relax SVN archive

Small change which should have been part of the last commit (r26360).

Added printouts for the rdc.calc_q_factors and pcs_calc_q_factors user functions.

These are activated by the new verbosity user function argument which defaults to 1. If the value
is greater than 0, then the backend will print out all the calculated Q factors.

Modifications to the new N_state_model.test_CaM_IQ_tensor_fit system test.

The system test now checks all of the optimised values to make sure the correct values have been
found. That will block any future regressions in this N-state model code path. The system test is
now also faster. And the pcs.structural_noise user function RMSD value has been set to 0.0 so that
the test no longer has a random component affecting the final optimised values.

The align_tensor.display user function now has more consistent section formatting.

The section() and subsection() functions of the lib.text.sectioning module are now being used to
standardise these custom printouts with the rest of relax.

Merged revisions 26334-26348 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26334 | bugman | 2014-10-22 09:47:22 +0200 (Wed, 22 Oct 2014) | 9 lines

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.
........
r26335 | bugman | 2014-10-22 10:08:50 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26336 | bugman | 2014-10-22 10:21:18 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26337 | bugman | 2014-10-22 10:47:48 +0200 (Wed, 22 Oct 2014) | 9 lines

The structure.load_spins user function now stores the number of states in cdp.N.

This is to help the specific analyses which handle ensembles of structures. With the introduction
of the from_mols argument to the structure.load_spins user function, the number of states is now not
equal to the number of structural models, as the states can now come from different structures of
the same model. Therefore the user function will now explicitly set cdp.N to the number of states
depending on how the spins were loaded.
........
r26338 | bugman | 2014-10-22 11:02:30 +0200 (Wed, 22 Oct 2014) | 7 lines

Clean up and speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

All output files are now set to 'devnull' so that the system test no longer creates any files within
the relax source directories. And the optimisation settings have been decreased to hugely speed up
the system test.
........
r26339 | bugman | 2014-10-22 11:36:57 +0200 (Wed, 22 Oct 2014) | 6 lines

Bug fix for the lib.arg_check.is_float_matrix() function.

The check for a numpy.ndarray data structure type was incorrect so that lists of numpy arrays were
failing in this function. Rank-2 arrays were not affected.
........
r26340 | bugman | 2014-10-22 11:38:09 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26341 | bugman | 2014-10-22 11:44:55 +0200 (Wed, 22 Oct 2014) | 8 lines

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).
........
r26342 | bugman | 2014-10-22 14:00:50 +0200 (Wed, 22 Oct 2014) | 5 lines

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

This is for better spacing for the next messages from the specific analysis.
........
r26343 | bugman | 2014-10-22 14:01:58 +0200 (Wed, 22 Oct 2014) | 5 lines

Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

This test is however still far too slow.
........
r26344 | bugman | 2014-10-22 14:22:11 +0200 (Wed, 22 Oct 2014) | 7 lines

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.
........
r26345 | bugman | 2014-10-22 14:26:17 +0200 (Wed, 22 Oct 2014) | 8 lines

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.
........
r26346 | bugman | 2014-10-22 14:34:35 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26347 | bugman | 2014-10-22 14:37:25 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26348 | bugman | 2014-10-22 14:52:21 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........

Merged revisions 26334-26348 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26334 | bugman | 2014-10-22 09:47:22 +0200 (Wed, 22 Oct 2014) | 9 lines

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.
........
r26335 | bugman | 2014-10-22 10:08:50 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26336 | bugman | 2014-10-22 10:21:18 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26337 | bugman | 2014-10-22 10:47:48 +0200 (Wed, 22 Oct 2014) | 9 lines

The structure.load_spins user function now stores the number of states in cdp.N.

This is to help the specific analyses which handle ensembles of structures. With the introduction
of the from_mols argument to the structure.load_spins user function, the number of states is now not
equal to the number of structural models, as the states can now come from different structures of
the same model. Therefore the user function will now explicitly set cdp.N to the number of states
depending on how the spins were loaded.
........
r26338 | bugman | 2014-10-22 11:02:30 +0200 (Wed, 22 Oct 2014) | 7 lines

Clean up and speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

All output files are now set to 'devnull' so that the system test no longer creates any files within
the relax source directories. And the optimisation settings have been decreased to hugely speed up
the system test.
........
r26339 | bugman | 2014-10-22 11:36:57 +0200 (Wed, 22 Oct 2014) | 6 lines

Bug fix for the lib.arg_check.is_float_matrix() function.

The check for a numpy.ndarray data structure type was incorrect so that lists of numpy arrays were
failing in this function. Rank-2 arrays were not affected.
........
r26340 | bugman | 2014-10-22 11:38:09 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26341 | bugman | 2014-10-22 11:44:55 +0200 (Wed, 22 Oct 2014) | 8 lines

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).
........
r26342 | bugman | 2014-10-22 14:00:50 +0200 (Wed, 22 Oct 2014) | 5 lines

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

This is for better spacing for the next messages from the specific analysis.
........
r26343 | bugman | 2014-10-22 14:01:58 +0200 (Wed, 22 Oct 2014) | 5 lines

Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.

This test is however still far too slow.
........
r26344 | bugman | 2014-10-22 14:22:11 +0200 (Wed, 22 Oct 2014) | 7 lines

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.
........
r26345 | bugman | 2014-10-22 14:26:17 +0200 (Wed, 22 Oct 2014) | 8 lines

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.
........
r26346 | bugman | 2014-10-22 14:34:35 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26347 | bugman | 2014-10-22 14:37:25 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........
r26348 | bugman | 2014-10-22 14:52:21 +0200 (Wed, 22 Oct 2014) | 6 lines

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.
........

Modified the Structure.test_load_spins_multi_mol system test for the spin.pos variable changes.

The atomic position for an ensemble of structures is now set to None rather than being missing, so
the system test has been updated to check for this.

Changed the spin_selection argument default in the interatom.define user function backend.

This now defaults to False to allow other parts of relax which call this function to operate as
previously. The default for the interatom.define user function is however still True.

Merged revisions 26332-26333 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26332 | bugman | 2014-10-22 08:50:36 +0200 (Wed, 22 Oct 2014) | 9 lines

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.
........
r26333 | bugman | 2014-10-22 09:27:01 +0200 (Wed, 22 Oct 2014) | 10 lines

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.
........

Merged revisions 26332-26333 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r26332 | bugman | 2014-10-22 08:50:36 +0200 (Wed, 22 Oct 2014) | 9 lines

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.
........
r26333 | bugman | 2014-10-22 09:27:01 +0200 (Wed, 22 Oct 2014) | 10 lines

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.
........