relax SVN archive

Bug fix for the structure.read_pdb user function parsing of CONECT records.

CONECT records pointing to ATOM records were not being read by the user function. As ATOM records
should not require CONECT records by their definition, this is only a minor problem affecting
synthetic edge cases.

Reintroduced the CONECT PDB records into the artificial diffusion tensor test suite data.

The uniform vector distributions have overlapping vectors. This causes the internal structural
object atom connection determining algorithm to fail, as this is distance-based rather than using
the PDB amino acid definitions for now.

Changed the synthetic PDB for the artificial diffusion tensor test suite data.

The nitrogen and proton positions are now shifted 10 Angstrom along the distribution vectors. This
is to avoid having all nitrogens positioned at the origin which causes the internal structural
object algorithm for determining which atoms are connected to fail.

Bug fix for the printouts from the relax_data.read user function.

This problem was introduced in the last relax release (at r26588). The problem is that the spin ID
in the loaded relaxation data printout is the same for all data, being the spin ID of the first
spin. This has no effect on how relax runs, it is only incorrect feedback.

Another update for the artificial diffusion tensor test suite data.

The number of increments on the sphere has been increased from 5 to 6, to make the vector
distribution truly uniform. All PDB files and relaxation data has been updated.

Updated the artificial diffusion tensor test suite data.

This is the data in test_suite/shared_data/diffusion_tensor. The residues in the PDB files are now
proper amino acids, so the HETATM records are now ATOM records, and the CONECT records have been
eliminated.

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.