relax SVN archive

Attempt at fixing the lib.structure.internal.coordinates.common_residues() function.

This function still does not work correctly.

Expanded the docstring of the Test_align_protein.test_align_multiple_from_pairwise unit test.

This is from the _lib._sequence_alignment.test_align_protein unit test module.

Simplified the Test_coordinates.test_common_residues unit test by removing many residues.

This is from the _lib._structure._internal.test_coordinates unit test module.

Created the Test_align_protein.test_align_multiple_from_pairwise unit test.

This is in the _lib._sequence_alignment.test_align_protein unit test module. This test checks the
operation of the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function, which
does not yet exist.

Modified the lib.structure.internal.coordinates.common_residues() function.

It now accepts the seq argument which will caused the gapped sequence strings to be returned. This
is to allow for checking in the unit tests.

Created the Test_coordinates.test_common_residues unit test.

This is from the _lib._structure._internal.test_coordinates unit test module. The test shows that
the lib.structure.internal.coordinates.common_residues() function is working correctly. However the
printout, which is not caught by the test, is incorrect.

Created empty unit test infrastructure for testing the lib.structure.internal.coordinates module.

Created the Structure.test_align_molecules_end_truncation system test.

This is to demonstrate a failure of the common residue detection algorithm using multiple pairwise
alignments in the backend of the structure.align and other multiple structure based user functions.

Fix for the Structure.test_displacement system test - the molecule IDs needed updating.

Large simplification of the atomic coordinate assembly code in the internal structural object.

This is in the lib.structure.internal.coordinates.assemble_coord_array() function. The logic of the
function has recently changed due to the introduction of the pairwise sequence alignments. This
caused a lot of code to now be redundant, and also incorrect in certain cases. This simplification
fixes the problem caught by the Structure.test_align_molecules2 system test.