Author: bugman Date: Fri Jan 23 17:11:18 2009 New Revision: 8640 URL: http://svn.gna.org/viewcvs/relax?rev=8640&view=rev Log: Merged revisions 8633-8635 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ r8633 | bugman | 2009-01-23 16:52:20 +0100 (Fri, 23 Jan 2009) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-8213" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/multi_structure ................ r8634 | bugman | 2009-01-23 17:06:01 +0100 (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@xxxxxxxxxxx/svn/relax/branches/multi_structure ........ 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. ........ 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. ........ 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. ........ 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. ........ r8220 | bugman | 2008-12-18 15:24:05 +0100 (Thu, 18 Dec 2008) | 3 lines Redesigned the structure.read_pdb() arguments and docstring. ........ 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(). ........ 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(). ........ 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. ........ 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. ........ 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. ........ r8336 | bugman | 2009-01-08 16:30:24 +0100 (Thu, 08 Jan 2009) | 3 lines Created the StructList data structure for holding different structures. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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(). ........ 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(). ........ r8405 | bugman | 2009-01-12 14:11:32 +0100 (Mon, 12 Jan 2009) | 3 lines Renamed Molecule_container to MolContainer. ........ 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. ........ 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. ........ 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. ........ 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() ........ 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. ........ 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. ........ 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. ........ r8413 | bugman | 2009-01-12 14:24:35 +0100 (Mon, 12 Jan 2009) | 3 lines Modified __atom_index() to work within the MolContainer. ........ 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. ........ r8416 | bugman | 2009-01-12 14:27:42 +0100 (Mon, 12 Jan 2009) | 3 lines Some copyright updates. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r8431 | bugman | 2009-01-13 16:12:27 +0100 (Tue, 13 Jan 2009) | 3 lines Fixes for the duplicate_data() method. ........ r8432 | bugman | 2009-01-13 16:12:39 +0100 (Tue, 13 Jan 2009) | 3 lines Fixes for the __compare_objects() method. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r8442 | bugman | 2009-01-14 17:23:18 +0100 (Wed, 14 Jan 2009) | 3 lines Bug fixes for the pack_structs() method. ........ r8443 | bugman | 2009-01-14 17:27:24 +0100 (Wed, 14 Jan 2009) | 3 lines Bug fixes for the load_pdb() method. ........ 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. ........ 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. ........ r8446 | bugman | 2009-01-14 17:56:43 +0100 (Wed, 14 Jan 2009) | 3 lines Removed a debugging print out. ........ 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(). ........ 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(). ........ 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! ........ 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). ........ 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. ........ 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. ........ 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. ........ r8454 | bugman | 2009-01-15 10:20:21 +0100 (Thu, 15 Jan 2009) | 3 lines Compacted some comments. ........ 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(). ........ 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. ........ 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(). ........ 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. ........ 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. ........ 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! ........ 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. ........ r8462 | bugman | 2009-01-15 11:45:01 +0100 (Thu, 15 Jan 2009) | 3 lines Fix for the test___residue_loop() unit test. ........ r8463 | bugman | 2009-01-15 11:50:27 +0100 (Thu, 15 Jan 2009) | 3 lines Fixes for the test_load_pdb() unit test. ........ 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! ........ 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. ........ 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 . ........ 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. ........ 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. ........ 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! ........ 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. ........ 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. ........ 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(). ........ r8478 | bugman | 2009-01-15 17:12:46 +0100 (Thu, 15 Jan 2009) | 3 lines Created the validate() method. ........ 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. ........ r8480 | bugman | 2009-01-15 17:15:59 +0100 (Thu, 15 Jan 2009) | 3 lines Bug fix for the new validate() method. ........ 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. ........ 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'. ........ 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. ........ 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. ........ 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. ........ 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. ........ r8487 | bugman | 2009-01-15 18:42:02 +0100 (Thu, 15 Jan 2009) | 3 lines Shifted __det_pdb_element() to the correct location. ........ r8488 | bugman | 2009-01-15 18:46:43 +0100 (Thu, 15 Jan 2009) | 3 lines Added 'SG' to the translation table. ........ 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. ........ 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! ........ 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(). ........ r8495 | bugman | 2009-01-16 13:44:47 +0100 (Fri, 16 Jan 2009) | 3 lines Docstring fixes for vectors(). ........ 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. ........ 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'. ........ 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(). ........ 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. ........ r8500 | bugman | 2009-01-16 17:49:22 +0100 (Fri, 16 Jan 2009) | 3 lines Removed some redundant code. ........ 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(). ........ 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!!! ........ r8504 | bugman | 2009-01-19 11:04:57 +0100 (Mon, 19 Jan 2009) | 3 lines Deleted the Scientific python structural object add_struct() method. ........ 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. ........ r8506 | bugman | 2009-01-19 11:11:29 +0100 (Mon, 19 Jan 2009) | 3 lines Fixed the API bond_vectors() method. ........ r8507 | bugman | 2009-01-19 11:15:15 +0100 (Mon, 19 Jan 2009) | 3 lines Fixed a call to bond_vectors(). ........ r8508 | bugman | 2009-01-19 11:18:00 +0100 (Mon, 19 Jan 2009) | 3 lines Bug fixes for bond_vectors(). ........ r8509 | bugman | 2009-01-19 11:21:07 +0100 (Mon, 19 Jan 2009) | 3 lines [... 635 lines stripped ...]