Blocked revisions 5400-5457 via svnmerge
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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.
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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!
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r5402 | bugman | 2008-04-08 10:27:16 +0200 (Tue, 08 Apr 2008) | 3 lines
Updated the command() function to the new relax design.
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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.
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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.
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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.
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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.
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r5407 | bugman | 2008-04-08 10:47:51 +0200 (Tue, 08 Apr 2008) | 3 lines
Updated the write() function to the new relax design.
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r5408 | bugman | 2008-04-08 10:48:20 +0200 (Tue, 08 Apr 2008) | 3 lines
Arg to keyword epydoc fix.
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r5409 | bugman | 2008-04-08 10:49:24 +0200 (Tue, 08 Apr 2008) | 3 lines
Added the return details to the create_macro() docstring.
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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.
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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.
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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.
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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().
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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().
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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().
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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().
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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.
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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.
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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.
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r5427 | bugman | 2008-04-08 14:32:38 +0200 (Tue, 08 Apr 2008) | 3 lines
Deletion of the sequence_exists() dummy function.
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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().
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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.
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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().
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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.
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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.
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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.
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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.
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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.
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r5436 | bugman | 2008-04-08 15:28:07 +0200 (Tue, 08 Apr 2008) | 3 lines
Added some missing imports.
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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.
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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.
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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.
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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.
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r5441 | bugman | 2008-04-08 15:54:12 +0200 (Tue, 08 Apr 2008) | 3 lines
Bug fix for the test_pdb() system test.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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!
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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.
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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.
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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.
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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.
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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.
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