relax SVN archive

Added the index_flag argument to all structural API atom_loop() methods.

Created 13 unit tests of the Internal._trim_helix() internal structural object method.

SHEET PDB records are now read, stored, and written out by the internal structural object.

This affects the structure.read_pdb and structure.write_pdb user functions. The sheet is stored as
a metadata type object - its elements do not correspond to the atoms in the structural object.

HELIX PDB records are now read, stored, and written out by the internal structural object.

This affects the structure.read_pdb and structure.write_pdb user functions. The helix is stored as
a metadata type object - its elements do not correspond to the atoms in the structural object.

Fix for the internal structural object _pdb_chain_id_to_mol_index() method.

This was accidentally set to be a method of the MolContainer class and not the internal object.

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.