relax SVN archive

Modification of the Needleman-Wunsch sequence alignment algorithm implementation.

This is in the lib.sequence_alignment.needleman_wunsch functions. Scoring matrices are now
supported, as well as a user supplied non-integer gap penalty. The algorithm for walking through
the traceback matrix has been fixed for a bug under certain conditions.

Fix for the lib.sequence_alignment.substitution_matrices.BLOSUM62_SEQ string.

Corrected the spelling of the BLOSUM62 matrix in lib.sequence_alignment.substitution_matrices.

Created the lib.sequence_alignment.substitution_matrices module.

This is for storing substitution matrices for use in sequence alignment. The module currently only
includes the BLOSSUM62 matrix.

Created a unit test for checking the Needleman-Wunsch sequence alignment algorithm.

This uses the DNA data from the example in the Wikipedia article at
https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm. The test shows that the
implementation of the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function is
correct.

Implementation of the Needleman-Wunsch sequence alignment algorithm.

This is located in the lib.sequence_alignment.needleman_wunsch module. This is implemented as
described in the Wikipedia article https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm.

Added the unit testing infrastructure for the new lib.sequence_alignment package.

Added the sequence_alignment package to the lib package __all__ list.

Created an empty lib.sequence_alignment relax library package.

This may be used in the future for implementing more advanced structural alignments (the current
method is simply to skip missing atoms, sequence numbering changes are not handled).

Better error handling in the structure.align user function.

If no common atoms can be found between the structures, a RelaxError is now raised for better user
feedback.