relax SVN archive

Reverted r27364 as this was recursive rubbish.

The command used was:
svn merge -r27364:r27363 .

.....
r27364 | bugman | 2015-01-29 17:38:25 +0100 (Thu, 29 Jan 2015) | 18 lines
Changed paths:
M /trunk/lib/sequence.py

Reverted r27291 as this was rubbish.

The command used was:
svn merge -r27291:r27290 .

.....
r27291 | bugman | 2015-01-23 15:38:21 +0100 (Fri, 23 Jan 2015) | 7 lines
Changed paths:
M /trunk/lib/sequence.py

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.
.....
.....

Bug fix for the structure.align user function.

The addition of the molecule name to the displacement ID is now correctly performed.

Added final printouts to the structure.rotate and structure.translate user function backends.

This is to give feedback to the user as to how many atoms were translated or rotated, to aid in
solving problems with the structure user functions. These backend functions are also used by the
structure.align and structure.superimpose user functions.

Created the Internal_selection.count_atoms() internal structural object selection method.

This counts the number of atoms in the current selection.

Reverted r27291 as this was rubbish.

The command used was:
svn merge -r27291:r27290 .

.....
r27291 | bugman | 2015-01-23 15:38:21 +0100 (Fri, 23 Jan 2015) | 7 lines
Changed paths:
M /trunk/lib/sequence.py

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.
.....

Fixes for the Structure.test_align_molecules_end_truncation system test.

This system test had only been partly converted from the old Structure.test_align_molecules2 system
test it had been copied from.

Better printout spacing in lib.sequence_alignment.msa.central_star().

Alphabetical ordering of all Structure system tests.

Deleted the Test_coordinates.test_common_residues unit test.

This is from the _lib._structure._internal.test_coordinates unit test module. The
lib.structure.internal.coordinates.common_residues() function no longer exists.

The assemble_coord_array() function is now using the central star multiple sequence alignment.

This is the function from the lib.structure.internal.coordinates module used to assemble common
atomic coordinate information, used by the structure.align, structure.atomic_fluctuations,
structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd,
structure.superimpose and structure.web_of_motion user functions.

The non-functional lib.structure.internal.coordinates.common_residues() function has been removed as
the lib.sequence_alignment.msa.central_star() function performs this functionality correctly.