relax SVN archive

Sequence alignment is now performed in lib.structure.internal.coordinates.assemble_coord_array().

This is a pairwise alignment to the first molecule of the list. The alignments are not yet used for
anything. The assemble_coord_array() function is used by the structure.align user function, as well
as a few other structure user functions.

Implemented the internal structural object one_letter_codes() method.

This will create a string of one letter residue codes for the given molecule. Only proteins are
currently supported. This method uses the new lib.sequence.aa_codes_three_to_one() relax library
function.

Implemented the internal structural object MolContainer.loop_residues() method.

This generator method is used to quickly loop over all residues of the molecule.

Created the lib.sequence.aa_codes_three_to_one() function.

The lib.sequence module now contains the AA_CODES dictionary which is a translation table for the 3
letter amino acid codes to the one letter codes. The new aa_codes_three_to_one() function performs
the conversion.

Copyright notice updates to 2015.

The sequence alignment arguments are now passed all the way to the internal structural object backend.

These are the arguments of the structure.align user function.

Removed the 'algorithm' argument from the Structure.test_align_CaM_BLOSUM62 system test script.

This is for the structure.align user function. The argument has not been implemented to save room
in the GUI, and as 'NW70' is currently the only choice.

Added the sequence alignment arguments to the back end of the structure.align user function.

This is to allow the code in trunk to be functional before the sequence alignment before
superimposition has been implemented.

Added the sequence alignment arguments to the structure.align user function front end.

This includes the 'matrix', 'gap_open_penalty', 'gap_extend_penalty', 'end_gap_open_penalty', and
'end_gap_extend_penalty' arguments. The 'algorithm' argument has not been added to save room, as
there is only one choice of 'NW70'. A paragraph has been added to the user function description to
explain the sequence alignment part of the user function.

Small docstring expansion for lib.sequence_alignment.align_protein.align_pairwise().