Author: bugman Date: Wed Apr 9 15:48:38 2008 New Revision: 5502 URL: http://svn.gna.org/viewcvs/relax?rev=5502&view=rev Log: 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. ........ Modified: 1.2/ (props changed) Propchange: 1.2/ ------------------------------------------------------------------------------ Binary property 'svnmerge-blocked' - no diff available.