relax SVN archive

Replaced all references to 'atomic_data' with 'structure'.

Removed a reference to atomic_data in a docstring.

Replaced the initialisation of the atomic_data dictionary with an instance of Internal_PDB.

Added a package docstring.

Reverted r5501, as the behaviour of the tested code has been reverted to the original.

The command used was:
svn merge -r5501:5500 .

Fixes for the deletion of the exists_xxx() functions.

These have been replaced by calls to the is_empty() data object methods.

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.

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.

Blocked revisions 5466-5501 via svnmerge

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r5466 | bugman | 2008-04-08 18:39:36 +0200 (Tue, 08 Apr 2008) | 3 lines

Added a missing RelaxError import.
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r5467 | bugman | 2008-04-08 18:40:04 +0200 (Tue, 08 Apr 2008) | 3 lines

Fixed the RelaxError import statement.
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r5468 | bugman | 2008-04-08 18:47:34 +0200 (Tue, 08 Apr 2008) | 3 lines

Fix for the setUp() method, as empty SpinContainers are now automatically overwritten.
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r5469 | bugman | 2008-04-08 18:48:51 +0200 (Tue, 08 Apr 2008) | 3 lines

Added a missing RelaxError import and the copyright statement.
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r5470 | semor | 2008-04-09 04:07:25 +0200 (Wed, 09 Apr 2008) | 11 lines

Added missing imports and corrected calls to modules from generic_fns.

In previous revisions (5258, 5259, 5260, 5261, 5264, 5265, 5276, 5282, 5283), as part of the
modifications to the new design, these calls to the modules were erroneously instantiated (as is
done for the modules from specific_fns).

The reasons for these changes were specified by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00029.html (# Message-id:
<7f080ed10804040101n5cc2c69flc3cf0a894389e8f1@...>)
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r5471 | semor | 2008-04-09 04:13:17 +0200 (Wed, 09 Apr 2008) | 3 lines

Added missing imports.
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r5472 | bugman | 2008-04-09 10:49:36 +0200 (Wed, 09 Apr 2008) | 6 lines

Created the SpinContainer.is_empty() method.

The molecule, residue, spin object stack in the relax data store is being modified, expect massive
breakages until this is resolved!
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r5473 | bugman | 2008-04-09 10:52:46 +0200 (Wed, 09 Apr 2008) | 5 lines

Fixes for the SpinContainer.__repr__() method.

This method was fubar!
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r5474 | bugman | 2008-04-09 10:53:34 +0200 (Wed, 09 Apr 2008) | 3 lines

Comment fix in the SpinList.add_item() method.
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r5475 | bugman | 2008-04-09 10:55:21 +0200 (Wed, 09 Apr 2008) | 3 lines

Improvements to the ResidueContainer.__repr__() method.
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r5476 | bugman | 2008-04-09 11:00:21 +0200 (Wed, 09 Apr 2008) | 3 lines

Created the ResidueContainer.is_empty() method.
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r5477 | bugman | 2008-04-09 11:02:33 +0200 (Wed, 09 Apr 2008) | 3 lines

Created the SpinList.is_empty() method.
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r5478 | bugman | 2008-04-09 11:05:36 +0200 (Wed, 09 Apr 2008) | 3 lines

Created the ResidueList.is_empty() method.
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r5479 | bugman | 2008-04-09 11:06:56 +0200 (Wed, 09 Apr 2008) | 3 lines

The SpinList add_item() method now uses the is_empty() method.
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r5480 | bugman | 2008-04-09 11:08:35 +0200 (Wed, 09 Apr 2008) | 3 lines

The ResidueList add_item() method now calls the is_empty() method.
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r5481 | bugman | 2008-04-09 11:10:34 +0200 (Wed, 09 Apr 2008) | 3 lines

Updated the MoleculeContainer.__repr__() method.
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r5482 | bugman | 2008-04-09 11:10:57 +0200 (Wed, 09 Apr 2008) | 3 lines

Fixed a comment in the ResidueContainer.__repr__() method.
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r5483 | bugman | 2008-04-09 11:13:23 +0200 (Wed, 09 Apr 2008) | 3 lines

Created the MoleculeContainer.is_empty() method.
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r5484 | bugman | 2008-04-09 11:14:09 +0200 (Wed, 09 Apr 2008) | 3 lines

Added a docstring to the MoleculeList.__repr__() method.
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r5485 | bugman | 2008-04-09 11:17:14 +0200 (Wed, 09 Apr 2008) | 3 lines

Updated the MoleculeList.add_item() method.
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r5486 | bugman | 2008-04-09 11:19:37 +0200 (Wed, 09 Apr 2008) | 3 lines

Created the MoleculeList.is_empty() method.
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r5487 | bugman | 2008-04-09 11:20:12 +0200 (Wed, 09 Apr 2008) | 3 lines

The MoleculeList add_item() method now calls the is_empty() method.
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r5488 | bugman | 2008-04-09 11:36:24 +0200 (Wed, 09 Apr 2008) | 3 lines

Fix for the Prototype.__deepcopy__() method. The 'is_empty' method is now skipped in the copying.
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r5489 | bugman | 2008-04-09 11:37:34 +0200 (Wed, 09 Apr 2008) | 3 lines

Fixed the module docsting and updated the copyright.
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r5490 | bugman | 2008-04-09 11:42:38 +0200 (Wed, 09 Apr 2008) | 3 lines

Fix for a RelaxError message.
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r5491 | bugman | 2008-04-09 13:49:04 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the return_residue() function.

Empty MoleculeContainers and ResidueContainers are skipped to avoid returning them.
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r5492 | bugman | 2008-04-09 13:50:52 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the return_molecule() function.

Empty MoleculeContainers are skipped to avoid returning them.
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r5493 | bugman | 2008-04-09 13:52:08 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the return_spin() function.

Empty MoleculeContainers, ResidueContainers, and SpinContainers are skipped to avoid returning them.
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r5494 | bugman | 2008-04-09 13:56:11 +0200 (Wed, 09 Apr 2008) | 3 lines

Bug fix in the setUp() method, the first molecule should be named before adding a second!
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r5495 | bugman | 2008-04-09 14:04:59 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the SpinList.add_item() method.

Unnumbered spins are allowed if the names are unique.
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r5496 | bugman | 2008-04-09 14:07:07 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the ResidueList.add_item() method.

Unnumbered residues are allowed if the names are unique.
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r5497 | bugman | 2008-04-09 14:07:36 +0200 (Wed, 09 Apr 2008) | 3 lines

Clean up: Empty line removal.
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r5498 | bugman | 2008-04-09 14:10:31 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the Test_selection.setUp() method.

The relax data storage object was not being correctly set up, as empty spins were being overwritten.
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r5499 | bugman | 2008-04-09 14:11:34 +0200 (Wed, 09 Apr 2008) | 3 lines

Bug fix in the test_spin_loop_no_selection() unit test.
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r5500 | bugman | 2008-04-09 14:16:42 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the exists_mol_res_spin_data() function.

The new cdp.mol.is_empty() method is being used to determine if data exists.
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r5501 | bugman | 2008-04-09 14:43:36 +0200 (Wed, 09 Apr 2008) | 5 lines

Bug fix for the test_return_spin() unit test.

selection.return_spin() should return nothing if the SpinContainer is empty.
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Merged revisions 5462-5465 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r5462 | bugman | 2008-04-08 18:29:26 +0200 (Tue, 08 Apr 2008) | 6 lines

Added a copyright statement to the noe.py sample script.

The purpose of this is so the user knows who the author of the script was and how ancient the script
is, as well as allowing the file to be redistributable.
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r5463 | bugman | 2008-04-08 18:31:34 +0200 (Tue, 08 Apr 2008) | 6 lines

Added a copyright statement to the relax_fit.py sample script.

The purpose of this is so the user knows who the author of the script was and how ancient the script
is, as well as allowing the file to be redistributable.
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r5464 | bugman | 2008-04-08 18:34:35 +0200 (Tue, 08 Apr 2008) | 6 lines

Added a copyright statement to the full_analysis.py sample script.

The purpose of this is so the user knows who the author of the script was and how ancient the script
is, as well as allowing the file to be redistributable.
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r5465 | bugman | 2008-04-08 18:37:27 +0200 (Tue, 08 Apr 2008) | 3 lines

Added the JBNMR reference to the full_analysis.py sample script.
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