svn+ssh://semor@.../svn/relax/1.3
................
r8470 | bugman | 2009-01-15 07:52:12 -0500 (Thu, 15 Jan 2009) | 6 lines
Modified parse_token() to allow for '-' characters in molecule names (derived from file names, etc.)
Instead of throwing a RelaxError if an invalid range is found, it is assumed that the '-' character
does not signify a range and is treated as a string character which is part of the token.
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r8471 | bugman | 2009-01-15 08:01:40 -0500 (Thu, 15 Jan 2009) | 6 lines
Deletion of the test_parse_token_range_failx() unit test.
parse_token() no longer raises RelaxErrors with invalid range tokens (as they are assumed to be
standard string characters instead).
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r8492 | semor | 2009-01-15 14:10:18 -0500 (Thu, 15 Jan 2009) | 3 lines
Corrected mistakes in English.
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r8501 | bugman | 2009-01-17 06:36:47 -0500 (Sat, 17 Jan 2009) | 3 lines
Updated the relax intro copyright notice for the relax development team to 2009!
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r8633 | bugman | 2009-01-23 10:52:20 -0500 (Fri, 23 Jan 2009) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-8213" from
svn+ssh://bugman@.../svn/relax/branches/multi_structure
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r8634 | bugman | 2009-01-23 11:06:01 -0500 (Fri, 23 Jan 2009) | 962 lines
Merged revisions 8214,8217-8223,8333-8334,8336,8341,8348-8350,8400-8414,8416,8419,8421-8425,8431-8432,8434,8438-8469,8475-8489,8493-8500,8502-8541,8547-8562,8574-8580,8584-8590,8593-8632 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/multi_structure
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r8214 | bugman | 2008-12-12 17:51:36 +0100 (Fri, 12 Dec 2008) | 3 lines
Redesign of the args for the structure.read_pdb() user function.
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r8217 | bugman | 2008-12-18 13:42:20 +0100 (Thu, 18 Dec 2008) | 3 lines
Created the new RelaxNoneStrListStrError error class and fixed the RelaxNoneStrListError print out.
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r8218 | bugman | 2008-12-18 13:43:09 +0100 (Thu, 18 Dec 2008) | 3 lines
Removed the model arg unit test of structure.read_pdb() and added 4 new tests.
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r8219 | bugman | 2008-12-18 15:23:31 +0100 (Thu, 18 Dec 2008) | 3 lines
Fixes for 4 of the structure.read_pdb() user function arg unit tests.
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r8220 | bugman | 2008-12-18 15:24:05 +0100 (Thu, 18 Dec 2008) | 3 lines
Redesigned the structure.read_pdb() arguments and docstring.
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r8221 | bugman | 2008-12-18 15:41:53 +0100 (Thu, 18 Dec 2008) | 3 lines
Passed the new args into generic_fns.structure.main.read_pdb().
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r8222 | bugman | 2008-12-18 17:03:27 +0100 (Thu, 18 Dec 2008) | 3 lines
Fixes for 3 model-free unit tests using generic_fns.structure.main.read_pdb().
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r8223 | bugman | 2008-12-18 17:16:03 +0100 (Thu, 18 Dec 2008) | 3 lines
Add structural object load_pdb() methods now take the read_mol, set_mol_name, read_model, set_model_num args.
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r8333 | bugman | 2009-01-08 15:57:58 +0100 (Thu, 08 Jan 2009) | 3 lines
Created the ModelList data structure for storing multiple models of the same molecule.
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r8334 | bugman | 2009-01-08 16:05:39 +0100 (Thu, 08 Jan 2009) | 3 lines
Created the ModelContainer data structure for holding all structures of the model.
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r8336 | bugman | 2009-01-08 16:30:24 +0100 (Thu, 08 Jan 2009) | 3 lines
Created the StructList data structure for holding different structures.
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r8341 | bugman | 2009-01-08 18:57:32 +0100 (Thu, 08 Jan 2009) | 3 lines
Removal of the __init__() methods so that the model-structure data structure is not automatically created.
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r8348 | bugman | 2009-01-09 10:23:51 +0100 (Fri, 09 Jan 2009) | 3 lines
Started to redesign the internal structural object load_pdb() method.
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r8349 | bugman | 2009-01-09 10:35:50 +0100 (Fri, 09 Jan 2009) | 5 lines
Wrote the internal structural object __parse_structs() method.
This is used to loop over the structures within a model or the whole PDB if no models exist.
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r8350 | bugman | 2009-01-09 17:55:39 +0100 (Fri, 09 Jan 2009) | 3 lines
Many fixes and much new code for the new structural container design.
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r8400 | bugman | 2009-01-12 10:18:13 +0100 (Mon, 12 Jan 2009) | 3 lines
Removed the struct_index arg from the base api structural object.
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r8401 | bugman | 2009-01-12 10:19:02 +0100 (Mon, 12 Jan 2009) | 3 lines
Removed the struct_index arg from the Scientific python structral object load_pdb() method.
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r8402 | bugman | 2009-01-12 10:26:56 +0100 (Mon, 12 Jan 2009) | 3 lines
Large renaming of 'structure' to 'molecule' for the structral objects.
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r8403 | bugman | 2009-01-12 10:31:06 +0100 (Mon, 12 Jan 2009) | 3 lines
Bug fix for the load_pdb() method call to MolList.add_item().
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r8404 | bugman | 2009-01-12 14:10:36 +0100 (Mon, 12 Jan 2009) | 3 lines
Passed the model_index and mol_index into __fill_object_from_pdb().
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r8405 | bugman | 2009-01-12 14:11:32 +0100 (Mon, 12 Jan 2009) | 3 lines
Renamed Molecule_container to MolContainer.
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r8406 | bugman | 2009-01-12 14:13:02 +0100 (Mon, 12 Jan 2009) | 3 lines
Shifted __fill_object_from_pdb() from the Internal class to MolContainer.
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r8407 | bugman | 2009-01-12 14:14:46 +0100 (Mon, 12 Jan 2009) | 3 lines
Shifted atom_add() and atom_connect() from the Internal class to the MolContainer.
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r8408 | bugman | 2009-01-12 14:15:39 +0100 (Mon, 12 Jan 2009) | 3 lines
Removed atom_add() and atom_connect() from the base API structure.
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r8409 | bugman | 2009-01-12 14:18:12 +0100 (Mon, 12 Jan 2009) | 3 lines
Renamed __fill_object_from_pdb() to fill_object_from_pdb()
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r8410 | bugman | 2009-01-12 14:19:16 +0100 (Mon, 12 Jan 2009) | 3 lines
Shifted __parse_pdb_record() from the Internal class to the MolContainer.
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r8411 | bugman | 2009-01-12 14:21:18 +0100 (Mon, 12 Jan 2009) | 3 lines
Shifted __atom_index() from the Internal class to the MolContainer.
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r8412 | bugman | 2009-01-12 14:23:39 +0100 (Mon, 12 Jan 2009) | 3 lines
Modified the atom_add() and atom_connect() methods to work within the MolContainer.
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r8413 | bugman | 2009-01-12 14:24:35 +0100 (Mon, 12 Jan 2009) | 3 lines
Modified __atom_index() to work within the MolContainer.
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r8414 | bugman | 2009-01-12 14:27:07 +0100 (Mon, 12 Jan 2009) | 3 lines
When no structure ID is given, the '.pdb' is now stripped from the file name before creating the ID.
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r8416 | bugman | 2009-01-12 14:27:42 +0100 (Mon, 12 Jan 2009) | 3 lines
Some copyright updates.
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r8419 | bugman | 2009-01-12 15:26:13 +0100 (Mon, 12 Jan 2009) | 3 lines
Converted the test_load_pdb() unit test to the new structural data design.
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r8421 | bugman | 2009-01-12 16:35:59 +0100 (Mon, 12 Jan 2009) | 3 lines
Modified the atom_loop() method to handle the new data structure design.
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r8422 | bugman | 2009-01-12 16:37:03 +0100 (Mon, 12 Jan 2009) | 3 lines
Fix for the test_atom_loop_spin_selection2() unit test for the molecule naming.
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r8423 | bugman | 2009-01-12 16:39:13 +0100 (Mon, 12 Jan 2009) | 3 lines
Fix for the test___parse_pdb_record() unit test. The method is in MolContainer now.
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r8424 | bugman | 2009-01-12 16:44:55 +0100 (Mon, 12 Jan 2009) | 3 lines
Fix for the test_duplicate_data_fail1() unit test for the new structural data structures.
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r8425 | bugman | 2009-01-12 18:57:10 +0100 (Mon, 12 Jan 2009) | 3 lines
Created a new private method, __compare_objects() to check if 2 objects are the same.
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r8431 | bugman | 2009-01-13 16:12:27 +0100 (Tue, 13 Jan 2009) | 3 lines
Fixes for the duplicate_data() method.
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r8432 | bugman | 2009-01-13 16:12:39 +0100 (Tue, 13 Jan 2009) | 3 lines
Fixes for the __compare_objects() method.
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r8434 | bugman | 2009-01-13 18:03:18 +0100 (Tue, 13 Jan 2009) | 5 lines
Redesigned the Scientific python structural object load_pdb() method.
The structural data structure is not yet created.
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r8438 | bugman | 2009-01-14 14:07:39 +0100 (Wed, 14 Jan 2009) | 7 lines
Created a new structural API method, pack_structs().
This has the fun job of mapping the original models and molecules of the PDB (or which ever other
file format is read in the future) into the models and molecules stored within relax. I.e.
molecules can be converted to models and vice versa.
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r8439 | bugman | 2009-01-14 14:48:19 +0100 (Wed, 14 Jan 2009) | 3 lines
Added a print out for the loading of structural data.
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r8440 | bugman | 2009-01-14 14:50:33 +0100 (Wed, 14 Jan 2009) | 7 lines
Deletion of commented out code.
This includes the pointers to other structural objects. These pointers, rather than using new
structures could be dangerous additional data is added to the object. Therefore this code must be
eliminated.
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r8441 | bugman | 2009-01-14 17:12:39 +0100 (Wed, 14 Jan 2009) | 3 lines
The internal structural object load_pdb() method now uses the pack_structs() base class method.
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r8442 | bugman | 2009-01-14 17:23:18 +0100 (Wed, 14 Jan 2009) | 3 lines
Bug fixes for the pack_structs() method.
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r8443 | bugman | 2009-01-14 17:27:24 +0100 (Wed, 14 Jan 2009) | 3 lines
Bug fixes for the load_pdb() method.
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r8444 | bugman | 2009-01-14 17:43:33 +0100 (Wed, 14 Jan 2009) | 3 lines
Another bug fix for the pack_structs() method, the MolList.add_item() was incorrectly being called.
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r8445 | bugman | 2009-01-14 17:44:07 +0100 (Wed, 14 Jan 2009) | 3 lines
Bug fix for the load_pdb() method in the MolContainer setup.
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r8446 | bugman | 2009-01-14 17:56:43 +0100 (Wed, 14 Jan 2009) | 3 lines
Removed a debugging print out.
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r8447 | bugman | 2009-01-14 17:58:37 +0100 (Wed, 14 Jan 2009) | 3 lines
Fixed the default value for the verbosity keyword to load_pdb().
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r8448 | bugman | 2009-01-14 18:55:55 +0100 (Wed, 14 Jan 2009) | 3 lines
The Scientific python structural object load_pdb() method now uses pack_structs().
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r8449 | bugman | 2009-01-15 10:01:00 +0100 (Thu, 15 Jan 2009) | 6 lines
A number of bug fixes for the Scientific python structural object load_pdb() method.
The molecules are now also taken from the peptide_chains and nucleotide_chains structures, as the
molecules dictionary doesn't contain proteins or RNA!
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r8450 | bugman | 2009-01-15 10:01:38 +0100 (Thu, 15 Jan 2009) | 3 lines
Removed some old, commented out code (and an old print out).
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r8451 | bugman | 2009-01-15 10:02:41 +0100 (Thu, 15 Jan 2009) | 3 lines
Bug fix for the set up of orig_mol_num.
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r8452 | bugman | 2009-01-15 10:17:48 +0100 (Thu, 15 Jan 2009) | 5 lines
The load_pdb() method now creates the set_mol_name structure.
Well, a new method is required in the API base class.
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r8453 | bugman | 2009-01-15 10:19:11 +0100 (Thu, 15 Jan 2009) | 3 lines
Created the API base method target_mol_name() for generating the list of molecule names.
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r8454 | bugman | 2009-01-15 10:20:21 +0100 (Thu, 15 Jan 2009) | 3 lines
Compacted some comments.
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r8455 | bugman | 2009-01-15 10:25:00 +0100 (Thu, 15 Jan 2009) | 3 lines
The correct target molecule name structure is now passed into pack_structs() from load_pdb().
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r8456 | bugman | 2009-01-15 10:27:18 +0100 (Thu, 15 Jan 2009) | 3 lines
Added checks for the presence of the molecular data structures in the Scientific python structure.
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r8457 | bugman | 2009-01-15 11:27:25 +0100 (Thu, 15 Jan 2009) | 11 lines
Massive redesign of the Scientific Python structural object atom_loop() method.
The new structural data data structure is now handled, and a number of changes have occurred to the
class methods:
__molecule_loop() has been deleted.
__residue_loop() has been heavily modified.
The method __ave_atom_pos() has been added to allow the ave arg to atom_loop() to be handled.
The molecule type is stored in the molecule containers by load_pdb().
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r8458 | bugman | 2009-01-15 11:28:15 +0100 (Thu, 15 Jan 2009) | 5 lines
Bug fix for the MolList.add_item() method.
The molecule name is now stored within the molecule containers.
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r8459 | bugman | 2009-01-15 11:32:19 +0100 (Thu, 15 Jan 2009) | 3 lines
Fixes for the Scientific python structural object __residue_loop() unit tests.
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r8460 | bugman | 2009-01-15 11:35:48 +0100 (Thu, 15 Jan 2009) | 5 lines
Deleted all unit tests for the ScientificPython structural object __molecule_loop() method.
This method no longer exists!
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r8461 | bugman | 2009-01-15 11:42:48 +0100 (Thu, 15 Jan 2009) | 5 lines
Simplification of the internal structural object atom_loop() method.
There is now only one block of code for the atom looping for the two options of the ave argument.
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r8462 | bugman | 2009-01-15 11:45:01 +0100 (Thu, 15 Jan 2009) | 3 lines
Fix for the test___residue_loop() unit test.
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r8463 | bugman | 2009-01-15 11:50:27 +0100 (Thu, 15 Jan 2009) | 3 lines
Fixes for the test_load_pdb() unit test.
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r8464 | bugman | 2009-01-15 11:53:23 +0100 (Thu, 15 Jan 2009) | 3 lines
Fix for the test_atom_loop_spin_selection2() unit test, the molecule now has a name!
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r8465 | bugman | 2009-01-15 11:53:55 +0100 (Thu, 15 Jan 2009) | 3 lines
Fix for the test_load_pdb() unit test, in the check of the molecule name.
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r8466 | bugman | 2009-01-15 13:23:58 +0100 (Thu, 15 Jan 2009) | 6 lines
Reverted r8458. The molecule name is only used as a check, it is stored by other parts of the code!
The command used was:
svn merge -r8458:8457 .
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r8467 | bugman | 2009-01-15 13:25:01 +0100 (Thu, 15 Jan 2009) | 3 lines
Fix for the 2 test_load_pdb() unit tests. The mol name is in the mol_name variable.
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r8468 | bugman | 2009-01-15 13:42:44 +0100 (Thu, 15 Jan 2009) | 6 lines
Redesign of the set up of the molecule container data structures.
The file info is now set by the pack_structs() base API method rather than the MolContainer internal
object or the ScientificPython code.
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r8469 | bugman | 2009-01-15 13:44:42 +0100 (Thu, 15 Jan 2009) | 5 lines
Fix for the test___residue_loop_selection() unit test.
The molecule name is now different!
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r8475 | bugman | 2009-01-15 16:57:25 +0100 (Thu, 15 Jan 2009) | 3 lines
Fixes for all the test_calc_unit_vectorsx() system tests.
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r8476 | bugman | 2009-01-15 17:09:10 +0100 (Thu, 15 Jan 2009) | 3 lines
Bug fix for an infinite loop in the structure loading.
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r8477 | bugman | 2009-01-15 17:09:45 +0100 (Thu, 15 Jan 2009) | 3 lines
Deletion of the API num_structures() method, and creation of num_models() and num_molecules().
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r8478 | bugman | 2009-01-15 17:12:46 +0100 (Thu, 15 Jan 2009) | 3 lines
Created the validate() method.
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r8479 | bugman | 2009-01-15 17:14:52 +0100 (Thu, 15 Jan 2009) | 3 lines
Modified the load_spins() function to use the new num_models() and num_molecules() methods.
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r8480 | bugman | 2009-01-15 17:15:59 +0100 (Thu, 15 Jan 2009) | 3 lines
Bug fix for the new validate() method.
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r8481 | bugman | 2009-01-15 17:17:55 +0100 (Thu, 15 Jan 2009) | 3 lines
The write_pdb() method now validates the structural data with validate() before doing anything.
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r8482 | bugman | 2009-01-15 17:19:30 +0100 (Thu, 15 Jan 2009) | 5 lines
Bug fix for the test_load_spins_from_small_molecule() system test.
The molecule name is now 'gromacs_phthalic_acid_mol1'.
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r8483 | bugman | 2009-01-15 17:37:00 +0100 (Thu, 15 Jan 2009) | 5 lines
Bug fix for the load_pdb() method.
Molecules other than proteins and RNA are now correctly stored and their type set in mol_type.
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r8484 | bugman | 2009-01-15 18:03:36 +0100 (Thu, 15 Jan 2009) | 5 lines
Bug fixes for the non-protein and non-RNA Scientific python molecules.
A new MolContainer list-type class has been added to store the molecules.
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r8485 | bugman | 2009-01-15 18:30:08 +0100 (Thu, 15 Jan 2009) | 3 lines
The internal PDB reader now has rudimentary support for element determination if that column is missing.
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r8486 | bugman | 2009-01-15 18:41:28 +0100 (Thu, 15 Jan 2009) | 3 lines
Added an amino acid translation table for determining elements from PDB atom names.
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r8487 | bugman | 2009-01-15 18:42:02 +0100 (Thu, 15 Jan 2009) | 3 lines
Shifted __det_pdb_element() to the correct location.
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r8488 | bugman | 2009-01-15 18:46:43 +0100 (Thu, 15 Jan 2009) | 3 lines
Added 'SG' to the translation table.
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r8489 | bugman | 2009-01-15 18:47:49 +0100 (Thu, 15 Jan 2009) | 3 lines
The "'" character is stripped so __det_pdb_element() better handles RNA.
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r8493 | bugman | 2009-01-16 11:26:44 +0100 (Fri, 16 Jan 2009) | 5 lines
Modified the prompt interface of the structure.vectors() user function.
The struct_index arg is dead! Long live the model arg!
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r8494 | bugman | 2009-01-16 13:43:37 +0100 (Fri, 16 Jan 2009) | 3 lines
Support for models vs. molecules and elimination of struct_index in vectors().
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r8495 | bugman | 2009-01-16 13:44:47 +0100 (Fri, 16 Jan 2009) | 3 lines
Docstring fixes for vectors().
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r8496 | bugman | 2009-01-16 13:48:17 +0100 (Fri, 16 Jan 2009) | 3 lines
Added a verbosity flag to parse_token() so that print outs are suppressed by default.
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r8497 | bugman | 2009-01-16 13:53:24 +0100 (Fri, 16 Jan 2009) | 5 lines
Fix for the struct_index arg unit test of structure.vectors().
The arg is now called 'model'.
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r8498 | bugman | 2009-01-16 16:57:01 +0100 (Fri, 16 Jan 2009) | 3 lines
Support for models vs. molecules and the elimination of struct_index in bond_vectors().
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r8499 | bugman | 2009-01-16 17:49:01 +0100 (Fri, 16 Jan 2009) | 6 lines
Started to redesign add_struct() to remove the struct_index arg and convert to the new model design.
The API base class function get_model() has been added to return or create the desired model. The
add_struct() method has been renamed to add_molecule(). Much work remains to be done.
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r8500 | bugman | 2009-01-16 17:49:22 +0100 (Fri, 16 Jan 2009) | 3 lines
Removed some redundant code.
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r8502 | bugman | 2009-01-19 10:54:09 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fix for one of the checks in pack_structs().
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r8503 | bugman | 2009-01-19 11:00:55 +0100 (Mon, 19 Jan 2009) | 3 lines
Redesigned add_molecule(). The method now is one line long!!!
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r8504 | bugman | 2009-01-19 11:04:57 +0100 (Mon, 19 Jan 2009) | 3 lines
Deleted the Scientific python structural object add_struct() method.
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r8505 | bugman | 2009-01-19 11:11:16 +0100 (Mon, 19 Jan 2009) | 3 lines
Modified the bond_vectors() method for the new structural object design.
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r8506 | bugman | 2009-01-19 11:11:29 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixed the API bond_vectors() method.
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r8507 | bugman | 2009-01-19 11:15:15 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixed a call to bond_vectors().
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r8508 | bugman | 2009-01-19 11:18:00 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fixes for bond_vectors().
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r8509 | bugman | 2009-01-19 11:21:07 +0100 (Mon, 19 Jan 2009) | 3 lines
More bug fixes for bond_vectors(). The index i no longer exists!
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r8510 | bugman | 2009-01-19 11:24:12 +0100 (Mon, 19 Jan 2009) | 3 lines
Modified __bonded_atom() and __find_bonded_atoms() for the new structural object design.
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r8511 | bugman | 2009-01-19 11:27:36 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fix for bond_vectors(), the molecule name was not correctly accessed.
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r8512 | bugman | 2009-01-19 11:36:33 +0100 (Mon, 19 Jan 2009) | 3 lines
Removed all dependence on the deleted __molecule_loop() method.
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r8513 | bugman | 2009-01-19 11:37:28 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixed the calls to __residue_loop().
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r8514 | bugman | 2009-01-19 11:39:32 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixes for the unpacking of the __residue_loop() results.
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r8515 | bugman | 2009-01-19 11:50:59 +0100 (Mon, 19 Jan 2009) | 3 lines
Added the is_empty() method.
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r8516 | bugman | 2009-01-19 11:51:50 +0100 (Mon, 19 Jan 2009) | 6 lines
Fix for the MolList.is_empty() method.
If the molecule container method is_empty() is missing, then the container is assumed to not be
empty (i.e. the case for the Scientific python objects).
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r8517 | bugman | 2009-01-19 11:52:37 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fix for the MolList.add_item() method.
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r8518 | bugman | 2009-01-19 13:21:04 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fix for the pack_structs() method. The wrong index was being used!
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r8519 | bugman | 2009-01-19 13:24:24 +0100 (Mon, 19 Jan 2009) | 3 lines
Bug fixes for the calls to __atom_index().
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r8520 | bugman | 2009-01-19 13:32:25 +0100 (Mon, 19 Jan 2009) | 3 lines
Clean up of the Base_struct_API.__init__() method.
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r8521 | bugman | 2009-01-19 13:38:42 +0100 (Mon, 19 Jan 2009) | 5 lines
Fixes for the Base_struct_API.to_xml() method.
There are no structures to pack up, so only call the ModelList.to_xml() method.
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r8522 | bugman | 2009-01-19 13:40:26 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the MolList.to_xml() method.
The MolContainer.to_xml() method is now properly called.
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r8523 | bugman | 2009-01-19 13:48:09 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixes for the MolContainer.is_empty() method.
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r8524 | bugman | 2009-01-19 13:49:00 +0100 (Mon, 19 Jan 2009) | 3 lines
Missing import.
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r8525 | bugman | 2009-01-19 14:04:03 +0100 (Mon, 19 Jan 2009) | 3 lines
Modified the Base_struct_API.to_xml() method to only call ModelList.to_xml() if structural data exists.
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r8526 | bugman | 2009-01-19 14:08:52 +0100 (Mon, 19 Jan 2009) | 5 lines
Bug fix for the Base_struct_API.to_xml() method.
The model XML elements are now children of the structure XML element.
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r8527 | bugman | 2009-01-19 14:31:07 +0100 (Mon, 19 Jan 2009) | 6 lines
Bug fix for the MolList.to_xml() method.
The molecule container data was been added by this method and then the MolContainer.to_xml() method
a second time!
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r8528 | bugman | 2009-01-19 14:33:03 +0100 (Mon, 19 Jan 2009) | 6 lines
Fixes for the Scientific python MolContainer usage.
Now all molecules are stored in the MolContainer object to allow for the to_xml() method, which has
now been added. The MolContainer is no longer a list type. These changes will break things!
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r8529 | bugman | 2009-01-19 14:34:00 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the load_pdb() method.
The 'other' molecule types are now added to a standard list in MolContainer.data.
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r8530 | bugman | 2009-01-19 14:37:21 +0100 (Mon, 19 Jan 2009) | 3 lines
Regenerated all the results files containing structural info.
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r8531 | bugman | 2009-01-19 14:39:52 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixes for __residue_loop(). The Scientific python data structure is now in MolContainer.data.
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r8532 | bugman | 2009-01-19 14:48:07 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixes for __ave_atom_pos(). The Scientific python data structure is now in MolContainer.data.
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r8533 | bugman | 2009-01-19 14:49:23 +0100 (Mon, 19 Jan 2009) | 3 lines
Another fix for __ave_atom_pos(), related to the last!
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r8534 | bugman | 2009-01-19 15:05:32 +0100 (Mon, 19 Jan 2009) | 5 lines
Renamed the MolContainer 'mol' element to 'mol_cont'.
This prevents a clash with the pipe container 'mol' structure.
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r8535 | bugman | 2009-01-19 15:06:40 +0100 (Mon, 19 Jan 2009) | 3 lines
Regenerated all the results files containing structural info.
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r8536 | bugman | 2009-01-19 15:45:03 +0100 (Mon, 19 Jan 2009) | 3 lines
Fixes for the Base_struct_API.from_xml() method.
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r8537 | bugman | 2009-01-19 15:45:26 +0100 (Mon, 19 Jan 2009) | 3 lines
Added a missing import.
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r8538 | bugman | 2009-01-19 15:47:27 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the ModelList.is_empty() method.
Now if no ModelContainers are in the list, the method returns True.
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r8539 | bugman | 2009-01-19 15:49:58 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the ModelList.add_item() method.
If no ModelContainers are present, then don't try to change the model number!
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r8540 | bugman | 2009-01-19 15:51:07 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the MolList.is_empty() method.
Now if no MolContainers are in the list, the method returns True.
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r8541 | bugman | 2009-01-19 15:52:16 +0100 (Mon, 19 Jan 2009) | 5 lines
Fix for the MolList.add_item() method.
If no MolContainers are present, then don't try to change the molecule name!
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r8547 | bugman | 2009-01-20 16:21:00 +0100 (Tue, 20 Jan 2009) | 5 lines
Some fixes for the test_load_scientific_results() system test.
This is for the new structural data data structure design.
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r8548 | bugman | 2009-01-20 16:24:06 +0100 (Tue, 20 Jan 2009) | 6 lines
Some fixes for the test_load_internal_results() system test.
This is for the new structural data data structure design, and matches r8547.
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r8549 | bugman | 2009-01-20 16:27:29 +0100 (Tue, 20 Jan 2009) | 3 lines
Fixes for the call to the structure.read_pdb() user function.
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r8550 | bugman | 2009-01-20 16:30:23 +0100 (Tue, 20 Jan 2009) | 3 lines
Fixes for all these system tests as the molecule name is not 'Ap4Aase_res1-12_mol1'.
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r8551 | bugman | 2009-01-20 16:36:43 +0100 (Tue, 20 Jan 2009) | 3 lines
Fixes for the create_run() and execute() functions for the new structural data design.
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r8552 | bugman | 2009-01-20 16:38:58 +0100 (Tue, 20 Jan 2009) | 3 lines
Missing import.
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r8553 | bugman | 2009-01-20 16:57:22 +0100 (Tue, 20 Jan 2009) | 3 lines
Bug fix for the MolList.__repr__() method, the molecule name is in 'mol_name'.
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r8554 | bugman | 2009-01-20 17:02:00 +0100 (Tue, 20 Jan 2009) | 5 lines
A fix for the __parse_mols() method.
The 'END' PDB record is no longer identified as a molecule!
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r8555 | bugman | 2009-01-21 17:26:00 +0100 (Wed, 21 Jan 2009) | 3 lines
Indentation fix.
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r8556 | bugman | 2009-01-21 17:53:00 +0100 (Wed, 21 Jan 2009) | 6 lines
Found and fixed the biggest pain in the ass bug ever (after 2 days of debugging)!
The model-free model index 'model_index' which was being passed into duplicate_data() was being
overwritten by the loop over structural models, which was also using 'model_index'!!!
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r8557 | bugman | 2009-01-21 17:54:07 +0100 (Wed, 21 Jan 2009) | 3 lines
Fix for a call to structure.read_pdb() in the system test script.
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r8558 | bugman | 2009-01-21 18:08:35 +0100 (Wed, 21 Jan 2009) | 6 lines
Fixes all over for the angles system test.
The sequence is no longer loaded as it doesn't have the molecule name and clashes with the
structure.load_spins() call. Hence the spin specific checks have been updated.
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r8559 | bugman | 2009-01-21 18:11:38 +0100 (Wed, 21 Jan 2009) | 3 lines
Fixes for the molecule name variable in pack_structs().
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r8560 | bugman | 2009-01-21 18:12:03 +0100 (Wed, 21 Jan 2009) | 3 lines
Fixes for the molecule name variable in MolList.add_item().
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r8561 | bugman | 2009-01-21 18:15:25 +0100 (Wed, 21 Jan 2009) | 3 lines
Fix for a call to the structure.read_pdb() user function.
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r8562 | bugman | 2009-01-21 18:20:03 +0100 (Wed, 21 Jan 2009) | 3 lines
Fix for calls to structure.read_pdb() in the setUp() method.
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r8574 | bugman | 2009-01-22 10:26:14 +0100 (Thu, 22 Jan 2009) | 5 lines
Fixes for the lactose N-state model system test.
The structures from different PDB files are now being sent to different models.
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r8575 | bugman | 2009-01-22 10:28:55 +0100 (Thu, 22 Jan 2009) | 3 lines
Bug fix for __update_model(). cdp.structure.num_structures() no longer exists.
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r8576 | bugman | 2009-01-22 10:44:36 +0100 (Thu, 22 Jan 2009) | 3 lines
Expanded the structural data validate() method to check molecule names.
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r8577 | bugman | 2009-01-22 10:52:56 +0100 (Thu, 22 Jan 2009) | 6 lines
Fix for the call to structure.read_pdb() in the lactose N-state model system test.
The molecule name must be explicitly set so that the same molecule in different models has the same
name.
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r8578 | bugman | 2009-01-22 10:54:23 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the calls to structure.load_spins().
The combine_models flag has to be set to False, to prevent the atom position from being averaged.
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r8579 | bugman | 2009-01-22 11:22:53 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the call to generic_fns.structure.main.read_pdb() in __load_structure().
This fixes the loading of relax 1.2 results files.
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r8580 | bugman | 2009-01-22 11:28:02 +0100 (Thu, 22 Jan 2009) | 3 lines
Fixes for the system test catching Tyler Reddy's bug report at https://gna.org/bugs/?12487.
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r8584 | bugman | 2009-01-22 14:18:51 +0100 (Thu, 22 Jan 2009) | 3 lines
Fix for a RelaxError print out.
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r8585 | bugman | 2009-01-22 14:36:04 +0100 (Thu, 22 Jan 2009) | 6 lines
Modified load_spins() to handle spin systems with the molecule unnamed.
If loading spins from a PDB file is used but the sequence already loaded (without the molecule ID
string), the molecule ID is now set instead of a new molecule container created.
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r8586 | bugman | 2009-01-22 14:47:36 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for create_vector_dist().
The presence of structures now is tested using cdp.structure.num_models().
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r8587 | bugman | 2009-01-22 14:54:21 +0100 (Thu, 22 Jan 2009) | 3 lines
Docstring fix for pack_structs().
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r8588 | bugman | 2009-01-22 14:56:15 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the Internal.add_molecule() method.
The orig_mol_num structure must be a list!
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r8589 | bugman | 2009-01-22 14:59:41 +0100 (Thu, 22 Jan 2009) | 5 lines
Fixes for create_vector_dist() for the new structural data design.
The atoms are added to the single molecule, and the struct_index has been eliminated.
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r8590 | bugman | 2009-01-22 15:01:11 +0100 (Thu, 22 Jan 2009) | 3 lines
Copyright updates.
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r8593 | bugman | 2009-01-22 15:45:02 +0100 (Thu, 22 Jan 2009) | 5 lines
A large number of fixes for the write_pdb() method.
It can now handle the new structural data design.
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r8594 | bugman | 2009-01-22 15:48:45 +0100 (Thu, 22 Jan 2009) | 3 lines
Modified create_diff_tensor_pdb() for the new structural data design.
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r8595 | bugman | 2009-01-22 15:54:08 +0100 (Thu, 22 Jan 2009) | 5 lines
Fixes for generate_vector_dist(), generate_vector_residues(), and stitch_cap_to_cone().
These now handle the MolContainer instance.
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r8596 | bugman | 2009-01-22 16:01:16 +0100 (Thu, 22 Jan 2009) | 3 lines
Fixes for the cone_pdb() method for the new structural data design.
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r8597 | bugman | 2009-01-22 16:05:50 +0100 (Thu, 22 Jan 2009) | 3 lines
Renamed the struct_index arg to model_num in write_pdb().
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r8598 | bugman | 2009-01-22 16:09:57 +0100 (Thu, 22 Jan 2009) | 3 lines
Changed the struct_index arg of the structure.write_pdb() user function to model_num.
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r8599 | bugman | 2009-01-22 16:11:57 +0100 (Thu, 22 Jan 2009) | 3 lines
cone_edge() now also handles the MolContainer.
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r8600 | bugman | 2009-01-22 16:12:58 +0100 (Thu, 22 Jan 2009) | 3 lines
Removed a ton of now dead struct_index args from function calls.
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r8601 | bugman | 2009-01-22 16:23:48 +0100 (Thu, 22 Jan 2009) | 3 lines
Removed the last remnants of struct_index from the comments of from_xml().
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r8602 | bugman | 2009-01-22 16:25:18 +0100 (Thu, 22 Jan 2009) | 3 lines
Deletion of the unused, commented out code in from_xml().
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r8603 | bugman | 2009-01-22 16:41:32 +0100 (Thu, 22 Jan 2009) | 3 lines
Bug fix for MolList.from_xml(). The mol_nodes already exists!
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r8604 | bugman | 2009-01-22 16:45:51 +0100 (Thu, 22 Jan 2009) | 3 lines
Fix for the ModelList.from_xml() method. The XML element is called mol_cont, not mol.
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r8605 | bugman | 2009-01-22 16:48:07 +0100 (Thu, 22 Jan 2009) | 5 lines
MolList.from_xml() now calls MolContainer.from_xml().
This will allow the different structural objects to set themselves up as appropriate.
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r8606 | bugman | 2009-01-22 16:49:09 +0100 (Thu, 22 Jan 2009) | 3 lines
Bug fix for MolList.from_xml(). The molecule name is no longer passed into eval().
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r8607 | bugman | 2009-01-22 16:50:44 +0100 (Thu, 22 Jan 2009) | 3 lines
Bug fix for MolList.from_xml(). The MolContainer is now correctly referenced.
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r8608 | bugman | 2009-01-22 16:56:14 +0100 (Thu, 22 Jan 2009) | 3 lines
The parser ID string is now passed all the way to the MolList.from_xml() method.
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r8609 | bugman | 2009-01-22 17:03:48 +0100 (Thu, 22 Jan 2009) | 3 lines
Docstring fixes.
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r8610 | bugman | 2009-01-22 17:04:19 +0100 (Thu, 22 Jan 2009) | 3 lines
The MolContainer instances are now being properly recreated.
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r8611 | bugman | 2009-01-22 17:08:18 +0100 (Thu, 22 Jan 2009) | 3 lines
The MolContainers are now properly set up. Before the wrong classes were initialised.
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r8612 | bugman | 2009-01-22 17:09:35 +0100 (Thu, 22 Jan 2009) | 3 lines
MolList.add_item() now sets the molecule name.
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r8613 | bugman | 2009-01-22 17:12:36 +0100 (Thu, 22 Jan 2009) | 3 lines
Reactivated the calling of the specific MolContainer from_xml() method.
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r8614 | bugman | 2009-01-22 17:19:47 +0100 (Thu, 22 Jan 2009) | 3 lines
Added the MolContainer.from_xml() method for the internal structural object.
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r8615 | bugman | 2009-01-22 17:20:27 +0100 (Thu, 22 Jan 2009) | 3 lines
Fix for the test_load_scientific_results() system test.
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r8616 | bugman | 2009-01-22 17:20:51 +0100 (Thu, 22 Jan 2009) | 3 lines
Fix for the test_load_internal_results() system test.
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r8617 | bugman | 2009-01-22 17:23:05 +0100 (Thu, 22 Jan 2009) | 3 lines
More fixes for the test_load_internal_results() system test.
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r8618 | bugman | 2009-01-22 18:08:22 +0100 (Thu, 22 Jan 2009) | 3 lines
Added an incomplete MolContainer.from_xml() method.
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r8619 | bugman | 2009-01-22 18:09:11 +0100 (Thu, 22 Jan 2009) | 5 lines
Fixes for the test_load_scientific_results() test.
The atom_loop() method is now called to loop over the residues (using '@N').
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r8620 | bugman | 2009-01-22 18:34:54 +0100 (Thu, 22 Jan 2009) | 3 lines
Created the MolContainer.reload_pdb() method to be used by from_xml().
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r8621 | bugman | 2009-01-22 18:43:40 +0100 (Thu, 22 Jan 2009) | 3 lines
Added a print out for MolContainer.reload_pdb().
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r8622 | bugman | 2009-01-22 18:49:23 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the MolContainer.reload_pdb() method.
The molecule number and not index should be checked!
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r8623 | bugman | 2009-01-22 18:49:51 +0100 (Thu, 22 Jan 2009) | 3 lines
Removed an empty line.
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r8624 | bugman | 2009-01-22 18:53:00 +0100 (Thu, 22 Jan 2009) | 3 lines
Changed the relax results file to include the full path to the PDB file.
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r8625 | bugman | 2009-01-22 18:53:32 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the test_load_scientific_results() system test.
The path is now set.
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r8626 | bugman | 2009-01-22 18:56:18 +0100 (Thu, 22 Jan 2009) | 5 lines
Fix for the test_load_scientific_results() system test.
The res_name was coming out as a tuple, so now it is unpacked.
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r8627 | bugman | 2009-01-23 11:23:12 +0100 (Fri, 23 Jan 2009) | 8 lines
Wrote 3 system tests for the new design of the structural data handling.
These include:
test_read_pdb_mol_2_model_internal()
test_read_pdb_model_2_mol_internal()
test_read_pdb_complex_internal()
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r8628 | bugman | 2009-01-23 11:33:10 +0100 (Fri, 23 Jan 2009) | 5 lines
Fixes for the test_read_pdb_mol_2_model_internal() system test.
The checks were incorrect.
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r8629 | bugman | 2009-01-23 11:43:09 +0100 (Fri, 23 Jan 2009) | 3 lines
A number of fixes for test_read_pdb_complex_internal().
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r8630 | bugman | 2009-01-23 15:33:46 +0100 (Fri, 23 Jan 2009) | 6 lines
Improvements to the internal load_pdb() method.
The molecule naming algorithm, when no name is given, is now aware of the names of previously loaded
molecules.
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r8631 | bugman | 2009-01-23 15:50:14 +0100 (Fri, 23 Jan 2009) | 5 lines
Added consistency checks for the packing of the structural data.
The names of molecules must now match in all models.
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r8632 | bugman | 2009-01-23 15:55:28 +0100 (Fri, 23 Jan 2009) | 5 lines
Fix for the lactose N-state model system test.
The tag structures are now all named the same things, as they are a series of models.
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r8635 | bugman | 2009-01-23 11:06:25 -0500 (Fri, 23 Jan 2009) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/multi_structure
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