Author: bugman
Date: Thu Feb 5 09:52:35 2015
New Revision: 27537
URL: http://svn.gna.org/viewcvs/relax?rev=27537&view=rev
Log:
Small edits for the relax 3.3.6 messages in the CHANGES document.
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=27537&r1=27536&r2=27537&view=diff
==============================================================================
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Thu Feb 5 09:52:35 2015
@@ -29,7 +29,7 @@
* 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.
* 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.
* Attempt at fixing the
lib.structure.internal.coordinates.common_residues() function. This function
still does not work correctly.
- * 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.
+ * 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.
* Added the
lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function.
This should have been committed earlier. The function is only partly
implemented.
* Initial lib.sequence_alignment.msa.central_star() function. This
was moved from
lib.sequence_alignment.align_protein.align_multiple_from_pairwise().
* Import fix for the _lib._sequence_alignment.test_align_protein
unit test module.
@@ -51,7 +51,7 @@
* Improvement for the lib.sequence_alignment.msa.central_star()
function. The strings and gap matrix returned by the function have been
reordered to match the input sequences.
* 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.
* 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.
- * 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.
+ * Created the new relax data store object for saving sequence
alignments. This is in the new data_store.seq_align module via the
Sequence_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.
* Added the seq_align module to the data_store package __all__ list.
* 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.
* 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.
@@ -92,7 +92,7 @@
* The residue number based sequence alignment is now executed when
assembling atomic coordinates. This is in the
assemble_structural_coordinates() function of the pipe_control.structure.main
module.
* Modified the internal structural object one_letter_codes() method.
This now validates the models to make sure all models match, and the method
requires the selection object so that residue subsets can be handled.
* The assemble_atomic_coordinates() function now calls
one_letter_codes() with the selection object. This is the
lib.structure.internal.coordinates module function.
- * Fix for the residue number based sequence alignment when
assembling structural coordinates. This is in the
assemble_structural_coordinates() function of the pipe_control.structure.main
module. The sequences of the different molecules can be of different lengths.
+ * Fix for the residue number based sequence alignment when
assembling structural coordinates. This is in the
assemble_structural_coordinates() function of the pipe_control.structure.main
module. The sequences of the different molecules can be of different lengths.
* Shifted the residue skipping data structure construction into the
relax library. The code was originally in
pipe_control.structure.main.assemble_structural_coordinates() but has been
shifted into the new lib.sequence_alignment.msa.msa_residue_skipping()
function. This will also for greater code reuse. The
lib.sequence_alignment.msa module is also a better location for such
functionality.
* Renamed the Structure.test_sequence_alignment_molecules system
test. The new name is
Structure.test_sequence_alignment_central_star_nw70_blosum62, to better
reflect what the test is doing.
* Modified the
Structure.test_sequence_alignment_central_star_nw70_blosum62 system test.
Some residues are now deleted so that the sequences are not identical.
@@ -104,7 +104,7 @@
* The structure.sequence_alignment user function now sets some
arguments to None before storage. This is for all arguments not used in the
sequence alignment. For example the residue number based alignment does not
use the gap penalties, pairwise alignment algorithm or the substitution
matrices.
* Fix for the lib.sequence_alignment.msa.msa_residue_skipping()
function. The sequences argument for passing in the one letter codes has
been removed. The per molecule loop should be over the alignment strings
rather than one letter codes, otherwise the loop will be too short.
* Fix for the internal structural object atomic coordinate assembly
function. This is the
pipe_control.structure.main.assemble_structural_coordinates() function. The
case of no sequence alignment being required as only models are being handled
is now functional. The strings and gaps data structures passed into the
lib.sequence_alignment.msa.msa_residue_skipping() function for generating the
residue skipping data structure are now set to the one letter codes and an
empty structure of zeros respectively.
- * Test data directory renaming. The
test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed
to spheroid_prolate. This is in preparation for creating oblate spheroid
diffusion relaxation data.
+ * Test data directory renaming. The
test_suite/shared_data/diffusion_tensor/spheroid directory has been renamed
to spheroid_prolate. This is in preparation for creating oblate spheroid
diffusion relaxation data.
* Creation of oblate spheroid diffusion relaxation data. This will
be used in the Structure.test_create_diff_tensor_pdb_oblate system test.
* Fix for the oblate spheroid diffusion relaxation data. The
diffusion parameters are constrained as Dx <= Dy <= Dz.
* More fixes for the Structure.test_create_diff_tensor_pdb_oblate
system test. The initial Diso value is now set to the real final Diso, and
the PDB file contents have been updated for the fixed oblate spheroidal
diffusion relaxation data.
@@ -181,11 +181,11 @@
* 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.
* Another fix for the Internal_selection.count_atoms() internal
structural object selection method.
* 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.
- * The Structure.test_create_diff_tensor_pdb_oblate now uses oblate
diffusion relaxation data. This fixes bug #23232
(https://gna.org/bugs/?23232), the failure of this system test on Mac OS X.
The problem was that the system test was previously using relaxation data for
prolate spheroidal diffusion and fitting an oblate tensor to that data. This
caused the solution to be slightly different on different CPUs, operating
systems, Python versions, etc. and hence the PDB file representation of the
diffusion would be slightly different.
+ * The Structure.test_create_diff_tensor_pdb_oblate system test now
uses oblate diffusion relaxation data. This fixes bug #23232
(https://gna.org/bugs/?23232), the failure of this system test on Mac OS X.
The problem was that the system test was previously using relaxation data for
prolate spheroidal diffusion and fitting an oblate tensor to that data. This
caused the solution to be slightly different on different CPUs, operating
systems, Python versions, etc. and hence the PDB file representation of the
diffusion would be slightly different.
* Big bug fix for the GUI tests on MS Windows systems. On MS
Windows systems, the GUI tests were unable to complete without crashing.
This is because each GUI element requires one 'User object', and MS Windows
has a maximum limit of 10,000 of these objects. The GUI tests were taking
more than 10,000 and then Windows would say - relax, you die now. The
solution is that after each GUI test, all user function windows are
destroyed. The user function page is a wx.Panel object, so this requires a
Destroy() call. But the window is a Uf_page instance which inherits from
Wiz_page which inherits from wx.Dialog. Calling Destroy() on MS Windows and
Linux works fine, but is fatal on Mac OS X systems. So the solution is to
call Close() instead.
* Fix for the default grid_inc argument for the relaxation
curve-fitting auto-analysis. This needs to be an integer.
* Fix for bug #23244 (https://gna.org/bugs/?23244). The relaxation
curve-fitting auto-analysis now outputs text files and Grace graphs for the
I0 parameter and the Iinf parameter if it exists.
- * Fixes for the package checking unit tests on MS Windows for the
target_functions package. The compiled relaxation curve-fitting file is
called target_functions\relax_fit.pyd on MS Windows. The package checking was
only taking into account *.so compiled files and not *.pyd file.
+ * Fixes for the package checking unit tests on MS Windows for the
target_functions package. The compiled relaxation curve-fitting file is
called target_functions\relax_fit.pyd on MS Windows. The package checking
was only taking into account *.so compiled files and not *.pyd file.
r27537 - /trunk/docs/CHANGES