relax SVN archive

Created the internal structural object _pdb_chain_id_to_mol_index() method.

This will be used to convert PDB chain IDs, which are used to indicate different molecules in the
PDB, into molecule indices for the internal structural object.

Trailing whitespace removal.

The Structure.test_read_write_pdb_1UBQ system test now checks for HELIX and SHEET records.

This is not implemented yet, but the idea is that the structure.read_pdb and structure.write_pdb
should preserve the helix and sheet information present in the original PDB and that the internal
structural object should store this information.

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.