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Commit Date  
[r27092] by bugman

Fix for the structure.align user function if no data pipes are supplied.

The pipes list was no longer being created as it was shifted to the assemble_coordinates() function,
however it is required for the translation and rotation function calls.

2014-12-11 15:03:42 Tree
[r27091] by bugman

Changed the design of the lib.structure.internal.coordinates.assemble_coord_array() function.

The elements_flag argument has been renamed to seq_info_flag. If this is set, then in addition to
the atomic elements, the molecule name, residue name, residue number, and atom name is now assembled
and returned. This information is now the common information between the structures, hence the
return values for the elements are a list of str rather than list of lists.

All of the code in pipe_control.structure.main has been updated for the change.

2014-12-11 15:00:21 Tree
[r27090] by bugman

Refactored the descriptions of a number of structure user functions.

This includes the structure.align, structure.displacement, structure.find_pivot, structure.rmsd and
structure.superimpose user functions. The paragraph_multi_struct and paragraph_atom_id module
strings have been created and are shared as two paragraphs for each of these user function
descriptions. This standardises the pipe/model/molecule/atom_id descriptions. The user function
wizard page sizes have been updated for these changes.

2014-12-11 12:40:41 Tree
[r27089] by bugman

Some docstring expansions for the pipe_control.structure.main module functions.

2014-12-11 12:13:19 Tree
[r27088] by bugman

Code refactorisation for the structure.align user function backend.

The looping over data pipes, model numbers, and molecule names, skipping those that don't match the
function arguments, has been shifted into the new structure_loop() generator function of the
pipe_control.structure.main module. This function assembles the data from the data store and then
calls the new loop_coord_structures() generator function of the lib.structure.internal.coordinates
module which does all of the work.

2014-12-11 11:25:03 Tree
[r27087] by bugman

Fixes for the structure.superimpose and structure.align user functions.

The fit_to_mean() and fit_to_first() functions of lib.structure.superimpose where being incorrectly
called, in that they expect a list of elements and not lists of lists.

2014-12-11 10:49:26 Tree
[r27086] by bugman

Modified the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

This now calls the structure.align user function after calling the structure.superimpose user
function to better test a condition that can trigger bugs.

2014-12-11 10:46:04 Tree
[r27085] by bugman

Documentation fix for the assemble_coord_array() function.

The return values for lib.structure.internal.coordinates.assemble_coord_array() were incorrectly
documented.

2014-12-11 10:42:40 Tree
[r27084] by bugman

Converted the structure.superimpose user function to the new pipes/models/molecules/atom_id design.

The user function arguments have not changed, however the backend now uses the new
pipe_control.structure.main.assemble_coordinates() function. This is to simply decrease the number
of failure points possible in the structure user functions. The change has no effect on the user
function use or results.

2014-12-11 10:37:33 Tree
[r27083] by bugman

Created the internal structural object model_list() method.

This is to simplify the assembly of a list of all current models in the structural object.

2014-12-11 10:34:24 Tree
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