relax SVN archive

Added the new 'atom_id' argument to the frame_order.distribute user function.

This uses the new inverse selection functionality recently introduced into the trunk to delete all
structural data not matching the atom_id from the copy of the loaded structural data string prior to
generating the distribution of structures.

Merged revisions 27717-27719 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27717 | bugman | 2015-02-24 12:08:43 +0100 (Tue, 24 Feb 2015) | 3 lines

Improvement for a RelaxError message when assembling structural data but no coordinates can be found.
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r27718 | bugman | 2015-02-25 13:46:35 +0100 (Wed, 25 Feb 2015) | 6 lines

Created a series of unit tests for implementing a new internal structural object feature.

These tests check a new 'inv' argument for the selection() structural object method for allowing all
atoms not matching the atom ID string to be selected.
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r27719 | bugman | 2015-02-25 13:58:45 +0100 (Wed, 25 Feb 2015) | 6 lines

Implemented the new 'inv' argument for the selection() structural object method.

This allows for all atoms not matching the atom ID string to be selected. The unit tests for this
argument now all pass, validating the implementation.
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Implemented the new 'inv' argument for the selection() structural object method.

This allows for all atoms not matching the atom ID string to be selected. The unit tests for this
argument now all pass, validating the implementation.

Created a series of unit tests for implementing a new internal structural object feature.

These tests check a new 'inv' argument for the selection() structural object method for allowing all
atoms not matching the atom ID string to be selected.

Improvement for a RelaxError message when assembling structural data but no coordinates can be found.

Merged revisions 27707-27714 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27707 | bugman | 2015-02-20 16:16:02 +0100 (Fri, 20 Feb 2015) | 6 lines

Python 3 fix for the new internal structural object MolContainer._sort() method.

The list() builtin function is required to convert the output of the range() function into a true
list in Python 3, so that the list.sort() method can be accessed.
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r27708 | bugman | 2015-02-20 16:46:14 +0100 (Fri, 20 Feb 2015) | 7 lines

Python 3 fix for the Test_msa.test_central_star unit test.

This is from the _lib._sequence_alignment.test_msa unit test module. The logic of range() + range()
does not work in Python 3, so the range function calls are now wrapped in list() function calls to
convert to the correct data structure type.
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r27709 | bugman | 2015-02-20 16:51:33 +0100 (Fri, 20 Feb 2015) | 6 lines

Python 3 fix for the internal structural object MolContainer._sort_key() method.

This method is used as the key for the sort() function. However in Python 3, the key cannot be
None. So now if the residue number is None, the value of 0 is returned instead.
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r27710 | bugman | 2015-02-20 16:54:24 +0100 (Fri, 20 Feb 2015) | 6 lines

Python 3 fix for the pipe_control.structure.main.assemble_structural_coordinates() function.

This affects most of the structure user functions. This was another case of requiring the list()
built in function to create a list object from an iterator.
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r27711 | bugman | 2015-02-20 16:56:44 +0100 (Fri, 20 Feb 2015) | 5 lines

Another Python 3 list() fix for the structure user functions.

This time the problem was in the pipe_control.structure.main.sequence_alignment() function.
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r27712 | bugman | 2015-02-23 10:06:59 +0100 (Mon, 23 Feb 2015) | 9 lines

Large speed up of the structure.web_of_motion user function.

With the introduction of the _sort() internal structural object method and it being called by the
add_atom(), the structure.web_of_motion user function was now painfully slow. As sorting the
structural data is unnecessary for the backend of this user function, the add_atom() boolean
argument 'sort' has been added to turn the sorting on and off, and the structure.web_of_motion
backend now sets this to False.
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r27713 | bugman | 2015-02-23 11:49:05 +0100 (Mon, 23 Feb 2015) | 6 lines

Fix for the internal structural object unit test Test_object.test_add_atom_sort.

This test of the _lib._structure._internal.test_object unit test module now requires the sort
argument set to True when calling the add_atom() method.
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r27714 | bugman | 2015-02-23 11:50:54 +0100 (Mon, 23 Feb 2015) | 3 lines

Fix for a RelaxError message from the internal structural object when validating models.
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Fix of a fatal bug preventing the frame order analysis to be run on a multi-processor system.

The multi-processor code was calling the count_sobol_points() function of the
specific_analyses.frame_order.optimisation module to give feedback when calling the minimise.execute
or minimise.calculate user functions. However this was run in the slave command run() method, hence
would be executed on the slave. The problem is that count_sobol_points() performs a number of
checks on the current data pipe, however the slaves do not have any data pipes set up.

Fix for a RelaxError message from the internal structural object when validating models.

Fix for the internal structural object unit test Test_object.test_add_atom_sort.

This test of the _lib._structure._internal.test_object unit test module now requires the sort
argument set to True when calling the add_atom() method.

Large speed up of the structure.web_of_motion user function.

With the introduction of the _sort() internal structural object method and it being called by the
add_atom(), the structure.web_of_motion user function was now painfully slow. As sorting the
structural data is unnecessary for the backend of this user function, the add_atom() boolean
argument 'sort' has been added to turn the sorting on and off, and the structure.web_of_motion
backend now sets this to False.