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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