relax SVN archive

Fix for the atomic position handling in pipe_control.structure.main.load_spins_multi_mol().

The dimensionality of the position structure returned by the structural object atom_loop() method
needed to be reduced.

Modified the interatom.unit_vectors user function backend to handle missing atomic positions.

This is to match the structure.load_spins user function change whereby missing atomic positions are
now set to the value of None.

Modified the atomic position handling in pipe_control.structure.main.load_spins_multi_mol().

The multiple molecule merging functionality of the structure.load_spins user function now handles
missing atomic positions differently. The aim is that the length of the spin container position
variable is fixed for all spins to the number of structures, as the N-state model analysis assumes
this equal length for all spins. When data is missing, the atomic position for that structure is
now set to None. This will require other modifications in relax to support this new design.

Final fix for bug #22849 (https://gna.org/bugs/?22849).

This is the failure of the N-state model analysis when optimising only alignment tensors using RDCs
and/or PCSs. The alignment tensor is no longer initialised to zero values. This is to allow the
skip_preset argument for the minimise.grid_search user function to be operational for the N-state
model, a feature introduced with the zooming grid search. The solution was to check for the
uninitialised tensor in the minimise_setup_fixed_tensors() method of the
specific_analyses.n_state_model.optimisation module.

Created the N_state_model.test_CaM_IQ_tensor_fit system test.

This is for catching bug #22849 (https://gna.org/bugs/?22849), the failure of the N-state model
analysis when optimising only alignment tensors using RDCs and/or PCSs.

This new test checks code paths unchecked in the rest of the test suite, and is therefore of high
value.

Merged revisions 26307-26312,26321-26329 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26307 | bugman | 2014-10-17 16:13:04 +0200 (Fri, 17 Oct 2014) | 3 lines

Fix for the gui.fonts module to allow it to be used outside of the GUI.
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r26308 | bugman | 2014-10-17 16:54:40 +0200 (Fri, 17 Oct 2014) | 5 lines

Updated all of the scripts in devel_scripts/gui/.

These have been non-functional since the merger of the bieri_gui back in January 2011.
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r26309 | bugman | 2014-10-17 16:55:44 +0200 (Fri, 17 Oct 2014) | 3 lines

The gui.misc.bitmap_setup() function can now be used outside of the GUI.
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r26310 | bugman | 2014-10-17 20:22:56 +0200 (Fri, 17 Oct 2014) | 3 lines

Fix for the GUI test base class new_analysis_wizard() method for relaxation dispersion analyses.
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r26311 | bugman | 2014-10-18 10:20:36 +0200 (Sat, 18 Oct 2014) | 5 lines

Modified the pipe_control.pipes.get_bundle() function to operate when no pipe is supplied.

In this case, the pipe bundle that the current data pipe belongs to will be returned.
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r26312 | bugman | 2014-10-18 10:22:07 +0200 (Sat, 18 Oct 2014) | 6 lines

Fix for the recently broken (r26306) Relax_disp.test_tp02_data_to_tp02 system test.

The data pipe bundle variable was no longer defined, so now it is retrieved using the
pipe_control.pipes.get_bundle() function.
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r26321 | bugman | 2014-10-21 08:58:14 +0200 (Tue, 21 Oct 2014) | 3 lines

Bug fix for the structure.align user function for when no data pipes are supplied.
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r26322 | bugman | 2014-10-21 13:52:10 +0200 (Tue, 21 Oct 2014) | 5 lines

Created the Periodic_table.has_element() method for the lib.periodic_table module.

This is used to simply check if a given symbol exists as an atom in the periodic table.
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r26323 | bugman | 2014-10-21 13:57:05 +0200 (Tue, 21 Oct 2014) | 3 lines

Added 4 unit tests to the _lib.test_periodic_table module for the Periodic_table.has_element() method.
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r26324 | bugman | 2014-10-21 14:17:49 +0200 (Tue, 21 Oct 2014) | 8 lines

Modified the internal structural object backend for the structure.read_pdb user function.

The MolContainer._det_pdb_element() method for handling PDB files with missing element information
has been updated to use the Periodic_table.has_element() method to check if the PDB atom name
corresponds to any atoms in the periodic table. This allows for far greater support for HETATOMS
and all of the metals.
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r26325 | bugman | 2014-10-21 14:43:36 +0200 (Tue, 21 Oct 2014) | 7 lines

Created the Structure.test_load_spins_multi_mol system test.

This is to test yet to be implemented functionality of the structure.load_spins user function. This
is the loading of spin information similar, but not necessarily identical molecules all loaded into
the same structural model. For this, the from_mols argument will be added.
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r26326 | bugman | 2014-10-21 15:55:05 +0200 (Tue, 21 Oct 2014) | 6 lines

Fixes for the Structure.test_load_spins_multi_mol system test.

The call to the structure.load_spins user function has also been modified so that all 3 spins are
loaded at the same time.
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r26327 | bugman | 2014-10-21 15:58:31 +0200 (Tue, 21 Oct 2014) | 8 lines

Implemented the multiple molecule merging functionality of the structure.load_spins user function.

The argument has been added to the user function frontend and a description added for this new
functionality. In the backend, the pipe_control.structure.main.load_spins() function will now call
the load_spins_multi_mol() function if from_mols is supplied. This alternative function is required
to handle missing atoms and differential atom numbering.
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r26328 | bugman | 2014-10-21 17:03:49 +0200 (Tue, 21 Oct 2014) | 8 lines

Modified the N_state_model.test_populations system test to test the grid search code paths.

This performs a grid search of one increment after minimisation, then switches to the 'fixed'
N-state model and performs a second grid search of one increment. This now tests currently untested
code paths in the grid_search() API method behind the minimise.grid_search user function. The test
demonstrates a bug in the N-state model which was not uncovered in the test suite.
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r26329 | bugman | 2014-10-21 17:56:08 +0200 (Tue, 21 Oct 2014) | 7 lines

Bug fix for the N-state model grid search when only alignment tensor parameters are optimised.

The algorithm for splitting up the grid search to optimise each tensor separately, hence massively
collapsing the dimensionality of the problem, was being performed incorrectly. The grid_search()
API method inc, lower, and upper arguments are lists of lists, but were only being treated as lists.
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Merged revisions 26305-26306 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26305 | bugman | 2014-10-17 14:58:52 +0200 (Fri, 17 Oct 2014) | 14 lines

Changed the logic for how the new analysis wizard in the GUI is destroyed.

This relates to bug #22818 (https://gna.org/bugs/?22818), the GUI test suite failures in MS Windows
- PyAssertionError: C++ assertion "Assert failure".

The Destroy() method has been added to the Analysis_wizard class to properly close all elements of
the wizard. This is now called from the menu_new() method of the Analysis_controller class, which
is the target of the menu item and toolbar button.

To allow the test suite to use this, the menu_new() method now accepts the destroy boolean argument.
The test suite can set this to False and then access the GUI elements after calling the method
(however the Destroy() method must be called by the test suite).
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r26306 | bugman | 2014-10-17 15:05:32 +0200 (Fri, 17 Oct 2014) | 16 lines

Resign of how the new analysis wizard is handled in the GUI tests.

This relates to bug #22818 (https://gna.org/bugs/?22818), the GUI test suite failures in MS Windows
- PyAssertionError: C++ assertion "Assert failure".

The GUI test base class method new_analysis_wizard() has been created to simplify the process. When
a new analysis is desired, this method should be called. It will return the analysis page GUI
element for use in the test. The method standardises the execution of the new analysis wizard and
sets up the analysis in the GUI. It also properly destroys the wizard to avoid the memory leaking
issues such as bug #22818.

All GUI tests have been converted to use new_analysis_wizard(). This allows the GUI tests to pass
on MS Windows. However there are still significant sources of memory leaks (the USER Objects count)
visible in the Windows Task Manager.
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Bug fix for the N-state model grid search when only alignment tensor parameters are optimised.

The algorithm for splitting up the grid search to optimise each tensor separately, hence massively
collapsing the dimensionality of the problem, was being performed incorrectly. The grid_search()
API method inc, lower, and upper arguments are lists of lists, but were only being treated as lists.

Modified the N_state_model.test_populations system test to test the grid search code paths.

This performs a grid search of one increment after minimisation, then switches to the 'fixed'
N-state model and performs a second grid search of one increment. This now tests currently untested
code paths in the grid_search() API method behind the minimise.grid_search user function. The test
demonstrates a bug in the N-state model which was not uncovered in the test suite.

Implemented the multiple molecule merging functionality of the structure.load_spins user function.

The argument has been added to the user function frontend and a description added for this new
functionality. In the backend, the pipe_control.structure.main.load_spins() function will now call
the load_spins_multi_mol() function if from_mols is supplied. This alternative function is required
to handle missing atoms and differential atom numbering.