Author: bugman
Date: Wed Feb 4 09:20:21 2015
New Revision: 27498
URL: http://svn.gna.org/viewcvs/relax?rev=27498&view=rev
Log:
Merged revisions 27426-27438 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27426 | bugman | 2015-01-31 13:13:38 +0100 (Sat, 31 Jan 2015) | 8 lines
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.
........
r27427 | bugman | 2015-01-31 15:07:35 +0100 (Sat, 31 Jan 2015) | 6 lines
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.
........
r27428 | bugman | 2015-01-31 15:15:17 +0100 (Sat, 31 Jan 2015) | 5 lines
Modified the Structure.test_sequence_alignment_central_star_nw70_blosum62
system test.
Some residues are now deleted so that the sequences are not identical.
........
r27429 | bugman | 2015-01-31 15:17:09 +0100 (Sat, 31 Jan 2015) | 7 lines
Created the Structure.test_sequence_alignment_residue_number system test.
This will be used to test the structure.sequence_alignment user function
together with the 'residue
number' MSA algorithm. This is simply a copy of the
Structure.test_sequence_alignment_central_star_nw70_blosum62 system test
with a few small changes.
........
r27430 | bugman | 2015-01-31 17:26:57 +0100 (Sat, 31 Jan 2015) | 3 lines
Corrections and simplifications for the
Structure.test_sequence_alignment_residue_number system test.
........
r27431 | bugman | 2015-01-31 17:33:38 +0100 (Sat, 31 Jan 2015) | 5 lines
Modified the structure.sequence_alignment user function arguments.
The pairwise_algorithm and matrix arguments can no be None, and they
default to None.
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r27432 | bugman | 2015-01-31 17:54:04 +0100 (Sat, 31 Jan 2015) | 6 lines
Updated the Structure.test_align_CaM_BLOSUM62 system test script.
The MSA algorithm and pairwise alignment algorithms are now specified in the
structure.sequence_alignment user function calls.
........
r27433 | bugman | 2015-01-31 17:56:51 +0100 (Sat, 31 Jan 2015) | 7 lines
Creation of the lib.sequence_alignment.msa.msa_general() function.
This consists of code from the structure.sequence_alignment user function
backend function
pipe_control.structure.main.sequence_alignment() for selecting between the
different sequence
alignment methods.
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r27434 | bugman | 2015-01-31 17:59:44 +0100 (Sat, 31 Jan 2015) | 6 lines
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.
........
r27435 | bugman | 2015-02-02 09:11:41 +0100 (Mon, 02 Feb 2015) | 7 lines
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.
........
r27436 | bugman | 2015-02-02 09:20:06 +0100 (Mon, 02 Feb 2015) | 9 lines
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.
........
r27437 | bugman | 2015-02-02 16:44:46 +0100 (Mon, 02 Feb 2015) | 6 lines
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.
........
r27438 | bugman | 2015-02-02 16:46:06 +0100 (Mon, 02 Feb 2015) | 5 lines
Creation of oblate spheroid diffusion relaxation data.
This will be used in the Structure.test_create_diff_tensor_pdb_oblate
system test.
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/diffusion_tensor/spheroid_oblate/
- copied from r27438,
trunk/test_suite/shared_data/diffusion_tensor/spheroid_oblate/
branches/frame_order_cleanup/test_suite/shared_data/diffusion_tensor/spheroid_prolate/
- copied from r27438,
trunk/test_suite/shared_data/diffusion_tensor/spheroid_prolate/
Removed:
branches/frame_order_cleanup/test_suite/shared_data/diffusion_tensor/spheroid/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/sequence_alignment/msa.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/user_functions/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/lib/sequence_alignment/msa.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/sequence_alignment/msa.py?rev=27498&r1=27497&r2=27498&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=27498&r1=27497&r2=27498&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/structure_align.py?rev=27498&r1=27497&r2=27498&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=27498&r1=27497&r2=27498&view=diff
Modified: branches/frame_order_cleanup/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=27498&r1=27497&r2=27498&view=diff
r27498 - in /branches/frame_order_cleanup: ./ lib/sequence_alignment/ pipe_control/structure/ test_suite/shared_data/diffusi...