Author: bugman
Date: Fri Jan 23 17:06:01 2009
New Revision: 8634
URL: http://svn.gna.org/viewcvs/relax?rev=8634&view=rev
Log:
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
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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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[... 592 lines stripped ...]
r8634 - in /1.3: ./ data/ generic_fns/ generic_fns/structure/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/shar...