relax SVN archive

Fixes for the data_store.seq_align.Alignment.generate_id() method.

These problems were identified by the _data_store.test_seq_align module
Test_seq_align.test_alignment_addition unit test.

Created the Test_seq_align.test_alignment_addition unit test.

This is in the _data_store.test_seq_align unit test module. This tests the setup of the sequence
alignment object via the data_store.seq_align.Sequence_alignment.add() method.

Spelling mistake in the Sequence_alignments class name.

Added the seq_align module to the data_store package __all__ list.

Created the new relax data store object for saving sequence alignments.

This is in the new data_store.seq_align module via the Seqence_alignments object, subclassed from
RelaxListType, for holding all alignments and the Alignment Element object, subclassed from Element,
for holding each individual alignment. The objects are currently unused.

Large speed up of the mol-res-spin selection object.

The Selection.contains_mol(), Selection.contains_res() and Selection.contains_spin() methods of the
lib.selection module have been redesigned for speed. Instead of setting a number of flags and
performing bit operations at the end of the method to return the correct Boolean value, each of the
multiple checks now simply returns a Boolean value, avoiding all subsequent checks. The check list
order has also been rearranged so that the least expensive checks are to the top and the most time
intensive checks are last.

Modified the Structure.test_align_molecules_end_truncation system test.

The calmodulin bound calciums are now deleted prior to the structure.align user function call. This
prevents these being labelled as '*' residues and aligning with real amino acids via the central
star multiple sequence alignment (MSA) algorithm.

Small fix for the lib.structure.internal.coordinates.assemble_coord_array() function.

The termination condition for determining the residues in common between all structures was
incorrect.

Merged revisions 27373-27375 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27373 | bugman | 2015-01-29 19:27:18 +0100 (Thu, 29 Jan 2015) | 6 lines

Fix for the new Internal_selection.count_atoms() internal structural object selection method.

The method was previously returning the total number of molecules, not the total number of atoms in
the selection.
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r27374 | bugman | 2015-01-29 19:28:34 +0100 (Thu, 29 Jan 2015) | 6 lines

Printout fix for the backend of the structure.translate and structure.rotate user functions.

Model numbers of zero were not correctly identified. This also affects the structure.align and
structure.superimpose user functions which uses this backend code.
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r27375 | bugman | 2015-01-29 19:34:32 +0100 (Thu, 29 Jan 2015) | 3 lines

Another fix for the Internal_selection.count_atoms() internal structural object selection method.
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Another fix for the Internal_selection.count_atoms() internal structural object selection method.