.save user functions (as well as the results.read and state.load user functions).

2014-10-22 09:44:55 Tree
[r26340] by bugman

Expanded the lib.arg_check.is_float_matrix() function by adding the none_elements argument.

This matches a number of the other module functions, and allows for entire rows of the matrix to be
None.

2014-10-22 09:38:09 Tree
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