relax SVN archive

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These have been replaced by calls to the is_empty() data object methods.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

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

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

Fixed the RelaxError import statement.
........
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.
........
r5469 | bugman | 2008-04-08 18:48:51 +0200 (Tue, 08 Apr 2008) | 3 lines

Added a missing RelaxError import and the copyright statement.
........
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@...>)
........
r5471 | semor | 2008-04-09 04:13:17 +0200 (Wed, 09 Apr 2008) | 3 lines

Added missing imports.
........
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!
........
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!
........
r5474 | bugman | 2008-04-09 10:53:34 +0200 (Wed, 09 Apr 2008) | 3 lines

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

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

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

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

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

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

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

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

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

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

Created the MoleculeList.is_empty() method.
........
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.
........
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.
........
r5489 | bugman | 2008-04-09 11:37:34 +0200 (Wed, 09 Apr 2008) | 3 lines

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

Fix for a RelaxError message.
........
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.
........
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.
........
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.
........
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!
........
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.
........
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.
........
r5497 | bugman | 2008-04-09 14:07:36 +0200 (Wed, 09 Apr 2008) | 3 lines

Clean up: Empty line removal.
........
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.
........
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.
........
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.
........
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.
........

Merged revisions 5462-5465 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
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.
........
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.
........
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.
........
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.
........

Blocked revisions 5458-5461 via svnmerge

........
r5458 | bugman | 2008-04-08 18:21:11 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated comment about pipe creation in the noe.py sample script.
........
r5459 | bugman | 2008-04-08 18:22:14 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the relax_fit.py sample script to use the new structure.load_spins() user function.
........
r5460 | bugman | 2008-04-08 18:23:30 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the relax_fit.py sample script to the new design (no more run args).
........
r5461 | bugman | 2008-04-08 18:25:11 +0200 (Tue, 08 Apr 2008) | 3 lines

A few fixes to the noe.py sample script, and removal of the 'name' variable.
........

Blocked revisions 5400-5457 via svnmerge

........
r5400 | bugman | 2008-04-08 10:24:30 +0200 (Tue, 08 Apr 2008) | 5 lines

Created the user function pymol.cone_pdb() for displaying the N-state model cone geometric object.

This is just the front end.
........
r5401 | bugman | 2008-04-08 10:25:57 +0200 (Tue, 08 Apr 2008) | 3 lines

Bug fix for the cartoon() function. This now works again!
........
r5402 | bugman | 2008-04-08 10:27:16 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the command() function to the new relax design.
........
r5403 | bugman | 2008-04-08 10:35:07 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the create_macro() function to the new relax design.
........
r5404 | bugman | 2008-04-08 10:37:54 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the macro_exec() function to the new relax design.
........
r5405 | bugman | 2008-04-08 10:40:18 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the tensor_pdb() function to the new relax design.
........
r5406 | bugman | 2008-04-08 10:42:32 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the vector_dist() function to the new relax design.
........
r5407 | bugman | 2008-04-08 10:47:51 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the write() function to the new relax design.
........
r5408 | bugman | 2008-04-08 10:48:20 +0200 (Tue, 08 Apr 2008) | 3 lines

Arg to keyword epydoc fix.
........
r5409 | bugman | 2008-04-08 10:49:24 +0200 (Tue, 08 Apr 2008) | 3 lines

Added the return details to the create_macro() docstring.
........
r5410 | bugman | 2008-04-08 10:55:40 +0200 (Tue, 08 Apr 2008) | 3 lines

Created the cone_pdb() function for displaying the N-state model cone object in PyMOL.
........
r5411 | bugman | 2008-04-08 10:56:14 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix for the cone_pdb() function.

'pdb_file' does not exist.
........
r5412 | bugman | 2008-04-08 10:56:49 +0200 (Tue, 08 Apr 2008) | 5 lines

Another bug fix for the cone_pdb() function.

The pymol 'load' command requires the full PDB file name.
........
r5413 | bugman | 2008-04-08 10:57:23 +0200 (Tue, 08 Apr 2008) | 3 lines

Same bug fix as in r5411 but for tensor_pdb().
........
r5414 | bugman | 2008-04-08 10:57:35 +0200 (Tue, 08 Apr 2008) | 3 lines

Same bug fix as in r5412 but for tensor_pdb().
........
r5415 | bugman | 2008-04-08 11:28:51 +0200 (Tue, 08 Apr 2008) | 7 lines

Bug fix for the internal relax PDB data object.

The object structural_data inside the data object was a class variable, and hence each instantiation
of Internal_PDB was not resetting the object. If the object was used twice, then the data from the
first would remain.
........
r5416 | bugman | 2008-04-08 11:30:10 +0200 (Tue, 08 Apr 2008) | 5 lines

Shifted structural_data from a class varible to an instance varible in the API base class.

This uses the __init__() function now.
........
r5417 | bugman | 2008-04-08 11:42:44 +0200 (Tue, 08 Apr 2008) | 3 lines

Modified the cone_pdb() function to decrease the bond widths.
........
r5418 | bugman | 2008-04-08 11:43:18 +0200 (Tue, 08 Apr 2008) | 3 lines

Changed the colour of the Average CoM-pivot point vector.
........
r5419 | bugman | 2008-04-08 11:49:58 +0200 (Tue, 08 Apr 2008) | 3 lines

The average CoM-pivot point vector is now labelled in PyMOL.
........
r5420 | bugman | 2008-04-08 12:28:20 +0200 (Tue, 08 Apr 2008) | 3 lines

Changed the force flag of the structure.create_diff_tensor_pdb() user function to a bool.
........
r5421 | bugman | 2008-04-08 14:17:30 +0200 (Tue, 08 Apr 2008) | 5 lines

Created the structure.load_spins() user function.

The back end does not exist yet.
........
r5422 | bugman | 2008-04-08 14:19:27 +0200 (Tue, 08 Apr 2008) | 6 lines

Updated the structure.read_pdb() user function.

The arguments load_seq and spin_id have been removed as this functionality has been shifted into the
new user function structure.load_spins().
........
r5423 | bugman | 2008-04-08 14:24:13 +0200 (Tue, 08 Apr 2008) | 3 lines

Spun out the code for loading spins from read_pdb() to load_spins().
........
r5424 | bugman | 2008-04-08 14:26:31 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix for the spin_id arg test of the structure.read_pdb() user function.

This now belongs to the structure.load_spins() user function.
........
r5425 | bugman | 2008-04-08 14:28:23 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix for the structure.read_pdb() user function.

Bad set up of the intro string.
........
r5426 | bugman | 2008-04-08 14:29:25 +0200 (Tue, 08 Apr 2008) | 5 lines

Deleted the load_seq arg unit test of the structure.read_pdb() user function.

The argument no longer exists.
........
r5427 | bugman | 2008-04-08 14:32:38 +0200 (Tue, 08 Apr 2008) | 3 lines

Deletion of the sequence_exists() dummy function.
........
r5428 | bugman | 2008-04-08 14:34:13 +0200 (Tue, 08 Apr 2008) | 3 lines

Replaced the call to sequence_exists() by generic_fns.selection.exists_mol_res_spin_data().
........
r5429 | bugman | 2008-04-08 14:36:46 +0200 (Tue, 08 Apr 2008) | 7 lines

Removed the call to load_PDB_sequence().

The main part of load_PDB_sequence() will shifted to this load_spins() function. Those parts
specific to the Scientific Python PDB representation will be shifted to the atom_loop() method of
the new scientific python data object.
........
r5430 | bugman | 2008-04-08 14:39:03 +0200 (Tue, 08 Apr 2008) | 3 lines

Merged generic_fns.sequence.load_PDB_sequence() into generic_fns.structure.main.load_spins().
........
r5431 | bugman | 2008-04-08 15:10:12 +0200 (Tue, 08 Apr 2008) | 10 lines

Completion of generic_fns.structure.main.load_spins() and allowed atom selections in atom_loop().

The generic_fns.structure.main.load_spins() function now uses the structural data object API method
atom_loop() to generate the molecule, residue, and spin sequence in the relax data store. The
sequence generation code is mainly from the old load_PDB_sequence() function.

The Scientific Python data object atom_loop() generator method has been updated to allow for only
selected atoms to be yielded.
........
r5432 | bugman | 2008-04-08 15:11:29 +0200 (Tue, 08 Apr 2008) | 3 lines

Removed the import of the now non-existant generic_fns.sequence.load_PDB_sequence() function.
........
r5433 | bugman | 2008-04-08 15:17:47 +0200 (Tue, 08 Apr 2008) | 3 lines

Fixes and expansion of the system test for the loading of a sequence from a PDB file.
........
r5434 | bugman | 2008-04-08 15:21:22 +0200 (Tue, 08 Apr 2008) | 3 lines

Added the atom_id keyword to the Scientific Python PDB data object atom_loop() method.
........
r5435 | bugman | 2008-04-08 15:26:13 +0200 (Tue, 08 Apr 2008) | 5 lines

Buf fix for the system test for the loading of a sequence from a PDB file.

The N atom was incorrectly specified.
........
r5436 | bugman | 2008-04-08 15:28:07 +0200 (Tue, 08 Apr 2008) | 3 lines

Added some missing imports.
........
r5437 | bugman | 2008-04-08 15:39:08 +0200 (Tue, 08 Apr 2008) | 3 lines

Modified load_spins() to handle a single molecule with no name.
........
r5438 | bugman | 2008-04-08 15:41:43 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix in the load_spins() function.

Renamed incorrectly named variables.
........
r5439 | bugman | 2008-04-08 15:44:15 +0200 (Tue, 08 Apr 2008) | 5 lines

Buf fix for the system test for the loading of a sequence from a PDB file.

Only 12 residues exist in the PDB file.
........
r5440 | bugman | 2008-04-08 15:53:22 +0200 (Tue, 08 Apr 2008) | 3 lines

Expanded the data structure testing in the system test for loading of a sequence from a PDB file.
........
r5441 | bugman | 2008-04-08 15:54:12 +0200 (Tue, 08 Apr 2008) | 3 lines

Bug fix for the test_pdb() system test.
........
r5442 | bugman | 2008-04-08 16:15:58 +0200 (Tue, 08 Apr 2008) | 3 lines

Added an ID string to load_spins() to fix a bug in the return_residue() and return_spin() calls.
........
r5443 | bugman | 2008-04-08 17:19:34 +0200 (Tue, 08 Apr 2008) | 7 lines

Code shift.

Shifted the residue number check (cannot have 2 residues with the same number) and 1st element
replacement (if that ResidueContainer is empty) code from generic_fns.residue.create() to the relax
data storage object (the ResidueContainer.add_item() method).
........
r5444 | bugman | 2008-04-08 17:38:00 +0200 (Tue, 08 Apr 2008) | 6 lines

Code shift, similar to r5443.

Shifted the 1st element replacement code (if the MolecularContainer is empty) from
generic_fns.molecule.create() to the relax data storage object MoleculeContainer.add_item() method.
........
r5445 | bugman | 2008-04-08 17:41:04 +0200 (Tue, 08 Apr 2008) | 7 lines

Code shift, similar to that of r5443.

Shifted the spin number check (cannot have 2 spin with the same number) and 1st element replacement
(if that SpinContainer is empty) code from generic_fns.spin.create() to the relax data storage
object SpinContainer.add_item() method.
........
r5446 | bugman | 2008-04-08 17:42:18 +0200 (Tue, 08 Apr 2008) | 3 lines

Bug fix for the SpinContainer.add_item() method, the select flag is now set when replacing element 0.
........
r5447 | bugman | 2008-04-08 17:43:07 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix for the ResidueContainer.add_item() method.

The select flag is now set when replacing element 0.
........
r5448 | bugman | 2008-04-08 17:44:07 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix for the MoleculeContainer.add_item() method.

The select flag is now set when replacing element 0.
........
r5449 | bugman | 2008-04-08 17:48:51 +0200 (Tue, 08 Apr 2008) | 3 lines

Bug fix for the system test of loading the protein backbone amide N spins from a loaded PDB file.
........
r5450 | bugman | 2008-04-08 17:52:50 +0200 (Tue, 08 Apr 2008) | 5 lines

Added the system test test_load_protein_gly_N_spins_from_pdb().

This tests the loading the glycine backbone amide N spins from a loaded protein PDB file.
........
r5451 | bugman | 2008-04-08 17:56:35 +0200 (Tue, 08 Apr 2008) | 5 lines

Created the test_load_protein_gly_N_Ca_spins_from_pdb() system test.

This tests the loading of glycine backbone amide N and Ca spins from a loaded protein PDB file.
........
r5452 | bugman | 2008-04-08 18:04:19 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix in the Scientific Python PDB object atom_loop() generator method.

The atom name is now returned rather than the element type!
........
r5453 | bugman | 2008-04-08 18:12:24 +0200 (Tue, 08 Apr 2008) | 6 lines

Created the test_load_protein_asp_atoms_from_pdb() system test.

This tests the loading of all aspartic acid atoms from the single residue in a loaded protein PDB
file.
........
r5454 | bugman | 2008-04-08 18:15:29 +0200 (Tue, 08 Apr 2008) | 3 lines

The position vector is added to the SpinContainer in the load_spins() function.
........
r5455 | bugman | 2008-04-08 18:16:05 +0200 (Tue, 08 Apr 2008) | 5 lines

Bug fix in the test_opendx_theta_phi_da() system test.

The load_seq arg to the structure.read_pdb() user function no longer exists.
........
r5456 | bugman | 2008-04-08 18:20:00 +0200 (Tue, 08 Apr 2008) | 3 lines

Updated the noe.py sample script to use the new structure.load_spins() user function.
........
r5457 | bugman | 2008-04-08 18:20:33 +0200 (Tue, 08 Apr 2008) | 3 lines

Removed all the run args to the user functions in the noe.py sample script.
........

Bug fix for the test_return_spin() unit test.

selection.return_spin() should return nothing if the SpinContainer is empty.

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.

Bug fix in the test_spin_loop_no_selection() unit test.