relax SVN archive

Modified the gap penalty arguments for the structure.align user function.

These now must always be supplied, as None is not handled by the backend
lib.sequence_alignment.needleman_wunsch module. The previous defaults of None are now set to 0.0.

More redirects for the relax HTML manual at http://www.nmr-relax.com/manual/index.html.

This is required as the latex2html program used to build the manual has been modified to not
excluded the 'common words' from the page titles (see docs/devel/latex2html/). These redirects are
linked from outside of http://www.nmr-relax.com, as identified by the Google Webmaster Tools.

This is for http://www.nmr-relax.com/manual/The_M61_skew_2_site_fast_exchange_R1_rho_model.html.

Fix for the lib.sequence.aa_codes_three_to_one() function.

Non-standard residues are now converted to the '*' code. The value of 'X' prevents any type of
alignment of a stretch of X residues as X to X in both the BLOSUM62 and PAM250 substitution matrices
are set to -1.

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.