relax SVN archive

Implemented the back-end of the frame_order.distribute user function.

This follows the design of the pseudo-Brownian simulation frame_order.simulate user function. The
specific_analyses.frame_order.uf.distribute() function has been created as a modified copy of the
simulate() function of the same module. This simply performs checks and assembles the data, passing
into the new lib.frame_order.simulate.uniform_distribution() function, which itself is a modified
copy of the brownian() function in the same module.

Added the frame_order.distribute user function to the auto-analysis results output.

This will allow both the pseudo-Brownian simulation and uniform distribution PDB files to be
available to the user in all results directories (excluding the intermediate results for speed).

Small modification of the frame_order.simulate user function.

The GUI file opening dialog wildcard selectors are now set to all PDB file types (plain text, bzip2
compressed, and gzip compressed).

Created the front-end of the frame_order.distribute user function.

This is a copy and modification of the frame_order.simulate user function, as the concepts are
similar.

Created a large set of system tests for implementing the frame_order.distribute user function.

This user function will be similar to frame_order.simulate. However instead of creating a PDB file
with models from a pseudo-Brownian simulation, the frame_order.distribute user function will
generate a PDB file of models forming a uniform distribution of structures covering the full frame
order motional space.

The new system tests are:

Frame_order.test_distribute_double_rotor_mode1_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode1_z_axis
Frame_order.test_distribute_double_rotor_mode2_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode2_z_axis
Frame_order.test_distribute_free_rotor_z_axis
Frame_order.test_distribute_iso_cone_z_axis
Frame_order.test_distribute_iso_cone_xz_plane_tilt
Frame_order.test_distribute_iso_cone_torsionless_z_axis
Frame_order.test_distribute_pseudo_ellipse_xz_plane_tilt
Frame_order.test_distribute_pseudo_ellipse_z_axis
Frame_order.test_distribute_pseudo_ellipse_free_rotor_z_axis
Frame_order.test_distribute_pseudo_ellipse_torsionless_z_axis
Frame_order.test_distribute_rotor_z_axis

These are aliases for the equivalent Frame_order.test_simulate_* system tests which have had the
'type' keyword argument added, defaulting to 'sim', which allows to switch between the
frame_order.simulate and frame_order.distribute user functions. The concept behind these system
tests are the same for both user functions, so the code is shared.

Merged revisions 27635-27639 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27635 | bugman | 2015-02-12 19:42:34 +0100 (Thu, 12 Feb 2015) | 10 lines

Created new system tests for implementing new functionality for the structure.mean user function.

This includes the Structure.test_mean_models and Structure.test_mean_molecules. The idea is to
convert the user function to the new pipes/models/molecules/atom_id design. This will allow
molecules with non-identical sequences and atomic compositions to be averaged. The set_mol_name and
set_model_num arguments from the structure.read_pdb, structure.read_gaussian, and structure.read_xyz
user functions will also be implemented to allow the mean structure to be stored alongside the other
molecules.
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r27636 | bugman | 2015-02-13 17:05:57 +0100 (Fri, 13 Feb 2015) | 3 lines

Some fixes for the checks in the Structure.test_mean_molecules system test.
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r27637 | bugman | 2015-02-13 17:06:35 +0100 (Fri, 13 Feb 2015) | 3 lines

Fix for the structure.mean user function call in the Structure.test_mean_models system test.
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r27638 | bugman | 2015-02-13 17:33:19 +0100 (Fri, 13 Feb 2015) | 7 lines

Expanded the checking in all the Structure.test_mean* system tests to cover all atomic information.

This includes the Structure.test_mean, Structure.test_mean_models, and Structure.test_mean_molecules
system tests. All structural data is now carefully checked to make sure that the structure.mean
user function operates correctly.
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r27639 | bugman | 2015-02-13 17:45:08 +0100 (Fri, 13 Feb 2015) | 15 lines

Converted the structure.mean user function to the new pipe/model/molecule/atom_id design.

This allows the average structure calculation to work on atomic coordinates from different data
pipes, different structural models, and different molecules. The user function backend uses the new
pipe_control.structure.main.assemble_structural_coordinates() function to assemble the common atom
coordinates, molecule names, residue names, residue numbers, atom names and elements. All this
information is then used to construct a new molecule container for storing the average structure in
the internal structural object.

To allow for the averaged structural data to be stored, the internal structural object method
add_coordinates() has been created. This is modelled on the PDB, Gaussian, and XYZ format loading
methods. The internal structural object mean() method is no longer used, but remains for anyone who
might have interest in the future (though as it is untested, bit-rot will be a problem).
........

Converted the structure.mean user function to the new pipe/model/molecule/atom_id design.

This allows the average structure calculation to work on atomic coordinates from different data
pipes, different structural models, and different molecules. The user function backend uses the new
pipe_control.structure.main.assemble_structural_coordinates() function to assemble the common atom
coordinates, molecule names, residue names, residue numbers, atom names and elements. All this
information is then used to construct a new molecule container for storing the average structure in
the internal structural object.

To allow for the averaged structural data to be stored, the internal structural object method
add_coordinates() has been created. This is modelled on the PDB, Gaussian, and XYZ format loading
methods. The internal structural object mean() method is no longer used, but remains for anyone who
might have interest in the future (though as it is untested, bit-rot will be a problem).

Expanded the checking in all the Structure.test_mean* system tests to cover all atomic information.

This includes the Structure.test_mean, Structure.test_mean_models, and Structure.test_mean_molecules
system tests. All structural data is now carefully checked to make sure that the structure.mean
user function operates correctly.

Fix for the structure.mean user function call in the Structure.test_mean_models system test.

Some fixes for the checks in the Structure.test_mean_molecules system test.