relax SVN archive

Modified all of the unit tests of the internal structural object _trim_helix() method.

The structure of the helix metadata in the internal structural object was not correctly mimicked.

Implemented the internal structural object _trim_helix() method.

This is used when the structure.delete user function is called to trim and remove the helix
metadata. For this to work, the additional method _residue_data() was written to create a
dictionary with residue numbers as keys and the residue names as numbers. This dictionary is used
by _trim_helix() to change the residue names in the helix metadata.

Fixes for some of the new unit tests of the internal structural object _trim_helix() method.

Fix for the unit test of the generic_fns.structure.pdb_write.helix() function.

The init_seq_id argument is now called init_seq_num to match the PDB notation.

Fixes for some unit tests of the internal structural object for the changes to the atom_loop().

Single elements are now returned as single elements rather than a tuple of length 1.

Docstring editing of the ScientificPython structural object atom_loop() method.

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.