relax SVN archive

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.

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

This time the problem was in the pipe_control.structure.main.sequence_alignment() function.

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.

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.

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.

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.

Merged revisions 27704 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27704 | bugman | 2015-02-20 16:02:29 +0100 (Fri, 20 Feb 2015) | 14 lines

Fix for bug #23295 (https://gna.org/bugs/?23295).

This is the PDB secondary structure HELIX and SHEET records not updating when merging molecules.
The problem was that the algorithm for changing the molecule numbers for the helix and sheet
metadata when calling the structure.read_pdb user function was far too simplistic. Therefore the
logic has been completely rewritten.

Now the helix and sheet metadata are stored in temporary data structures in the _parse_pdb_ss()
method. As the molecules are being read from the PDB records, new data structures containing the
original molecule numbers and new molecule numbers are created. The helix and sheet metadata is
then stored in the internal structural object via the pack_structs() method, and the molecule
indices of the metadata changed based on the two molecule number remapping data structures.
........

Merged revisions 27704 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27704 | bugman | 2015-02-20 16:02:29 +0100 (Fri, 20 Feb 2015) | 14 lines

Fix for bug #23295 (https://gna.org/bugs/?23295).

This is the PDB secondary structure HELIX and SHEET records not updating when merging molecules.
The problem was that the algorithm for changing the molecule numbers for the helix and sheet
metadata when calling the structure.read_pdb user function was far too simplistic. Therefore the
logic has been completely rewritten.

Now the helix and sheet metadata are stored in temporary data structures in the _parse_pdb_ss()
method. As the molecules are being read from the PDB records, new data structures containing the
original molecule numbers and new molecule numbers are created. The helix and sheet metadata is
then stored in the internal structural object via the pack_structs() method, and the molecule
indices of the metadata changed based on the two molecule number remapping data structures.
........

Fix for bug #23295 (https://gna.org/bugs/?23295).

This is the PDB secondary structure HELIX and SHEET records not updating when merging molecules.
The problem was that the algorithm for changing the molecule numbers for the helix and sheet
metadata when calling the structure.read_pdb user function was far too simplistic. Therefore the
logic has been completely rewritten.

Now the helix and sheet metadata are stored in temporary data structures in the _parse_pdb_ss()
method. As the molecules are being read from the PDB records, new data structures containing the
original molecule numbers and new molecule numbers are created. The helix and sheet metadata is
then stored in the internal structural object via the pack_structs() method, and the molecule
indices of the metadata changed based on the two molecule number remapping data structures.