relax SVN archive

Merged revisions 27620-27629 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27620 | bugman | 2015-02-10 13:24:55 +0100 (Tue, 10 Feb 2015) | 6 lines

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.
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r27621 | bugman | 2015-02-11 09:25:58 +0100 (Wed, 11 Feb 2015) | 3 lines

Created the unit test infrastructure for the lib.structure.internal.object module.
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r27622 | bugman | 2015-02-11 09:55:57 +0100 (Wed, 11 Feb 2015) | 8 lines

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.
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r27623 | bugman | 2015-02-11 10:17:07 +0100 (Wed, 11 Feb 2015) | 9 lines

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.
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r27624 | bugman | 2015-02-11 10:23:45 +0100 (Wed, 11 Feb 2015) | 6 lines

The loading of structural data now sorts the data if the merge flag is True.

The pack_structs() method for sorting the data will now call the new MolContainer._sort() function
is the data is being merged. This is to ensure that the final structural data is correctly ordered.
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r27625 | bugman | 2015-02-11 10:29:27 +0100 (Wed, 11 Feb 2015) | 3 lines

Fixes for a number of Structure system tests for the sorted structural data changes.
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r27626 | bugman | 2015-02-11 10:48:24 +0100 (Wed, 11 Feb 2015) | 7 lines

Modified the structure.read_pdb user function backend to skip water molecules.

All residues with the name 'HOH' are now skipped when loading PDB files. This is implemented in the
MolContainer.fill_object_from_pdb() method, and a RelaxWarning is printed listing the residue
numbers of all skipped waters.
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r27627 | bugman | 2015-02-11 10:49:57 +0100 (Wed, 11 Feb 2015) | 6 lines

Modified the Structure.test_read_pdb_1UBQ system test for the new water skipping feature.

As the structure.read_pdb user function will now skip waters, the last atom in the structural object
will now be the last ubiquitin atom and not the last water atom.
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r27628 | bugman | 2015-02-11 11:25:41 +0100 (Wed, 11 Feb 2015) | 7 lines

Modified the Test_object.test_add_atom_sort unit test to check atom connectivities.

This is from the _lib._structure._internal.test_object unit test module. The problem is that the
MolContainer._sort() method for sorting the structural data currently does not correctly update the
bonded data structure.
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r27629 | bugman | 2015-02-11 11:28:15 +0100 (Wed, 11 Feb 2015) | 6 lines

Completed the implementation of the sorting of structural data in the internal structural object.

The MolContainer._sort() private method now changes the connect atom indices in the bonded data
structure to the new sorted indices.
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Completed the implementation of the sorting of structural data in the internal structural object.

The MolContainer._sort() private method now changes the connect atom indices in the bonded data
structure to the new sorted indices.

Modified the Test_object.test_add_atom_sort unit test to check atom connectivities.

This is from the _lib._structure._internal.test_object unit test module. The problem is that the
MolContainer._sort() method for sorting the structural data currently does not correctly update the
bonded data structure.

Modified the Structure.test_read_pdb_1UBQ system test for the new water skipping feature.

As the structure.read_pdb user function will now skip waters, the last atom in the structural object
will now be the last ubiquitin atom and not the last water atom.

Modified the structure.read_pdb user function backend to skip water molecules.

All residues with the name 'HOH' are now skipped when loading PDB files. This is implemented in the
MolContainer.fill_object_from_pdb() method, and a RelaxWarning is printed listing the residue
numbers of all skipped waters.

Fixes for a number of Structure system tests for the sorted structural data changes.

The loading of structural data now sorts the data if the merge flag is True.

The pack_structs() method for sorting the data will now call the new MolContainer._sort() function
is the data is being merged. This is to ensure that the final structural data is correctly ordered.

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.