Author: bugman
Date: Tue Nov 13 22:39:40 2007
New Revision: 3527
URL: http://svn.gna.org/viewcvs/relax?rev=3527&view=rev
Log:
Blocked revisions 3379,3382-3524 via svnmerge
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r3379 | bugman | 2007-10-28 18:55:32 +0100 (Sun, 28 Oct 2007) | 8 lines
Fix for bug #9389 (https://gna.org/bugs/?9389).
This bug was caused by the move away from using the __builtin__ namespace.
As the file is now
treated as a module from which errors must be imported, the AllRelaxErrors
object was not being
created. The solution was to add the function 'all_errors()' which returns
a list of all the
RelaxError objects.
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r3382 | bugman | 2007-10-28 20:29:06 +0100 (Sun, 28 Oct 2007) | 3 lines
Added two unit tests for the, as of yet, non-existent
'generic_fns.residue.rename()' function.
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r3383 | bugman | 2007-10-28 20:32:32 +0100 (Sun, 28 Oct 2007) | 7 lines
Removed the 'residue.merge()' from the data model redesign document.
I cannot see the purpose of this function, as it would probably duplicate
the functionality of
'residue.copy()' function. It was first mentioned by Chris MacRaild in the
post at
https://mail.gna.org/public/relax-devel/2006-10/msg00061.html.
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r3384 | bugman | 2007-10-29 15:02:21 +0100 (Mon, 29 Oct 2007) | 3 lines
Added a unit test for renaming multiple residues simultaneously through
'residue.rename()'.
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r3385 | bugman | 2007-10-29 15:03:53 +0100 (Mon, 29 Oct 2007) | 3 lines
Fixed a bug in the 'test_rename' unit test.
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r3386 | bugman | 2007-10-29 15:07:45 +0100 (Mon, 29 Oct 2007) | 3 lines
Added 3 unit tests for the non-existant residue.renumber() function.
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r3387 | bugman | 2007-11-03 14:09:28 +0100 (Sat, 03 Nov 2007) | 3 lines
Created the generic_fns.residue.rename() function and fixed the
corresponding unit tests.
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r3388 | bugman | 2007-11-03 16:04:48 +0100 (Sat, 03 Nov 2007) | 3 lines
Implemented the generic_fns.residue.renumber() function and fixed its unit
tests.
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r3389 | bugman | 2007-11-03 17:46:41 +0100 (Sat, 03 Nov 2007) | 3 lines
Added the rudimentary beginnings of the molecule user function class.
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r3390 | bugman | 2007-11-03 18:36:21 +0100 (Sat, 03 Nov 2007) | 3 lines
Alphabetical arrangement of the residue user functions.
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r3391 | bugman | 2007-11-03 18:37:32 +0100 (Sat, 03 Nov 2007) | 3 lines
Spelling correction.
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r3392 | bugman | 2007-11-03 19:25:57 +0100 (Sat, 03 Nov 2007) | 6 lines
More unit tests for the generic_fns.residue.copy() function.
The current test was renamed. Two new tests were added for copying between
molecules and copying
between data pipes.
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r3393 | bugman | 2007-11-03 23:37:13 +0100 (Sat, 03 Nov 2007) | 5 lines
A large number of changes to make the residue.copy() user function fully
functional.
Now residue data can be copied within a single molecule, between molecules,
and between data pipes.
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r3394 | bugman | 2007-11-04 11:55:51 +0100 (Sun, 04 Nov 2007) | 6 lines
Added a test for the failure of the generic_fns.selection.return_residue()
function.
This tests the failure of asking for a non-existent data pipe and the
function has been fixed to
fail appropriately.
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r3395 | bugman | 2007-11-04 13:15:18 +0100 (Sun, 04 Nov 2007) | 3 lines
Added another unit test for the generic_fns.selection.return_residue()
function.
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r3396 | bugman | 2007-11-04 13:19:36 +0100 (Sun, 04 Nov 2007) | 5 lines
Added two unit tests for the generic_fns.selection.return_molecule()
function.
Also made the function fail properly when no data pipe exists.
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r3397 | bugman | 2007-11-04 13:27:15 +0100 (Sun, 04 Nov 2007) | 3 lines
Added two unit tests for the
generic_fns.selection.return_single_residue_info() function.
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r3398 | bugman | 2007-11-04 13:36:57 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxNoRunError to RelaxNoPipeError, and updated
the error message.
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r3399 | bugman | 2007-11-04 13:39:20 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxRunError with RelaxPipeError, and modified
the error message.
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r3400 | bugman | 2007-11-04 13:42:08 +0100 (Sun, 04 Nov 2007) | 3 lines
Replaced all mention of 'run' from the RelaxError system and replaced it
with 'pipe'.
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r3401 | bugman | 2007-11-04 13:51:00 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed dud user functions from 'residue' which remained from the copy of
'sequence'.
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r3402 | bugman | 2007-11-04 13:51:37 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the docstring modifications of the 'residue' user function class.
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r3403 | bugman | 2007-11-04 13:57:38 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the residue.rename() user function.
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r3404 | bugman | 2007-11-04 14:01:46 +0100 (Sun, 04 Nov 2007) | 3 lines
Created the residue.renumber() user function.
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r3405 | bugman | 2007-11-04 14:37:59 +0100 (Sun, 04 Nov 2007) | 6 lines
Created the residue.display() user function.
This has been added to the data model redesign document. Two unit tests
have also been created for
the function.
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r3406 | bugman | 2007-11-04 14:39:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Fixed a typo in the docstrings of the unit tests for the
generic_fns.residue functions.
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r3407 | bugman | 2007-11-04 14:49:55 +0100 (Sun, 04 Nov 2007) | 3 lines
Modified the data model redesign document to show that the residue user
function class is finished.
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r3408 | bugman | 2007-11-04 14:56:03 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed junk code, left over from the copy from 'generic_fns/sequence.py'.
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r3409 | bugman | 2007-11-04 14:58:41 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some no longer used RelaxError imports.
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r3410 | bugman | 2007-11-04 15:38:46 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a module docstring.
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r3411 | bugman | 2007-11-04 15:40:29 +0100 (Sun, 04 Nov 2007) | 3 lines
Spacing.
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r3412 | bugman | 2007-11-04 15:41:08 +0100 (Sun, 04 Nov 2007) | 3 lines
Created the module docstring.
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r3413 | bugman | 2007-11-04 15:42:22 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the setUp and tearDown functions for the generic_fns.molecule
function unit tests.
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r3414 | bugman | 2007-11-04 15:43:40 +0100 (Sun, 04 Nov 2007) | 5 lines
Replace the contents of 'generic_fns/molecule.py' with those of
'generic_fns/residue.py'.
The file originated from 'generic_fns/residue.py' but was unmodified and
out of date.
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r3415 | bugman | 2007-11-04 17:14:57 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the module names in '__init__.py'.
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r3416 | bugman | 2007-11-04 17:28:45 +0100 (Sun, 04 Nov 2007) | 6 lines
Created the molecule.create() user function.
The user function and the function generic_fns.molecule.create() have been
written. Two unit tests
for the function have been created.
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r3417 | bugman | 2007-11-04 17:30:29 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed the useless molecule user functions remaining from the copy from
'prompt/sequence.py'.
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r3418 | bugman | 2007-11-04 17:31:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed the user function 'molecule.add()' to 'molecule.create()' in the
redesign doc.
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r3419 | bugman | 2007-11-04 17:58:21 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the copying of the molecule data between different
data pipes.
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r3420 | bugman | 2007-11-04 18:00:03 +0100 (Sun, 04 Nov 2007) | 6 lines
Added the 'return_single_molecule_info()' function and fixed the
'return_molecule()' function.
The 'return_molecule()' function was returning a molecule container when no
molecule selection was
given. Now None is returned.
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r3421 | bugman | 2007-11-04 18:01:59 +0100 (Sun, 04 Nov 2007) | 6 lines
Modified the 'generic_fns.residue.copy()' function to work with the
modified 'return_molecule()' fn.
Five unit test were failing due to the previous commit. This was because
of a problem in
'generic_fns.residue.copy()' that wasn't previously detected.
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r3422 | bugman | 2007-11-04 18:04:22 +0100 (Sun, 04 Nov 2007) | 3 lines
Another fix for the 'return_molecule()' function.
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r3423 | bugman | 2007-11-04 18:10:46 +0100 (Sun, 04 Nov 2007) | 3 lines
A few more fixes to the 'return_molecule()' function.
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r3424 | bugman | 2007-11-04 18:11:21 +0100 (Sun, 04 Nov 2007) | 3 lines
Wrote the generic_fns.molecule.copy() function.
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r3425 | bugman | 2007-11-04 18:14:20 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test to test the failure of copying molecule data to a
non-existent data pipe.
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r3426 | bugman | 2007-11-04 18:23:47 +0100 (Sun, 04 Nov 2007) | 3 lines
Added two more unit tests for the generic_fns.molecule.copy() function.
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r3427 | bugman | 2007-11-04 18:53:24 +0100 (Sun, 04 Nov 2007) | 3 lines
Created the molecule.copy() user function interface.
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r3428 | bugman | 2007-11-04 18:54:23 +0100 (Sun, 04 Nov 2007) | 3 lines
A few changes to the residue.copy() user function RelaxError messages.
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r3429 | bugman | 2007-11-04 19:02:46 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the generic_fns.molecule.delete() function.
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r3430 | bugman | 2007-11-04 19:07:43 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the deletion of all molecules.
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r3431 | bugman | 2007-11-04 19:10:12 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the failure of the generic_fns.molecule.delete()
function.
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r3432 | bugman | 2007-11-04 19:16:58 +0100 (Sun, 04 Nov 2007) | 3 lines
Implemented the generic_fns.molecule.delete() function.
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r3433 | bugman | 2007-11-04 19:17:35 +0100 (Sun, 04 Nov 2007) | 3 lines
Fixed a problem in the 'test_delete_all()' unit test.
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r3434 | bugman | 2007-11-04 19:20:18 +0100 (Sun, 04 Nov 2007) | 3 lines
Added 2 unit tests for the generic_fns.molecule.display() function.
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r3435 | bugman | 2007-11-04 19:26:18 +0100 (Sun, 04 Nov 2007) | 3 lines
A small change to a generic_fns.molecule.display() unit test.
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r3436 | bugman | 2007-11-04 19:26:42 +0100 (Sun, 04 Nov 2007) | 3 lines
Wrote the generic_fns.molecule.display() function.
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r3437 | bugman | 2007-11-04 19:28:43 +0100 (Sun, 04 Nov 2007) | 3 lines
Debugged the generic_fns.molecule.display() function.
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r3438 | bugman | 2007-11-04 19:29:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some debugging print statements.
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r3439 | bugman | 2007-11-04 19:33:54 +0100 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.delete() user function.
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r3440 | bugman | 2007-11-04 19:36:00 +0100 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.display() user function.
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r3441 | bugman | 2007-11-04 19:38:07 +0100 (Sun, 04 Nov 2007) | 3 lines
Modified the molecule user functions to include the identification string
documentation.
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r3442 | bugman | 2007-11-04 19:38:59 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a missing import statement.
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r3443 | bugman | 2007-11-04 19:41:53 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the generic_fns.molecule.rename() function.
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r3444 | bugman | 2007-11-04 19:47:00 +0100 (Sun, 04 Nov 2007) | 3 lines
Implemented the generic_fns.molecule.rename() function.
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r3445 | bugman | 2007-11-04 19:50:28 +0100 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.rename() user function.
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r3446 | bugman | 2007-11-04 19:56:29 +0100 (Sun, 04 Nov 2007) | 3 lines
Added 2 unit tests for the failure of the generic_fns.molecule.rename()
function.
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r3447 | bugman | 2007-11-04 19:57:43 +0100 (Sun, 04 Nov 2007) | 3 lines
Fixed a bug in generic_fns.molecule.rename() found using the previously
committed unit tests.
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r3448 | bugman | 2007-11-04 19:58:53 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed the user function molecule.info() to molecule.display() in the
redesign document.
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r3449 | bugman | 2007-11-04 19:59:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the molecule.rename() user function to the redesign document.
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r3450 | bugman | 2007-11-04 20:12:54 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the redesign document to show that the molecule user functions are
all implemented.
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r3451 | bugman | 2007-11-04 20:13:24 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
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r3452 | bugman | 2007-11-04 20:14:23 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
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r3453 | bugman | 2007-11-04 20:15:11 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
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r3454 | bugman | 2007-11-04 20:48:09 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed the out of date spin system module.
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r3455 | bugman | 2007-11-04 20:49:37 +0100 (Sun, 04 Nov 2007) | 6 lines
Copied, for a second time, generic_fns/residue.py to generic_fns/spin.py.
This had previously been done, but the copied file was now well out of date
and useless. It has
been replaced with a newer version.
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r3456 | bugman | 2007-11-04 20:51:15 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the copyright notice.
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r3457 | bugman | 2007-11-04 20:51:53 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the module docstring.
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r3458 | bugman | 2007-11-04 20:53:49 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the 'self.setup_data()' docstring.
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r3459 | bugman | 2007-11-04 20:54:45 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a docstring to the 'self.setup_data()' function.
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r3460 | bugman | 2007-11-04 20:56:55 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the setUp, tearDown, and setup_data functions for the unit tests of
'generic_fns.spin'.
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r3461 | bugman | 2007-11-06 20:32:19 +0100 (Tue, 06 Nov 2007) | 3 lines
Copied the GPL 'COPYING' file to the 'minimise' dir to prepare to copy this
code to the minfx project.
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r3462 | bugman | 2007-11-11 10:56:15 +0100 (Sun, 11 Nov 2007) | 5 lines
Removed the useless read(), sort(), and write() spin user functions.
These were remnants of the copy from the original sequence user function
module.
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r3463 | bugman | 2007-11-11 10:57:42 +0100 (Sun, 11 Nov 2007) | 3 lines
Removed the prompt.spin module. This will be replaced by the current
residue module instead.
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r3464 | bugman | 2007-11-11 10:58:12 +0100 (Sun, 11 Nov 2007) | 3 lines
Copied the residue user function module to the spin module.
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r3465 | bugman | 2007-11-11 11:00:16 +0100 (Sun, 11 Nov 2007) | 3 lines
The spin user function class is now accessible from the prompt.
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r3466 | bugman | 2007-11-11 11:12:44 +0100 (Sun, 11 Nov 2007) | 3 lines
Wrote a unit test for checking the copying of spin data between molecules.
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r3467 | bugman | 2007-11-11 12:14:24 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a unit test for copying spins between residues and improvements to
'test_spin.py'.
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r3468 | bugman | 2007-11-11 12:19:14 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a unit test for copying spin data between data pipes.
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r3469 | bugman | 2007-11-11 12:21:26 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a unit test for the failure of copying spin data to a non-existent
data pipe.
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r3470 | bugman | 2007-11-11 12:26:55 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a unit test for various types of failure of copying spin data.
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r3471 | bugman | 2007-11-11 12:30:17 +0100 (Sun, 11 Nov 2007) | 3 lines
Added the missing RelaxError import statement.
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r3472 | bugman | 2007-11-11 12:35:26 +0100 (Sun, 11 Nov 2007) | 3 lines
Updated the generic_fns.spin.copy() function to be spin specific rather
than residue specific.
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r3473 | bugman | 2007-11-11 12:37:50 +0100 (Sun, 11 Nov 2007) | 3 lines
Added the function generic_fns.selection.return_single_spin_info().
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r3474 | bugman | 2007-11-11 12:41:03 +0100 (Sun, 11 Nov 2007) | 3 lines
Created the function generic_fns.selection.return_spin().
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r3475 | bugman | 2007-11-11 12:44:55 +0100 (Sun, 11 Nov 2007) | 3 lines
Added the missing return_spin import.
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r3476 | bugman | 2007-11-11 12:59:27 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a docstring and comments to the selection class method __contains__().
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r3477 | bugman | 2007-11-11 13:06:33 +0100 (Sun, 11 Nov 2007) | 3 lines
Fixed up the data setup for the spin.copy() unit function tests.
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r3478 | bugman | 2007-11-11 13:08:31 +0100 (Sun, 11 Nov 2007) | 3 lines
More fixes for the data setup for the spin.copy() unit function tests.
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r3479 | bugman | 2007-11-11 13:10:25 +0100 (Sun, 11 Nov 2007) | 3 lines
Fixes to the spin.copy() unit test 'test_copy_between_molecules'.
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r3480 | bugman | 2007-11-11 13:14:24 +0100 (Sun, 11 Nov 2007) | 3 lines
Fixed a small bug in the spin.copy() unit test 'test_copy_between_residues'.
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r3481 | bugman | 2007-11-11 13:16:57 +0100 (Sun, 11 Nov 2007) | 3 lines
Fixed a number of bugs in the generic_fns.spin unit test setup_data
function.
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r3482 | bugman | 2007-11-11 13:21:21 +0100 (Sun, 11 Nov 2007) | 3 lines
Bug fixes for the spin.copy() unit test 'test_copy_between_residues'.
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r3483 | bugman | 2007-11-11 13:26:26 +0100 (Sun, 11 Nov 2007) | 3 lines
Added another check in the spin.copy unit test 'test_copy_fail'.
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r3484 | bugman | 2007-11-11 13:29:30 +0100 (Sun, 11 Nov 2007) | 3 lines
Split the generic_fns.spin.copy() unit test 'test_copy_fail' into four unit
tests.
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r3485 | bugman | 2007-11-11 13:31:01 +0100 (Sun, 11 Nov 2007) | 3 lines
Bug fix for the spin.copy() unit test 'test_copy_between_residues'.
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r3486 | bugman | 2007-11-11 13:33:07 +0100 (Sun, 11 Nov 2007) | 3 lines
Added a test for the existence of the target residue.
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r3487 | bugman | 2007-11-11 13:34:42 +0100 (Sun, 11 Nov 2007) | 3 lines
A number of bug fixes to the spin.copy() function.
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r3488 | bugman | 2007-11-11 13:38:43 +0100 (Sun, 11 Nov 2007) | 3 lines
Fixed the last of the bugs in the generic_fns.spin.copy() function.
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r3489 | bugman | 2007-11-11 13:44:34 +0100 (Sun, 11 Nov 2007) | 6 lines
Removed the spin.read(), spin.sort(), and spin.write() user function from
the redesign document.
These can be implemented in a single user function class which handles
molecules, residues, and
spins together.
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r3490 | bugman | 2007-11-11 17:46:23 +0100 (Sun, 11 Nov 2007) | 5 lines
Added a new point in the data model redesign document - the new sequence
user function class.
The idea is that this is a class that handles the whole of the
molecule-residue-spin structure.
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r3491 | bugman | 2007-11-11 20:29:26 +0100 (Sun, 11 Nov 2007) | 3 lines
Split the 'test_copy_within_molecule_fail' unit test in two, for the 2
failures.
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r3492 | bugman | 2007-11-11 20:35:30 +0100 (Sun, 11 Nov 2007) | 5 lines
Wrote 2 unit tests for the generic_fns.spin.create() function.
One tests that the function works correctly, the second that it fails
correctly.
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r3493 | bugman | 2007-11-11 20:44:20 +0100 (Sun, 11 Nov 2007) | 3 lines
Changed one of the spin creation unit tests to send the spin to a different
molecule and residue.
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r3494 | bugman | 2007-11-11 20:51:26 +0100 (Sun, 11 Nov 2007) | 3 lines
[... 143 lines stripped ...]
r3527 - /1.2/