Author: bugman
Date: Sun Apr 13 11:16:29 2008
New Revision: 5613
URL: http://svn.gna.org/viewcvs/relax?rev=5613&view=rev
Log:
Blocked revisions 5506-5603,5605-5610 via svnmerge
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r5506 | bugman | 2008-04-09 16:56:46 +0200 (Wed, 09 Apr 2008) | 9 lines
Reverted r5491, r5492, and r5493 as these introduced a bug.
The command used was:
svn merge -r5493:5490 .
The problem is that empty MoleculeContainers, ResidueContainers, and
SpinContainers should be
returned when the selection identifier only selects a higher structure.
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r5507 | bugman | 2008-04-09 17:04:22 +0200 (Wed, 09 Apr 2008) | 5 lines
Deleted the exists_mol_data(), exists_res_data(), and exists_spin_data()
functions.
These are now redundant because of the is_empty() methods of the
mol-res-spin data object stack.
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r5508 | bugman | 2008-04-09 17:07:24 +0200 (Wed, 09 Apr 2008) | 5 lines
Fixes for the deletion of the exists_xxx() functions.
These have been replaced by calls to the is_empty() data object methods.
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r5509 | bugman | 2008-04-09 17:13:10 +0200 (Wed, 09 Apr 2008) | 6 lines
Reverted r5501, as the behaviour of the tested code has been reverted to
the original.
The command used was:
svn merge -r5501:5500 .
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r5510 | bugman | 2008-04-09 17:16:40 +0200 (Wed, 09 Apr 2008) | 3 lines
Added a package docstring.
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r5511 | bugman | 2008-04-09 17:22:32 +0200 (Wed, 09 Apr 2008) | 3 lines
Replaced the initialisation of the atomic_data dictionary with an instance
of Internal_PDB.
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r5512 | bugman | 2008-04-09 17:24:26 +0200 (Wed, 09 Apr 2008) | 3 lines
Removed a reference to atomic_data in a docstring.
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r5513 | bugman | 2008-04-09 17:25:29 +0200 (Wed, 09 Apr 2008) | 3 lines
Replaced all references to 'atomic_data' with 'structure'.
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r5514 | bugman | 2008-04-09 17:27:03 +0200 (Wed, 09 Apr 2008) | 3 lines
Added the missing import of Internal_PDB.
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r5515 | bugman | 2008-04-09 17:28:23 +0200 (Wed, 09 Apr 2008) | 6 lines
Bug fix for the calling of terminate().
This is now an object method which is part of the structural data API,
rather than a module
function.
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r5516 | bugman | 2008-04-10 11:05:05 +0200 (Thu, 10 Apr 2008) | 6 lines
Made the structural API method atom_loop() much more flexible.
Each part of the tuple of atomic information can be individually selected
to be yielded, and the
element name is now also returned.
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r5517 | bugman | 2008-04-10 11:07:06 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the call to the atom_loop() method in the centre_of_mass() function.
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r5518 | bugman | 2008-04-10 11:09:03 +0200 (Thu, 10 Apr 2008) | 6 lines
Made the call to the atom_loop() method in the centre_of_mass() function
more robust.
By setting all the flags, the returned tuple should always be the correct
size, even if additional
atomic data is specified in the API method.
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r5519 | bugman | 2008-04-10 11:10:34 +0200 (Thu, 10 Apr 2008) | 6 lines
All the atom_loop() args in the API have been set to False.
This will make the method more robust as the caller will get exactly what
it asks for, i.e. the
tuple will be of the right size.
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r5520 | bugman | 2008-04-10 11:19:07 +0200 (Thu, 10 Apr 2008) | 5 lines
Updated the Scientific Python structural API atom_loop() method.
All the flags are now accepted, and the appropriate tuple is now built.
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r5521 | bugman | 2008-04-10 11:22:40 +0200 (Thu, 10 Apr 2008) | 5 lines
Added '_flag' to the end of all the flag args in the atom_loop() structural
API method.
This will avoid many bugs with the flags being overwritten by other
variables.
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r5522 | bugman | 2008-04-10 11:25:24 +0200 (Thu, 10 Apr 2008) | 3 lines
'_flag' has been added to all of the Scientific Python atom_loop() API
method flags.
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r5523 | bugman | 2008-04-10 11:26:31 +0200 (Thu, 10 Apr 2008) | 3 lines
The Scientific atom_loop() structural API method now properly returns the
element name.
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r5524 | bugman | 2008-04-10 11:28:00 +0200 (Thu, 10 Apr 2008) | 3 lines
Added the 'atom_id' arg to the structural API atom_loop() generator method
stub.
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r5525 | bugman | 2008-04-10 11:29:51 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixed the atom_loop() call in load_spins().
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r5526 | bugman | 2008-04-10 11:30:21 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixed the atom_loop() call in centre_of_mass().
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r5527 | bugman | 2008-04-10 11:31:15 +0200 (Thu, 10 Apr 2008) | 3 lines
Variable name fixes for the load_spins() function.
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r5528 | bugman | 2008-04-10 11:32:05 +0200 (Thu, 10 Apr 2008) | 3 lines
The element name rather than atom name is being passed into the
return_atomic_mass() function now.
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r5529 | bugman | 2008-04-10 11:45:30 +0200 (Thu, 10 Apr 2008) | 3 lines
Created the write_header() function.
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r5530 | bugman | 2008-04-10 11:47:11 +0200 (Thu, 10 Apr 2008) | 3 lines
The write_body() function now calls write_header().
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r5531 | bugman | 2008-04-10 11:49:01 +0200 (Thu, 10 Apr 2008) | 3 lines
Renamed all flag args in the write_body() function from '*_col' to '*_flag'.
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r5532 | bugman | 2008-04-10 11:51:02 +0200 (Thu, 10 Apr 2008) | 3 lines
Shifted all flag args to the end of the write_body() and write_header()
functions.
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r5533 | bugman | 2008-04-10 11:53:53 +0200 (Thu, 10 Apr 2008) | 3 lines
Epydoc fixes in the docstrings of write_body() and write_header().
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r5534 | bugman | 2008-04-10 12:03:01 +0200 (Thu, 10 Apr 2008) | 3 lines
Created the write_line() function for writing a single line of sequence
data.
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r5535 | bugman | 2008-04-10 12:04:25 +0200 (Thu, 10 Apr 2008) | 3 lines
The write_body() function now calls write_line() for each spin.
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r5536 | bugman | 2008-04-10 12:15:34 +0200 (Thu, 10 Apr 2008) | 5 lines
Modified the test_display_protein_sequence() and
test_write_protein_sequence() unit tests.
The behaviour of the functions is changing.
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r5537 | bugman | 2008-04-10 12:20:07 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the write() function.
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r5538 | bugman | 2008-04-10 12:21:00 +0200 (Thu, 10 Apr 2008) | 3 lines
Changed the default vals of the write() flag args to bools.
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r5539 | bugman | 2008-04-10 12:21:47 +0200 (Thu, 10 Apr 2008) | 3 lines
Changed all the '*_flag' arg default values from True to False.
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r5540 | bugman | 2008-04-10 12:23:34 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the display() function.
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r5541 | bugman | 2008-04-10 12:29:25 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the sequence.display() user function.
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r5542 | bugman | 2008-04-10 12:33:55 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the sequence.write() user function.
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r5543 | bugman | 2008-04-10 12:34:41 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix for the write_line() function.
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r5544 | bugman | 2008-04-10 12:36:48 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixes for all the sequence.display() user function arg unit tests.
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r5545 | bugman | 2008-04-10 12:38:59 +0200 (Thu, 10 Apr 2008) | 3 lines
More fixes for the sequence.display() user function arg unit tests.
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r5546 | bugman | 2008-04-10 12:40:52 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixes for the sequence.write() user function arg unit tests.
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r5547 | bugman | 2008-04-10 12:41:21 +0200 (Thu, 10 Apr 2008) | 3 lines
Added a missing RelaxError import.
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r5548 | bugman | 2008-04-10 14:30:17 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix for the write_line() function.
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r5549 | bugman | 2008-04-10 14:30:42 +0200 (Thu, 10 Apr 2008) | 3 lines
Changed all the sequence user function '*_flag' args to the default of
False.
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r5550 | bugman | 2008-04-10 14:33:09 +0200 (Thu, 10 Apr 2008) | 5 lines
Bug fix for the force arg test of the structure.create_diff_tensor_pdb()
user function.
This should be a bool arg.
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r5551 | bugman | 2008-04-10 14:36:03 +0200 (Thu, 10 Apr 2008) | 5 lines
Changed the flag args of the structre.create_vect_dist() user function to
bools.
The flags args have been shifted to the end as well.
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r5552 | bugman | 2008-04-10 14:38:03 +0200 (Thu, 10 Apr 2008) | 5 lines
Fixes for the symmetry and force arg unit tests of the
structure.create_vector_dist() user function.
These should now be bools.
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r5553 | bugman | 2008-04-10 16:24:47 +0200 (Thu, 10 Apr 2008) | 5 lines
Bug fix in the force arg test of the structure.create_diff_tensor_pdb()
user function.
RelaxBoolError should be raised.
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r5554 | bugman | 2008-04-10 16:27:20 +0200 (Thu, 10 Apr 2008) | 5 lines
Bug fix for the force arg test of the sequence.write() user function.
The arg should be a bool.
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r5555 | bugman | 2008-04-10 16:34:04 +0200 (Thu, 10 Apr 2008) | 5 lines
load_state() now throws a RelaxError when the state is incompatible.
The error says that the relax version in incompatible.
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r5556 | bugman | 2008-04-10 16:44:54 +0200 (Thu, 10 Apr 2008) | 5 lines
Added a relax script to regenerate
'test_suite/shared_data/saved_states/basic_single_pipe.bz2'.
This can be used when ever this saved state becomes incompatible with relax.
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r5557 | bugman | 2008-04-10 16:45:20 +0200 (Thu, 10 Apr 2008) | 3 lines
Updated the 'basic_single_pipe.bz2' to be compatible with the current relax
revision.
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r5558 | bugman | 2008-04-10 16:54:04 +0200 (Thu, 10 Apr 2008) | 3 lines
Epydoc fixes.
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r5559 | bugman | 2008-04-10 17:01:35 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the align_tensor.init() errors argument to a bool.
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r5560 | bugman | 2008-04-10 17:03:24 +0200 (Thu, 10 Apr 2008) | 3 lines
Fix for the errors arg test of the align_tensor.init() user function.
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r5561 | bugman | 2008-04-10 17:05:51 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the fixed arg to the diffusion_tensor.init() user function to be
a bool.
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r5562 | bugman | 2008-04-10 17:07:21 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixes for the docstring of the diffusion_tensor.init() user function.
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r5563 | bugman | 2008-04-10 17:10:05 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix for the fixed arg test of the diffusion_tensor.init() user function.
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r5564 | bugman | 2008-04-10 17:11:39 +0200 (Thu, 10 Apr 2008) | 3 lines
Fixed all calls to diffusion_tensor.init().
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r5565 | bugman | 2008-04-10 17:14:15 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the relax_data.write() force arg to a bool.
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r5566 | bugman | 2008-04-10 17:20:22 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the results.write() force arg to a bool.
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r5567 | bugman | 2008-04-10 17:25:05 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted all class methods to module functions.
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r5568 | bugman | 2008-04-10 17:32:36 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the write() function to the new relax design.
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r5569 | bugman | 2008-04-10 17:33:26 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix: Removed an old line of code from the write() function.
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r5570 | bugman | 2008-04-10 17:42:39 +0200 (Thu, 10 Apr 2008) | 5 lines
Bug fix for the AIC model selection between two diffusion tensors system
test.
The diffusion_tensor.init() fixed arg is now passed in as a bool.
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r5571 | bugman | 2008-04-10 17:43:09 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the get_specific_fn() raise_error arg to a bool.
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r5572 | bugman | 2008-04-10 17:49:25 +0200 (Thu, 10 Apr 2008) | 3 lines
Converted the read() function to the new relax design.
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r5573 | bugman | 2008-04-10 17:52:46 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix, the diffusion_tensor.init() fixed flag is now a bool.
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r5574 | bugman | 2008-04-10 17:53:56 +0200 (Thu, 10 Apr 2008) | 3 lines
Bug fix, the diffusion_tensor.init() fixed flag is now a bool.
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r5575 | bugman | 2008-04-10 17:57:19 +0200 (Thu, 10 Apr 2008) | 3 lines
Fix for the test_angles() system test. The spins are now loaded.
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r5576 | bugman | 2008-04-11 12:39:08 +0200 (Fri, 11 Apr 2008) | 3 lines
Updated the load_spins() function to print out a list of spins appended to
the data store.
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r5577 | bugman | 2008-04-11 12:40:13 +0200 (Fri, 11 Apr 2008) | 3 lines
Added the missing import of generic_fns.sequence.write_line().
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r5578 | bugman | 2008-04-11 12:41:00 +0200 (Fri, 11 Apr 2008) | 3 lines
Bug fix for the write_line() function.
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r5579 | bugman | 2008-04-11 14:21:38 +0200 (Fri, 11 Apr 2008) | 5 lines
Fix for the print out of the load_spins() function.
Now only when a new SpinContainer is created is the spin system information
written to stdout.
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r5580 | bugman | 2008-04-11 14:38:17 +0200 (Fri, 11 Apr 2008) | 5 lines
Improvements to the Scientific Python structural object atom_loop() method.
Multiple molecules of different types are now simultaneously supported.
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r5581 | bugman | 2008-04-11 14:40:55 +0200 (Fri, 11 Apr 2008) | 3 lines
Readded the condition to catch if no molecules can be identified in
atom_loop().
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r5582 | bugman | 2008-04-11 14:42:49 +0200 (Fri, 11 Apr 2008) | 3 lines
Non protein/RNA/DNA molecules are now supported in the atom_loop() API
method.
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r5583 | bugman | 2008-04-11 14:53:13 +0200 (Fri, 11 Apr 2008) | 3 lines
A few fixes for the atom_loop() structural API method (for Scientific).
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r5584 | bugman | 2008-04-11 16:30:20 +0200 (Fri, 11 Apr 2008) | 5 lines
Created the private __molecule_loop() method.
This is for looping over the individual molecules of the scientific data
structures.
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r5585 | bugman | 2008-04-11 16:33:51 +0200 (Fri, 11 Apr 2008) | 3 lines
atom_loop() now calls __molecule_loop().
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r5586 | bugman | 2008-04-11 16:41:09 +0200 (Fri, 11 Apr 2008) | 3 lines
Created the __residue_loop() method and have it called from atom_loop().
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r5587 | semor | 2008-04-11 16:46:39 +0200 (Fri, 11 Apr 2008) | 3 lines
Aliased the current data pipe and removed the run arguments.
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r5588 | semor | 2008-04-11 16:52:51 +0200 (Fri, 11 Apr 2008) | 3 lines
Modified the 'nucleus' variable to its new designation.
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r5589 | semor | 2008-04-11 16:58:03 +0200 (Fri, 11 Apr 2008) | 3 lines
Modified the 'nucleus' variable to its new designations as part of the move
to the new design.
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r5590 | semor | 2008-04-11 17:13:42 +0200 (Fri, 11 Apr 2008) | 3 lines
Removed an empty line.
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r5591 | bugman | 2008-04-11 17:35:45 +0200 (Fri, 11 Apr 2008) | 3 lines
Fixes for the looping over non-protein/RNA/DNA residues.
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r5592 | bugman | 2008-04-11 17:36:05 +0200 (Fri, 11 Apr 2008) | 3 lines
Removed a debugging print out.
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r5593 | bugman | 2008-04-11 18:04:06 +0200 (Fri, 11 Apr 2008) | 3 lines
Changed the default value of the spin_id arg to None in the
structure.load_spins() user function.
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r5594 | semor | 2008-04-11 20:43:28 +0200 (Fri, 11 Apr 2008) | 7 lines
Converted some 'instance' arguments to calls to 'spin' and removed some now
unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
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r5595 | semor | 2008-04-12 02:02:23 +0200 (Sat, 12 Apr 2008) | 7 lines
Added a missing argument to the set_error() method.
This omission was spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00053.html (# Message-id:
<7f080ed10804111525p48f7bc6aq10189644ae5d736b@xxxxxxxxxxxxxx>)
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r5596 | semor | 2008-04-12 02:05:26 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5597 | semor | 2008-04-12 02:07:39 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5598 | semor | 2008-04-12 02:17:04 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5599 | semor | 2008-04-12 16:39:27 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5600 | semor | 2008-04-12 16:41:34 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5601 | semor | 2008-04-12 16:44:13 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin' and removed
some now unused 'cdp' calls.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5602 | semor | 2008-04-12 20:08:45 +0200 (Sat, 12 Apr 2008) | 7 lines
Converted some more 'instance' arguments to calls to 'spin'.
This is a small part of what Edward d'Auvergne noticed in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00010.html (# Message-id:
<7f080ed10804030909m3b540ee3y1d60009542c09694@xxxxxxxxxxxxxx>)
........
r5603 | semor | 2008-04-12 20:11:28 +0200 (Sat, 12 Apr 2008) | 3 lines
Removed one unused run argument.
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r5605 | bugman | 2008-04-12 22:28:30 +0200 (Sat, 12 Apr 2008) | 18 lines
Manually merged r5603 from the 1.2 line.
The command used was:
svn merge -r5603:5604
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2/specific_fns/model_free.py
specific_fns/model_free/mf_minimise.py
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r5604 | bugman | 2008-04-12 22:20:59 +0200 (Sat, 12 Apr 2008) | 7 lines
Changed paths:
M /1.2/specific_fns/model_free.py
Fix for bug #11476 (https://gna.org/bugs/index.php?11476).
This bug is fatal for Monte Carlo simulations if model m0 is encountered.
The problem was that
there was a 'return' statement instead of 'continue' which caused the
Monte Carlo simulation
optimisation as soon as model m0 is encountered.
.....
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r5606 | semor | 2008-04-12 22:29:26 +0200 (Sat, 12 Apr 2008) | 7 lines
[... 45 lines stripped ...]
r5613 - /1.2/