relax SVN archive

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.

Merged revisions 27698-27701 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27698 | bugman | 2015-02-20 14:56:11 +0100 (Fri, 20 Feb 2015) | 5 lines

Added one more check to the Structure.test_bug_23295_ss_metadata_merge system test.

The test would pass if no HELIX or SHEET records were to be written to the PDB file.
........
r27699 | bugman | 2015-02-20 15:41:11 +0100 (Fri, 20 Feb 2015) | 3 lines

Fix for the Structure.test_bug_23295_ss_metadata_merge system test and additional printouts.
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r27700 | bugman | 2015-02-20 15:49:23 +0100 (Fri, 20 Feb 2015) | 9 lines

Bug fix for the SHEET PDB records created by the structure.write_pdb user function.

The current and previous atom parts of the record were not being correctly formatted. This was
simply using the %4s formatting string. However the PDB atom format is rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to the
lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for
consistently formatting the atom name field.
........
r27701 | bugman | 2015-02-20 15:50:52 +0100 (Fri, 20 Feb 2015) | 6 lines

Fix for the Structure.test_pdb_combined_secondary_structure system test.

The SHEET PDB record check was incorrect and was checking for the improperly formatted atom name
field, which has now been fixed in relax.
........

Merged revisions 27698-27701 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27698 | bugman | 2015-02-20 14:56:11 +0100 (Fri, 20 Feb 2015) | 5 lines

Added one more check to the Structure.test_bug_23295_ss_metadata_merge system test.

The test would pass if no HELIX or SHEET records were to be written to the PDB file.
........
r27699 | bugman | 2015-02-20 15:41:11 +0100 (Fri, 20 Feb 2015) | 3 lines

Fix for the Structure.test_bug_23295_ss_metadata_merge system test and additional printouts.
........
r27700 | bugman | 2015-02-20 15:49:23 +0100 (Fri, 20 Feb 2015) | 9 lines

Bug fix for the SHEET PDB records created by the structure.write_pdb user function.

The current and previous atom parts of the record were not being correctly formatted. This was
simply using the %4s formatting string. However the PDB atom format is rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to the
lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for
consistently formatting the atom name field.
........
r27701 | bugman | 2015-02-20 15:50:52 +0100 (Fri, 20 Feb 2015) | 6 lines

Fix for the Structure.test_pdb_combined_secondary_structure system test.

The SHEET PDB record check was incorrect and was checking for the improperly formatted atom name
field, which has now been fixed in relax.
........

Fix for the Structure.test_pdb_combined_secondary_structure system test.

The SHEET PDB record check was incorrect and was checking for the improperly formatted atom name
field, which has now been fixed in relax.

Bug fix for the SHEET PDB records created by the structure.write_pdb user function.

The current and previous atom parts of the record were not being correctly formatted. This was
simply using the %4s formatting string. However the PDB atom format is rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to the
lib.structure.pdb_write module. This is now used in the atom() and sheet() functions for
consistently formatting the atom name field.