relax SVN archive

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.
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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

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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.
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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.

Merged revisions 27612 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27612 | bugman | 2015-02-10 12:05:01 +0100 (Tue, 10 Feb 2015) | 10 lines

Huge speed up for the assembly of atomic coordinates from a large number of structures.

The internal structural object validate_models() method was being called once for each structure
when assembling the atomic coordinates. This resulted in the _translate() internal structural
object method, which converts all input data to formatted strings, being called hundreds of millions
of times. The problem was in lib.structure.internal.coordinates.assemble_atomic_coordinates(), in
that the one_letter_codes() method, which calls validate_models(), was called for each molecule
encountered. The solution was not to validate models in one_letter_codes().
........