relax SVN archive

Implementation of methods for sorting sequence data in the internal structural object.

The information is sorted in the molecule container level using the new MolContainer._sort() private
method. This uses the _sort_key() helper method which determines what the new order should be.
This is used as the 'key' argument for the Python sort() method. Instead of list shuffling, new
lists in the correct order are created. Although not memory efficient, this might be faster than
shuffling.

Created the Test_object.test_add_atom_sort unit test.

This is from the _lib._structure._internal.test_object unit test module. The test will be used to
implement the sorting of input data by residue number in the add_atom() internal structural object
method. This will mean that added atoms will be placed in residue sequence order, so that output
PDB files are correctly ordered.

Created the unit test infrastructure for the lib.structure.internal.object module.

Fix for the Structure.test_atomic_fluctuations_no_match system test.

The structure.atomic_fluctuations user function will now raise a RelaxError when no data
corresponding to the atom ID can be found, so the test now checks for this.

Merged revisions 27616-27618 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27616 | bugman | 2015-02-10 13:08:00 +0100 (Tue, 10 Feb 2015) | 6 lines

Created the Structure.test_atomic_fluctuations_no_match system test.

This demonstrates a failure in the operation of the structure.atomic_fluctuations user function when
the supplied atom ID matches no atoms.
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r27617 | bugman | 2015-02-10 13:15:55 +0100 (Tue, 10 Feb 2015) | 6 lines

Fixes for the lib.structure.internal.coordinates.assemble_coord_array() function.

The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The
function can now handle no data being passed in.
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r27618 | bugman | 2015-02-10 13:19:26 +0100 (Tue, 10 Feb 2015) | 8 lines

Fixes for the pipe_control.structure.main.assemble_structural_coordinates() function.

The function will now raise a RelaxError if no structural data matching the atom ID can be found.
The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The fix
affects the structure.atomic_fluctuations, structure.displacement, structure.find_pivot,
structure.rmsd, structure.superimpose, and structure.web_of_motion user functions.
........

Fixes for the pipe_control.structure.main.assemble_structural_coordinates() function.

The function will now raise a RelaxError if no structural data matching the atom ID can be found.
The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The fix
affects the structure.atomic_fluctuations, structure.displacement, structure.find_pivot,
structure.rmsd, structure.superimpose, and structure.web_of_motion user functions.

Fixes for the lib.structure.internal.coordinates.assemble_coord_array() function.

The problem was uncovered by the Structure.test_atomic_fluctuations_no_match system test. The
function can now handle no data being passed in.

Created the Structure.test_atomic_fluctuations_no_match system test.

This demonstrates a failure in the operation of the structure.atomic_fluctuations user function when
the supplied atom ID matches no atoms.

Merged revisions 27614 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27614 | bugman | 2015-02-10 12:54:17 +0100 (Tue, 10 Feb 2015) | 8 lines

Huge speed up of the internal structural object validate_models() method.

The string formatting to create pseudo-PDB records and the large number of calls to the _translate()
method for atomic information string formatting has been shifted to only be called when atomic
information does not match. Instead the structural information is directly compared within a large
if-else statement.
........

Huge speed up of the internal structural object validate_models() method.

The string formatting to create pseudo-PDB records and the large number of calls to the _translate()
method for atomic information string formatting has been shifted to only be called when atomic
information does not match. Instead the structural information is directly compared within a large
if-else statement.