Author: bugman
Date: Thu Oct 2 13:11:33 2014
New Revision: 26132
URL: http://svn.gna.org/viewcvs/relax?rev=26132&view=rev
Log:
Merged revisions 26096-26127 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26096 | bugman | 2014-09-30 15:32:36 +0200 (Tue, 30 Sep 2014) | 6 lines
Created the Structure.test_mean system test.
This is to test the functionality of a planned new feature, the
structure.mean user function. This
is an analysis aid that will calculate the mean structure from all loaded
models.
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r26097 | bugman | 2014-09-30 15:50:08 +0200 (Tue, 30 Sep 2014) | 5 lines
Implemented the structure.mean user function frontend.
The backend is currently just a stub function.
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r26098 | bugman | 2014-09-30 16:56:28 +0200 (Tue, 30 Sep 2014) | 5 lines
Fixes and simplifications for the pipe_control.pipes.check_pipe() checking
object.
One of the RelaxError classes were not initialised and the docstring was
incorrect.
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r26099 | bugman | 2014-09-30 17:26:24 +0200 (Tue, 30 Sep 2014) | 6 lines
Created the pipe_control.structure.main.check_structure() checking object.
This will be used for providing much more detailed feedback for when
structural information is
missing.
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r26100 | bugman | 2014-09-30 17:31:30 +0200 (Tue, 30 Sep 2014) | 5 lines
Converted all of the pipe_control.strucuture.main functions to use the
check_structure() object.
This standardises and improves all of the checks.
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r26101 | bugman | 2014-09-30 17:32:11 +0200 (Tue, 30 Sep 2014) | 3 lines
Import fix for r26099.
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r26102 | bugman | 2014-09-30 18:07:02 +0200 (Tue, 30 Sep 2014) | 3 lines
Some fixes and additional checks for the Structure.test_mean system test.
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r26103 | bugman | 2014-09-30 18:08:57 +0200 (Tue, 30 Sep 2014) | 7 lines
Implemented the backend of the structure.mean user function.
This primarily occurs within the internal structural object in the new
mean() method. The
pipe_control.structure.main.mean() function simply checks if the current
data pipe is correctly set
up and then calls the structural object mean() method.
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r26104 | bugman | 2014-10-01 19:44:08 +0200 (Wed, 01 Oct 2014) | 5 lines
Created the Structure.test_align system test.
This will be used to test the yet to be implemented structure.align user
function. This user
function will be similar to the structure.superimpose user function but
will be designed so that
structures with different primary and atomic sequences can be superimposed.
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r26105 | bugman | 2014-10-01 19:44:10 +0200 (Wed, 01 Oct 2014) | 4 lines
Created the frontend of the structure.align user function.
This is almost the same as that of the structure.superimpose user function
except that the pipes
argument has been added and the titles and description changed to indicate
the differences.
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r26106 | bugman | 2014-10-01 19:44:12 +0200 (Wed, 01 Oct 2014) | 4 lines
Registered the new user function argument type 'int_list_of_lists' in the
prompt UI.
This is to allow for lists of lists of integers, as used for the model
argument in the new
structure.align user function.
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r26107 | bugman | 2014-10-01 19:44:13 +0200 (Wed, 01 Oct 2014) | 4 lines
Modified the lib.arg_check.is_int_list() function to accept the
list_of_lists Boolean argument.
This updates the function to have the same functionality as is_str_list(),
allows for lists of lists
of int to be checked.
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r26108 | bugman | 2014-10-01 19:44:15 +0200 (Wed, 01 Oct 2014) | 1 line
Whitespace fixes for the lib.arg_check module.
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r26109 | bugman | 2014-10-01 19:44:16 +0200 (Wed, 01 Oct 2014) | 1 line
Fix for the pipes argument for the structure.align user function in the GUI.
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r26110 | bugman | 2014-10-01 19:44:20 +0200 (Wed, 01 Oct 2014) | 4 lines
Extended the Structure.test_align system test to throughly check the
structural data.
This includes changing the structure.align user function call to use 'fit
to first' and carefully
checking the new atomic coordinates.
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r26111 | bugman | 2014-10-01 19:44:22 +0200 (Wed, 01 Oct 2014) | 4 lines
Modified the Structure.test_align system test so that translations and
rotations match the algorithm.
This allows the output of the structure.align user function to be checked
to see if the rotation
matrix and translation vector found match that used to shift the original
structures.
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r26112 | bugman | 2014-10-01 19:44:24 +0200 (Wed, 01 Oct 2014) | 4 lines
Implemented the structure.align user function backend.
This is similar to the structure.superimpose user function, however the
coordinate data structure
only contains atoms which are in common to all structures.
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r26113 | bugman | 2014-10-01 19:44:25 +0200 (Wed, 01 Oct 2014) | 4 lines
The pipe_control.structure.main functions translate() and rotate() now
accept the pipe_name argument.
This is used to translate and rotate structures in different data pipes, as
required by the
structure.align user function.
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r26114 | bugman | 2014-10-01 19:44:27 +0200 (Wed, 01 Oct 2014) | 4 lines
The pipe_control.structure.main.check_structure() checking object now
accepts the pipe_name argument.
This allows structural data to be checked for in different data pipes
without having to switch to
them.
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r26115 | bugman | 2014-10-01 19:44:29 +0200 (Wed, 01 Oct 2014) | 1 line
Small whitespace fix.
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r26116 | bugman | 2014-10-01 19:44:30 +0200 (Wed, 01 Oct 2014) | 4 lines
Modified the Structure.test_align system test to call the
structure.write_pdb user function.
This sets the file name to sys.stdout so that the original structure and
the final aligned
structures are output to STDOUT for debugging purposes.
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r26117 | bugman | 2014-10-01 19:44:32 +0200 (Wed, 01 Oct 2014) | 4 lines
Bug fix for the structure.delete user function.
When individual atoms are deleted, the bonded atom data structure is no
correctly updated to remove
the now non-existent atom.
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r26118 | bugman | 2014-10-01 19:44:34 +0200 (Wed, 01 Oct 2014) | 3 lines
Created the Structure.test_delete_atom system test.
This is used to test the deletion of a single atom using the
structure.delete user function.
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r26119 | bugman | 2014-10-01 19:44:35 +0200 (Wed, 01 Oct 2014) | 4 lines
Expanded the Structure.test_delete_atom system test.
This is to show that the structure.write_pdb user function fails after a
call to the
structure.delete user function to delete individual atoms.
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r26120 | bugman | 2014-10-01 19:44:37 +0200 (Wed, 01 Oct 2014) | 4 lines
Another bug fix for the structure.delete user function when deleting
individual atoms.
The bonded atom data structure consisting of indices requires all indices
after the deleted atom to
be decremented by 1.
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r26121 | bugman | 2014-10-01 19:44:39 +0200 (Wed, 01 Oct 2014) | 4 lines
Bug fix for the CONECT records created by the structure.write_pdb user
function.
The atom numbers inside the structural object were being used for the
CONECT records rather than the
atom numbers used within the PDB file.
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r26122 | bugman | 2014-10-01 19:44:41 +0200 (Wed, 01 Oct 2014) | 4 lines
Fix for the new structure.align user function.
The translation and rotation of the structures at the end to the aligned
positions was being
incorrectly performed.
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r26123 | bugman | 2014-10-01 19:44:43 +0200 (Wed, 01 Oct 2014) | 4 lines
Loosened some checks in the Structure.test_align system test to allow it to
pass.
Some self.assertEqual() checks for the atomic coordinates have been
replaced by
self.assertAlmostEqual() to allow for small machine precision differences.
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r26124 | bugman | 2014-10-01 19:44:45 +0200 (Wed, 01 Oct 2014) | 3 lines
Modified the lib.arg_check.is_str_or_inst() to handle cStringIO objects.
This allows sys.stdout to be used as a file object in the relax test suite.
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r26125 | bugman | 2014-10-01 19:50:20 +0200 (Wed, 01 Oct 2014) | 3 lines
Removed a debugging printout fatal for Python3.
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r26126 | bugman | 2014-10-01 19:55:36 +0200 (Wed, 01 Oct 2014) | 3 lines
Removal of another temporary debugging printout.
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r26127 | bugman | 2014-10-01 19:56:54 +0200 (Wed, 01 Oct 2014) | 6 lines
Modified the lib.arg_check.is_str_or_inst() function to work with Python 3.
Instead of checking for cStringIO.OutputType, which does not exist in
Python 3, the argument is
simply checked to see if it has a write() method.
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Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/arg_check.py
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/pipe_control/pipes.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/prompt/uf_objects.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/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/arg_check.py?rev=26132&r1=26131&r2=26132&view=diff
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=26132&r1=26131&r2=26132&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pipes.py?rev=26132&r1=26131&r2=26132&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=26132&r1=26131&r2=26132&view=diff
Modified: branches/frame_order_cleanup/prompt/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/prompt/uf_objects.py?rev=26132&r1=26131&r2=26132&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=26132&r1=26131&r2=26132&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=26132&r1=26131&r2=26132&view=diff
r26132 - in /branches/frame_order_cleanup: ./ lib/ lib/structure/internal/ pipe_control/ pipe_control/structure/ prompt/ tes...