Merged revisions 27325,27331,27336-27368 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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r27325 | bugman | 2015-01-27 11:35:39 +0100 (Tue, 27 Jan 2015) | 6 lines
Disabled the General.test_bug_23187_residue_delete_gui GUI test.
This is essential as a wxPython bug in Mac OS X systems causes this test to trigger a 'Bus Error'
every time the GUI tests are run, killing relax.
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r27331 | bugman | 2015-01-27 15:58:24 +0100 (Tue, 27 Jan 2015) | 6 lines
Backported the relax 3.3.5 CHANGES file changes to trunk.
The command used was:
svn merge -r27329:27330 svn+ssh://bugman@.../svn/relax/tags/3.3.5 .
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r27336 | bugman | 2015-01-28 09:47:07 +0100 (Wed, 28 Jan 2015) | 3 lines
Spelling fixes for the CHANGES document.
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r27337 | bugman | 2015-01-28 11:48:50 +0100 (Wed, 28 Jan 2015) | 5 lines
Created the Structure.test_align_molecules2 system test.
This is to demonstrate a failure condition in the structure.align user function.
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r27338 | bugman | 2015-01-28 12:29:05 +0100 (Wed, 28 Jan 2015) | 8 lines
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.
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r27339 | bugman | 2015-01-28 12:29:54 +0100 (Wed, 28 Jan 2015) | 3 lines
Fix for the Structure.test_displacement system test - the molecule IDs needed updating.
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r27340 | bugman | 2015-01-28 13:07:29 +0100 (Wed, 28 Jan 2015) | 6 lines
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.
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r27341 | bugman | 2015-01-28 14:41:51 +0100 (Wed, 28 Jan 2015) | 3 lines
Created empty unit test infrastructure for testing the lib.structure.internal.coordinates module.
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r27342 | bugman | 2015-01-28 15:02:11 +0100 (Wed, 28 Jan 2015) | 7 lines
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.
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r27343 | bugman | 2015-01-28 15:15:13 +0100 (Wed, 28 Jan 2015) | 6 lines
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.
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r27344 | bugman | 2015-01-28 18:24:15 +0100 (Wed, 28 Jan 2015) | 7 lines
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.
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r27345 | bugman | 2015-01-29 13:23:58 +0100 (Thu, 29 Jan 2015) | 5 lines
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.
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r27346 | bugman | 2015-01-29 13:24:59 +0100 (Thu, 29 Jan 2015) | 5 lines
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.
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r27347 | bugman | 2015-01-29 13:26:00 +0100 (Thu, 29 Jan 2015) | 5 lines
Attempt at fixing the lib.structure.internal.coordinates.common_residues() function.
This function still does not work correctly.
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r27348 | bugman | 2015-01-29 13:33:32 +0100 (Thu, 29 Jan 2015) | 9 lines
Renamed the Test_align_protein.test_align_multiple_from_pairwise unit test.
This is now the Test_msa.test_central_star unit test of the _lib._sequence_alignment.test_msa unit
test module (it was originally in the _lib._sequence_alignment.test_align_protein unit test module).
This is in preparation for converting the
lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function into the
lib.sequence_alignment.msa.central_star() function.
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r27349 | bugman | 2015-01-29 13:34:38 +0100 (Thu, 29 Jan 2015) | 5 lines
Added the lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function.
This should have been committed earlier. The function is only partly implemented.
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r27350 | bugman | 2015-01-29 13:37:46 +0100 (Thu, 29 Jan 2015) | 5 lines
Initial lib.sequence_alignment.msa.central_star() function.
This was moved from lib.sequence_alignment.align_protein.align_multiple_from_pairwise().
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r27351 | bugman | 2015-01-29 13:38:31 +0100 (Thu, 29 Jan 2015) | 3 lines
Import fix for the _lib._sequence_alignment.test_align_protein unit test module.
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r27352 | bugman | 2015-01-29 14:16:23 +0100 (Thu, 29 Jan 2015) | 5 lines
Added the verbosity argument to lib.sequence_alignment.align_protein.align_pairwise().
If set to zero, all printouts are suppressed.
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r27353 | bugman | 2015-01-29 15:36:05 +0100 (Thu, 29 Jan 2015) | 6 lines
The Needleman-Wunsch sequence alignment algorithm now calculates and returns an alignment score.
This is in the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function. The score
is calculated as the sum of the Needleman-Wunsch matrix elements along the traceback path.
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r27354 | bugman | 2015-01-29 15:37:23 +0100 (Thu, 29 Jan 2015) | 6 lines
The protein pairwise sequence alignment function now returns the alignment score.
This is in the lib.sequence_alignment.align_protein.align_pairwise() function. The score from the
Needleman-Wunsch sequence alignment algorithm is simply passed along.
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r27355 | bugman | 2015-01-29 15:39:38 +0100 (Thu, 29 Jan 2015) | 6 lines
Fix for the Test_msa.test_central_star unit test.
This is from the _lib._sequence_alignment.test_msa unit test module. Some of the real gap matrix
indices were incorrect.
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r27356 | bugman | 2015-01-29 15:48:34 +0100 (Thu, 29 Jan 2015) | 10 lines
Complete implementation of the central star multiple sequence alignment algorithm.
This includes all the four major steps - pairwise alignment between all sequence pairs, finding the
central sequence, iteratively aligning the sequences to the gapped central sequence, and introducing
gaps in previous alignments during the iterative alignment.
The correctness of the implementation is verified by the Test_msa.test_central_star unit test of the
_lib._sequence_alignment.test_msa module.
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r27357 | bugman | 2015-01-29 15:52:16 +0100 (Thu, 29 Jan 2015) | 7 lines
Fixes for the unit tests of the _lib._sequence_alignment.test_align_protein module.
The Test_align_protein.test_align_pairwise_PAM250 unit test was accidentally duplicated due to a
copy and paste error. And the lib.sequence_alignment.align_protein.align_pairwise() function now
also returns the alignment score.
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r27358 | bugman | 2015-01-29 15:53:41 +0100 (Thu, 29 Jan 2015) | 6 lines
Fixes for the unit tests of the _lib._sequence_alignment.test_needleman_wunsch module.
The lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function now returns the
alignment score.
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r27359 | bugman | 2015-01-29 16:19:17 +0100 (Thu, 29 Jan 2015) | 11 lines
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.
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r27360 | bugman | 2015-01-29 16:20:54 +0100 (Thu, 29 Jan 2015) | 6 lines
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.
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r27361 | bugman | 2015-01-29 16:25:29 +0100 (Thu, 29 Jan 2015) | 3 lines
Alphabetical ordering of all Structure system tests.
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r27362 | bugman | 2015-01-29 16:37:32 +0100 (Thu, 29 Jan 2015) | 3 lines
Better printout spacing in lib.sequence_alignment.msa.central_star().
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r27363 | bugman | 2015-01-29 17:17:34 +0100 (Thu, 29 Jan 2015) | 6 lines
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.
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r27364 | bugman | 2015-01-29 17:38:25 +0100 (Thu, 29 Jan 2015) | 18 lines
Reverted r27291 as this was rubbish.
The command used was:
svn merge -r27291:r27290 .
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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.
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r27365 | bugman | 2015-01-29 17:50:31 +0100 (Thu, 29 Jan 2015) | 5 lines
Created the Internal_selection.count_atoms() internal structural object selection method.
This counts the number of atoms in the current selection.
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r27366 | bugman | 2015-01-29 17:59:21 +0100 (Thu, 29 Jan 2015) | 7 lines
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.
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r27367 | bugman | 2015-01-29 18:16:04 +0100 (Thu, 29 Jan 2015) | 5 lines
Bug fix for the structure.align user function.
The addition of the molecule name to the displacement ID is now correctly performed.
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r27368 | bugman | 2015-01-29 18:22:32 +0100 (Thu, 29 Jan 2015) | 29 lines
Reverted r27364 as this was recursive rubbish.
The command used was:
svn merge -r27364:r27363 .
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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 .
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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.
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