relax SVN archive

Created the Structure.test_read_write_pdb_1UBQ system test.

This is for checking the use of the structure.delete user function with the atom ID argument.

Sections of molecules can now be deleted using the structure.delete user function.

The atom ID argument has been added and this is now propagated into the internal structural object.
This ID string can be used to delete subsets of the 3D structural data in the relax data store.

Proper fix for the pack_structs() structural API method.

This was incorrectly done in r18858, but now the index of the new molecule is handled correctly.

Reverted r18858 as this change was incorrect.

The command used was:
svn merge -r18858:r18857 .

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r18858 | bugman | 2013-03-18 15:27:56 +0100 (Mon, 18 Mar 2013) | 5 lines
Changed paths:
M /trunk/generic_fns/structure/api_base.py

Bug fix for the structural data consistency test in the pack_structs() structural API method.

The index was not correct causing failures in certain rare cases.
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Implemented the average structure creation component of the frame_order.pdb_model user function.

This is the implementation of the _pdb_ave_pos() frame order specific method. The loaded structure
is simply copied, rotated, translated, and then written out as a PDB file.

Split up the frame_order.pdb_model user function backend into three components.

The main _pdb_model() method now consists of calls to three new methods _pdb_ave_pos(),
_pdb_geometric_rep() and _pdb_distribution(). The _pdb_geometric_rep() method is simply the
contents of the old _pdb_model() method and the two other methods are currently stubs.

More changes to the frame_order.pdb_model user function.

The idea is that a 3D structure file of the domains moved to the average position will be created
using the new 'ave_pos_file' argument. The 'file' argument has been renamed to 'rep_file' as this
will simply contain the geometric object representation.

The frame order auto-analysis 'results_dir' argument is now used by the auto-analysis.

The frame order PDB representation and visualisation script are now created after optimisation.

This is for the frame order auto-analysis. The optimise() method has therefore been renamed to
nested_models() as it now does more than just optimisation.

Merged revisions 18847-18859 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18847 | bugman | 2013-03-18 13:19:29 +0100 (Mon, 18 Mar 2013) | 11 lines

Added a comment to the output from value.display and value.write to describe the parameter.

This idea is discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428.

The idea is to take the parameter description from the specific analysis API and add it to the top
of the file or output. This is to help understand what the Rex value are. For example for the Rex
parameter the first line would be:

# Parameter description: Chemical exchange relaxation (sigma_ex = Rex / omega**2).
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r18848 | bugman | 2013-03-18 13:34:02 +0100 (Mon, 18 Mar 2013) | 8 lines

Created the Structure.test_read_merge system test to test a new concept - merging of structures.

The idea is to add the merge argument to the structure.read_pdb user function to allow two different
structures in two PDB files to be merged. This is useful if structures of individual domains have
have been solved separately and are located in two PDB files. Then with the merge flag, you will
not need to use and external program or hand edit PDB files to join them.
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r18849 | bugman | 2013-03-18 13:41:23 +0100 (Mon, 18 Mar 2013) | 5 lines

Added the merge flag to the structure.read_pdb user function.

This currently does nothing.
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r18850 | bugman | 2013-03-18 13:42:16 +0100 (Mon, 18 Mar 2013) | 3 lines

Docstring fix for the structure.read_pdb user function backend.
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r18851 | bugman | 2013-03-18 13:51:56 +0100 (Mon, 18 Mar 2013) | 5 lines

The merge flag for the structure.read_pdb user function is now propaged to the pack_structs() method.

This structure API method calls the ModelList.merge_item() method which is yet to be implemented.
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r18852 | bugman | 2013-03-18 13:56:17 +0100 (Mon, 18 Mar 2013) | 6 lines

The MolList.add_item() structural API method now returns the added molecule container.

This is used by the pack_structs() method to alias the molecule, and will be required when structure
merging is implemented.
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r18853 | bugman | 2013-03-18 14:10:36 +0100 (Mon, 18 Mar 2013) | 3 lines

Replaced many instances of the tab character '\t' with 4 spaces.
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r18854 | bugman | 2013-03-18 14:25:05 +0100 (Mon, 18 Mar 2013) | 3 lines

Fix for a copy and paste error in the Structure.test_read_merge system test.
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r18855 | bugman | 2013-03-18 14:48:13 +0100 (Mon, 18 Mar 2013) | 5 lines

Fixes for all the Ap4Aase truncated PDB files.

The atom numbers are now sequential, as defined by the PDB standard.
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r18856 | bugman | 2013-03-18 14:48:59 +0100 (Mon, 18 Mar 2013) | 5 lines

Implemented the merging of structural objects.

This allows the merge flag of the structure.read_pdb user function to work.
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r18857 | bugman | 2013-03-18 15:18:36 +0100 (Mon, 18 Mar 2013) | 3 lines

Fixes for the test suite for the changes to the Ap4Aase PDB file atom numbering at r18855.
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r18858 | bugman | 2013-03-18 15:27:56 +0100 (Mon, 18 Mar 2013) | 5 lines

Bug fix for the structural data consistency test in the pack_structs() structural API method.

The index was not correct causing failures in certain rare cases.
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r18859 | bugman | 2013-03-18 15:31:04 +0100 (Mon, 18 Mar 2013) | 5 lines

The printouts from the structure.read_pdb user function are now different with the merge flag set.

The text now says that the molecules are being merged rather than added.
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