relax SVN archive

Merged revisions 27635-27639,27654-27655 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).
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r27654 | bugman | 2015-02-17 09:27:42 +0100 (Tue, 17 Feb 2015) | 3 lines

Small correction for the structure.read_pdb user function description.
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r27655 | bugman | 2015-02-17 09:31:42 +0100 (Tue, 17 Feb 2015) | 6 lines

Created the Structure.test_read_merge_simultaneous system test.

This is to demonstrate a failure in the structure.read_pdb user function when merging multiple
molecules from one file into one molecule simultaneously with a single user function call.
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Merged revisions 27656 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27656 | bugman | 2015-02-17 09:44:53 +0100 (Tue, 17 Feb 2015) | 7 lines

Fix for bug #23288 (https://gna.org/bugs/?23288).

This is the failure of the structure.read_pdb user function when simultaneously merging multiple
molecules from one file. The set_mol_name and set_model_num arguments are now converted to lists
equal to the length of the read_mol and read_model arguments simultaneously, if supplied.
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Merged revisions 27654-27655 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27654 | bugman | 2015-02-17 09:27:42 +0100 (Tue, 17 Feb 2015) | 3 lines

Small correction for the structure.read_pdb user function description.
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r27655 | bugman | 2015-02-17 09:31:42 +0100 (Tue, 17 Feb 2015) | 6 lines

Created the Structure.test_read_merge_simultaneous system test.

This is to demonstrate a failure in the structure.read_pdb user function when merging multiple
molecules from one file into one molecule simultaneously with a single user function call.
........

Fix for bug #23288 (https://gna.org/bugs/?23288).

This is the failure of the structure.read_pdb user function when simultaneously merging multiple
molecules from one file. The set_mol_name and set_model_num arguments are now converted to lists
equal to the length of the read_mol and read_model arguments simultaneously, if supplied.

Created the Structure.test_read_merge_simultaneous system test.

This is to demonstrate a failure in the structure.read_pdb user function when merging multiple
molecules from one file into one molecule simultaneously with a single user function call.

Small correction for the structure.read_pdb user function description.

Deleted a number of Frame_order.test_distribute* system tests.

These are the four double rotor model tests. The frame_order.distribute user function cannot
operate on these test cases as one of the two torsion angles are set to zero in the tests.

The frame_order.distribute user function now warns when the maximum rotations are reached.

Changed the default max_rotations argument value to 100,000 in the frame_order.distribute user function.

This decrease from one million is so the user function completes in a reasonable amount of time.

The Frame_order.test_auto_analysis system test now sets the results file compression type to bzip2.