Author: bugman
Date: Thu Jan 29 18:28:21 2015
New Revision: 27369
URL: http://svn.gna.org/viewcvs/relax?rev=27369&view=rev
Log:
Merged revisions 27325,27331,27336-27368 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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@xxxxxxxxxxx/svn/relax/tags/3.3.5 .
........
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 .
.....
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.
.....
.....
........
Added:
branches/frame_order_cleanup/lib/sequence_alignment/msa.py
- copied unchanged from r27368, trunk/lib/sequence_alignment/msa.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_msa.py
- copied unchanged from r27368,
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_msa.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
- copied unchanged from r27368,
trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/docs/CHANGES
branches/frame_order_cleanup/lib/sequence_alignment/__init__.py
branches/frame_order_cleanup/lib/sequence_alignment/align_protein.py
branches/frame_order_cleanup/lib/sequence_alignment/needleman_wunsch.py
branches/frame_order_cleanup/lib/structure/internal/coordinates.py
branches/frame_order_cleanup/lib/structure/internal/selection.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/test_suite/gui_tests/general.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/__init__.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_structure/_internal/__init__.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/CHANGES?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/lib/sequence_alignment/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence_alignment/__init__.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/lib/sequence_alignment/align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence_alignment/align_protein.py?rev=27369&r1=27368&r2=27369&view=diff
Modified:
branches/frame_order_cleanup/lib/sequence_alignment/needleman_wunsch.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence_alignment/needleman_wunsch.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/lib/structure/internal/coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/coordinates.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/lib/structure/internal/selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/selection.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/test_suite/gui_tests/general.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/gui_tests/general.py?rev=27369&r1=27368&r2=27369&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=27369&r1=27368&r2=27369&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/__init__.py?rev=27369&r1=27368&r2=27369&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py?rev=27369&r1=27368&r2=27369&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py?rev=27369&r1=27368&r2=27369&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_structure/_internal/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_structure/_internal/__init__.py?rev=27369&r1=27368&r2=27369&view=diff
r27369 - in /branches/frame_order_cleanup: ./ docs/ lib/sequence_alignment/ lib/structure/internal/ pipe_control/structure/ ...