Blocked revisions 5793,5795-5814,5825-5968 via svnmerge
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r5793 | bugman | 2008-04-16 21:37:24 +0200 (Wed, 16 Apr 2008) | 3 lines
Converted the class docstring to a module docstring.
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r5795 | bugman | 2008-04-16 21:40:23 +0200 (Wed, 16 Apr 2008) | 3 lines
Converted all class methods into module functions.
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r5796 | bugman | 2008-04-16 21:44:17 +0200 (Wed, 16 Apr 2008) | 3 lines
Replaced the redundant module function open_file() with relax_io.open_write_file().
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r5797 | bugman | 2008-04-16 21:46:12 +0200 (Wed, 16 Apr 2008) | 3 lines
Fixed the usage of the relax_io module.
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r5798 | bugman | 2008-04-16 21:47:50 +0200 (Wed, 16 Apr 2008) | 3 lines
The mkdir() function is now called relax_io.mkdir_nofail().
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r5799 | bugman | 2008-04-16 21:49:55 +0200 (Wed, 16 Apr 2008) | 3 lines
Removed all references to 'self' in the create() function.
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r5800 | bugman | 2008-04-16 21:52:13 +0200 (Wed, 16 Apr 2008) | 3 lines
Removed all references to 'self' in the extract() function.
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r5801 | bugman | 2008-04-16 21:58:14 +0200 (Wed, 16 Apr 2008) | 3 lines
Converted the line_positions() to the new design.
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r5802 | bugman | 2008-04-16 21:58:47 +0200 (Wed, 16 Apr 2008) | 3 lines
Fixed the call to line_positions().
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r5803 | bugman | 2008-04-16 22:03:23 +0200 (Wed, 16 Apr 2008) | 6 lines
Removed the tests in extract() for the presence of a model-free model and relaxation data.
These tests reduce flexibility as these can be set later, and the reading of the mfout file does not
depend on these.
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r5804 | bugman | 2008-04-16 22:08:51 +0200 (Wed, 16 Apr 2008) | 6 lines
Reintroduced the test for the model-free model but with a RelaxError now thrown.
This test was important as the model is necessary to differentiate between te and ts in the mfout
file!
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r5805 | bugman | 2008-04-16 22:10:35 +0200 (Wed, 16 Apr 2008) | 3 lines
Fixes for the extract() function.
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r5806 | bugman | 2008-04-16 22:11:44 +0200 (Wed, 16 Apr 2008) | 3 lines
Fix for the get_mf_data() function.
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r5807 | bugman | 2008-04-16 22:12:28 +0200 (Wed, 16 Apr 2008) | 3 lines
Fixed all the calls to get_mf_data().
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r5808 | bugman | 2008-04-16 22:24:57 +0200 (Wed, 16 Apr 2008) | 3 lines
Fix for extract() to handle residue misalignment between mfout and the relax data store.
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r5809 | bugman | 2008-04-16 22:37:18 +0200 (Wed, 16 Apr 2008) | 3 lines
Prepared for a new structural API method, num_str(), for counting the number of structures.
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r5810 | bugman | 2008-04-16 22:43:03 +0200 (Wed, 16 Apr 2008) | 5 lines
Added the structural API base class method num_str().
This base class method is not a stub, but returns the length of 'self.structural_data'.
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r5811 | bugman | 2008-04-16 22:43:45 +0200 (Wed, 16 Apr 2008) | 3 lines
Modified the module docsting to say that the methods aren't all prototypes.
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r5812 | bugman | 2008-04-16 22:45:17 +0200 (Wed, 16 Apr 2008) | 3 lines
Fix for the vectors() function.
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r5813 | bugman | 2008-04-17 00:03:36 +0200 (Thu, 17 Apr 2008) | 3 lines
Small fix for the xh_vector() method.
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r5814 | bugman | 2008-04-18 14:17:16 +0200 (Fri, 18 Apr 2008) | 3 lines
Converted the uniform vector distribution object into a list of numpy float64 arrays.
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r5825 | bugman | 2008-04-20 11:46:20 +0200 (Sun, 20 Apr 2008) | 5 lines
Added the sequence.read() user function to the angles calculation system test.
This just adds a check that sequence.read() can be used in combination with structure.load_spins().
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r5826 | bugman | 2008-04-20 11:59:47 +0200 (Sun, 20 Apr 2008) | 3 lines
Redesigned the structure.vectors() user function again, again removing the heteronuc arg.
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r5827 | bugman | 2008-04-20 12:01:53 +0200 (Sun, 20 Apr 2008) | 3 lines
Removed the heteronuc arg from vectors(), and placed the proton name into spin.attached_proton.
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r5828 | bugman | 2008-04-20 12:04:22 +0200 (Sun, 20 Apr 2008) | 3 lines
Added the unit arg to the vectors() fn. This might be useful in the future.
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r5829 | bugman | 2008-04-20 12:23:56 +0200 (Sun, 20 Apr 2008) | 3 lines
Modified the Scientific Python API atom_loop() method to return the model number when asked.
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r5830 | bugman | 2008-04-20 12:25:41 +0200 (Sun, 20 Apr 2008) | 3 lines
Modified the structural API stub method atom_loop() to accept the model_num_flag arg.
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r5831 | bugman | 2008-04-20 12:29:25 +0200 (Sun, 20 Apr 2008) | 5 lines
Fixed the angles.py script used in the system tests.
The heteronuc arg to structure.vectors() has been removed.
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r5832 | bugman | 2008-04-20 12:31:59 +0200 (Sun, 20 Apr 2008) | 3 lines
Renamed the structural API base class method num_str() to num_models().
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r5833 | bugman | 2008-04-20 12:45:08 +0200 (Sun, 20 Apr 2008) | 3 lines
Added the structural API atom_loop() call to the vectors() function.
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r5834 | bugman | 2008-04-20 12:51:34 +0200 (Sun, 20 Apr 2008) | 6 lines
Renamed generate_spin_id() to generate_spin_id_data_array(), and created a new generate_spin_id().
The generate_spin_id_data_array() function generates the spin_id string from a data array whereas
generate_spin_id() generates the spin_id string from the argument values passed into it.
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r5835 | bugman | 2008-04-20 12:52:51 +0200 (Sun, 20 Apr 2008) | 3 lines
Fixed the call to generate_spin_id() in the return_spin_from_index() function.
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r5836 | bugman | 2008-04-20 12:54:02 +0200 (Sun, 20 Apr 2008) | 3 lines
The generate_spin_id_data_array() fn is now called in the read() method.
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r5837 | bugman | 2008-04-20 12:55:22 +0200 (Sun, 20 Apr 2008) | 3 lines
The generate_spin_id() fn is now being called by the vectors() fn.
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r5838 | bugman | 2008-04-20 13:26:25 +0200 (Sun, 20 Apr 2008) | 5 lines
Shifted the XH vector calculation from the xh_vector() structural API method to the vector() fn.
This calculation can be done independently from the type of the structural data object.
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r5839 | bugman | 2008-04-20 13:27:34 +0200 (Sun, 20 Apr 2008) | 3 lines
Deleted the xh_vector() method from the API base class and Scientific Python PDB data object.
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r5840 | bugman | 2008-04-20 13:32:46 +0200 (Sun, 20 Apr 2008) | 6 lines
Added the full_info flag arg to return_spin() to allow more info to be returned when desired.
This flag will cause the molecule name, residue number and residue name to be returned in addition
to the spin container.
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r5841 | bugman | 2008-04-20 13:36:54 +0200 (Sun, 20 Apr 2008) | 3 lines
The full spin info is now returned from return_spin() and the modified spins written to stdout.
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r5842 | bugman | 2008-04-20 14:30:59 +0200 (Sun, 20 Apr 2008) | 6 lines
Started to recode the vectors() function.
The structural API atom_loop() approach is completely wrong, so the spin_loop() will be used
instead.
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r5843 | bugman | 2008-04-20 14:45:03 +0200 (Sun, 20 Apr 2008) | 3 lines
Started to write the new structural API method attached_atom().
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r5844 | bugman | 2008-04-20 14:45:30 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the atom_id string.
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r5845 | bugman | 2008-04-20 17:03:46 +0200 (Sun, 20 Apr 2008) | 3 lines
Added the start of the regular expression description in the id_string_doc string.
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r5846 | bugman | 2008-04-20 17:04:43 +0200 (Sun, 20 Apr 2008) | 3 lines
Wrote the test_Selection_full_spin_id() for testing the string identifier '#Ap4Aase:2&:Glu@...&@NH'.
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r5847 | bugman | 2008-04-20 17:08:02 +0200 (Sun, 20 Apr 2008) | 5 lines
Fixed all the unit tests of generic_fns.selection.generate_spin_id_data_array().
The function was recently renamed from generate_spin_id() to generate_spin_id_data_array().
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r5848 | bugman | 2008-04-20 17:09:08 +0200 (Sun, 20 Apr 2008) | 5 lines
Removed the heteronuc arg test of the structure.vectors() user function.
This argument is no longer present.
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r5849 | bugman | 2008-04-20 17:13:56 +0200 (Sun, 20 Apr 2008) | 3 lines
Improved the test_Selection_full_spin_id() unit test to test all spins.
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r5850 | bugman | 2008-04-20 17:53:45 +0200 (Sun, 20 Apr 2008) | 6 lines
Split up the Selection.__contains__() method to allow for string comparisons as well.
The MoleculeContainer, ResidueContainer, and/or SpinContainer comparison has been shifted to the
method Selection.__contains_mol_res_spin_containers().
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r5851 | bugman | 2008-04-20 18:05:51 +0200 (Sun, 20 Apr 2008) | 3 lines
Started an implementation of Selection.__contains_spin_id().
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r5852 | bugman | 2008-04-20 18:11:54 +0200 (Sun, 20 Apr 2008) | 3 lines
Docstring fix for the __residue_loop() method.
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r5853 | bugman | 2008-04-20 18:17:59 +0200 (Sun, 20 Apr 2008) | 3 lines
Added the directory for the unit tests of the generic_fns.structure package.
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r5854 | bugman | 2008-04-20 18:21:31 +0200 (Sun, 20 Apr 2008) | 3 lines
Added the _structure directory to the __all__ list.
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r5855 | bugman | 2008-04-20 18:37:37 +0200 (Sun, 20 Apr 2008) | 5 lines
Added the framework for the unit tests of the Scietific Python PDB structural object.
Included is a test of the load_structures() method.
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r5856 | bugman | 2008-04-20 18:39:13 +0200 (Sun, 20 Apr 2008) | 3 lines
Shifted the 'test.pdb' file into the directory for data shared between the system and unit tests.
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r5857 | bugman | 2008-04-20 18:45:36 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the test_load_structures() unit test.
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r5858 | bugman | 2008-04-20 18:47:07 +0200 (Sun, 20 Apr 2008) | 3 lines
Started the replacement of the use of tokenise() by the full selection object.
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r5859 | bugman | 2008-04-20 18:50:59 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the load_structures() method, the model arg should be a keyword arg.
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r5860 | bugman | 2008-04-20 18:54:43 +0200 (Sun, 20 Apr 2008) | 3 lines
Added some checks to the test_load_structures() unit test.
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r5861 | bugman | 2008-04-20 18:57:16 +0200 (Sun, 20 Apr 2008) | 3 lines
Added a unit test for the Scientific_data.atom_loop() method.
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r5862 | bugman | 2008-04-20 19:02:39 +0200 (Sun, 20 Apr 2008) | 3 lines
Added a unit test for the private Scientific_data.__molecule_loop() method.
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r5863 | bugman | 2008-04-20 19:06:15 +0200 (Sun, 20 Apr 2008) | 5 lines
Fixes for the __molecule_loop() method.
The selection object is now used for comparisons.
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r5864 | bugman | 2008-04-20 19:10:33 +0200 (Sun, 20 Apr 2008) | 3 lines
Added some checks to the test___molecule_loop() unit test.
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r5865 | bugman | 2008-04-20 19:12:51 +0200 (Sun, 20 Apr 2008) | 5 lines
Fix for the __molecule_loop() method.
Molecule names of None are now caught.
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r5866 | bugman | 2008-04-20 19:16:55 +0200 (Sun, 20 Apr 2008) | 3 lines
Wrote a unit test for the private Scientific_data.__molecule_loop() method with a selection object.
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r5867 | bugman | 2008-04-20 19:19:29 +0200 (Sun, 20 Apr 2008) | 3 lines
Wrote a unit test for the Scientific_data.__molecule_loop() method with a non-matching selection object.
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r5868 | bugman | 2008-04-20 19:48:10 +0200 (Sun, 20 Apr 2008) | 5 lines
Created the Selection.contains_mol() method.
This is for testing if a molecule name, in string form, is contained in the selection object.
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r5869 | bugman | 2008-04-20 19:55:37 +0200 (Sun, 20 Apr 2008) | 3 lines
Added 5 unit test for the Selection.contains_mol() method.
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r5870 | bugman | 2008-04-20 19:57:44 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for Selection.contains_mol(). The mol arg is now a keyword arg which defaults to None.
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r5871 | bugman | 2008-04-20 19:59:07 +0200 (Sun, 20 Apr 2008) | 3 lines
Bug fix for the Selection.contains_mol() method. The recursive call was misspelt.
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r5872 | bugman | 2008-04-20 20:02:22 +0200 (Sun, 20 Apr 2008) | 6 lines
Fix for the Selection.contains_mol() method.
If the molecule name is None and there are no molecules in the selection object, the function
returns True.
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r5873 | bugman | 2008-04-20 20:04:37 +0200 (Sun, 20 Apr 2008) | 5 lines
Fix for the Scientific_data.__molecule_loop() method.
The Selection.contains_mol() method is being used to identify matching molecules.
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r5874 | bugman | 2008-04-20 20:30:44 +0200 (Sun, 20 Apr 2008) | 3 lines
Wrote 6 unit tests for the currently non-existent Selection.contains_res() method.
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r5875 | bugman | 2008-04-20 20:41:53 +0200 (Sun, 20 Apr 2008) | 3 lines
Added another unit test of the Selection.contains_res() method.
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r5876 | bugman | 2008-04-20 21:02:04 +0200 (Sun, 20 Apr 2008) | 3 lines
Implemented the Selection.contains_res() method.
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r5877 | bugman | 2008-04-20 21:08:52 +0200 (Sun, 20 Apr 2008) | 5 lines
Fixes for the __residue_loop() method.
The selection object is now used for comparison.
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r5878 | bugman | 2008-04-20 21:24:59 +0200 (Sun, 20 Apr 2008) | 3 lines
Wrote 3 unit tests for the Scientific_data.__residue_loop() method.
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r5879 | bugman | 2008-04-20 22:08:00 +0200 (Sun, 20 Apr 2008) | 3 lines
Fixes for all the unit tests of the Selection.contains_res() method.
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r5880 | bugman | 2008-04-20 22:10:34 +0200 (Sun, 20 Apr 2008) | 3 lines
Fixes for the Selection.contains_res() method.
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r5881 | bugman | 2008-04-20 22:24:11 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the test___residue_loop_selection() unit test.
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r5882 | bugman | 2008-04-20 22:24:54 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the Selection.contains_res() method.
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r5883 | bugman | 2008-04-20 22:26:03 +0200 (Sun, 20 Apr 2008) | 3 lines
Fix for the Selection.contains_mol() method.
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r5884 | bugman | 2008-04-20 23:53:22 +0200 (Sun, 20 Apr 2008) | 3 lines
Modified the Scientific_data.atom_loop() method to call the non-existent Selection.contains_spin().
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r5885 | bugman | 2008-04-20 23:57:08 +0200 (Sun, 20 Apr 2008) | 3 lines
Implemented the Selection.contains_spin() method.
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r5886 | bugman | 2008-04-20 23:59:40 +0200 (Sun, 20 Apr 2008) | 3 lines
Fixed the test_atom_loop() unit test.
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r5887 | bugman | 2008-04-21 00:14:37 +0200 (Mon, 21 Apr 2008) | 3 lines
Wrote 5 unit tests for the Scientific_data.atom_loop() method using spin selections.
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r5888 | bugman | 2008-04-21 00:16:40 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixed all of the system tests which use the shifted 'test.pdb' data file.
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r5889 | bugman | 2008-04-21 00:18:45 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixed the angles system test reading of the 'test.pdb' file.
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r5890 | bugman | 2008-04-21 00:21:33 +0200 (Mon, 21 Apr 2008) | 3 lines
A number of fixes for the Scientific_data.attached_atom() method.
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r5891 | bugman | 2008-04-21 00:24:21 +0200 (Mon, 21 Apr 2008) | 3 lines
The Scientific_data.attached_atom() method now returns the atom information.
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r5892 | bugman | 2008-04-21 00:27:27 +0200 (Mon, 21 Apr 2008) | 3 lines
Renamed the angles() user function to angle_diff_frame().
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r5893 | bugman | 2008-04-21 00:28:57 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixed the loading of the angle_diff_frame() user function into the interpreter.
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r5894 | bugman | 2008-04-21 00:30:02 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the angles system test. The angle_diff_frame() user function is now called.
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r5895 | bugman | 2008-04-21 00:35:30 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixes for the angle_diff_frame() function.
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r5896 | bugman | 2008-04-21 00:41:34 +0200 (Mon, 21 Apr 2008) | 3 lines
The spheroid_frame() function has been converted to the new design.
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r5897 | bugman | 2008-04-21 10:27:36 +0200 (Mon, 21 Apr 2008) | 3 lines
Improvements to warning message in the spheroid_frame() function.
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r5898 | bugman | 2008-04-21 10:29:53 +0200 (Mon, 21 Apr 2008) | 3 lines
Added the sequence.display() user function call to the angles system test.
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r5899 | bugman | 2008-04-21 10:33:04 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the sequence.display() user function intro printout.
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r5900 | bugman | 2008-04-21 10:41:01 +0200 (Mon, 21 Apr 2008) | 3 lines
Changed the defaults of the sequence.display() user function so that everything is shown.
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r5901 | bugman | 2008-04-21 10:41:36 +0200 (Mon, 21 Apr 2008) | 3 lines
Copyright notice update.
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r5902 | bugman | 2008-04-21 10:48:00 +0200 (Mon, 21 Apr 2008) | 3 lines
A few small changes to the vectors() function.
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r5903 | bugman | 2008-04-21 11:21:52 +0200 (Mon, 21 Apr 2008) | 5 lines
Modified the attached_atom() method and created the __find_bonded_atom() method.
The attached atom is now isolated correctly and returned.
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r5904 | bugman | 2008-04-21 11:33:49 +0200 (Mon, 21 Apr 2008) | 3 lines
Some improvements to the vectors() function. It doesn't work yet though.
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r5905 | bugman | 2008-04-21 11:40:39 +0200 (Mon, 21 Apr 2008) | 3 lines
Modified the attached_atom() method to handle multiple models.
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r5906 | bugman | 2008-04-21 11:41:43 +0200 (Mon, 21 Apr 2008) | 3 lines
Modified the vectors() function to handle the atom position being a list.
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r5907 | bugman | 2008-04-21 11:44:33 +0200 (Mon, 21 Apr 2008) | 3 lines
Modified the vectors() function to call the non-existant structural API bond_vectors() method.
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r5908 | bugman | 2008-04-21 11:46:49 +0200 (Mon, 21 Apr 2008) | 3 lines
Added the attached_atom() prototype method to the structural API base class.
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r5909 | bugman | 2008-04-21 11:57:29 +0200 (Mon, 21 Apr 2008) | 3 lines
Created the Scientific Python structural API method bond_vectors().
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r5910 | bugman | 2008-04-21 11:59:20 +0200 (Mon, 21 Apr 2008) | 3 lines
Added the bond_vectors() prototype method to the structural API base class.
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r5911 | bugman | 2008-04-21 13:21:46 +0200 (Mon, 21 Apr 2008) | 6 lines
Completed the vectors() function.
The vector is now fetched, averaged over all models, and placed into spin.xh_vect. All the old code
has been axed.
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r5912 | bugman | 2008-04-21 14:02:54 +0200 (Mon, 21 Apr 2008) | 3 lines
Added many checks to the angles calculation system test.
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r5913 | bugman | 2008-04-21 14:05:22 +0200 (Mon, 21 Apr 2008) | 3 lines
Removed a newline character from the RelaxWarning system printout.
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r5914 | bugman | 2008-04-21 14:20:14 +0200 (Mon, 21 Apr 2008) | 3 lines
STDERR is now being caught by the relax test suite TextTestRunner replacement.
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r5915 | bugman | 2008-04-21 14:30:19 +0200 (Mon, 21 Apr 2008) | 3 lines
Wrote the RelaxTestRunner.addFailure() replacement method to prepend STDERR/STDOUT to the message.
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r5916 | bugman | 2008-04-21 14:33:27 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the test_atom_loop_spin_selection1() unit test.
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r5917 | bugman | 2008-04-21 14:36:03 +0200 (Mon, 21 Apr 2008) | 3 lines
Sorted some import statements.
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r5918 | bugman | 2008-04-21 14:38:30 +0200 (Mon, 21 Apr 2008) | 5 lines
Fixed the setup of the maths_fns.consistency_tests.Consistency object.
This mimicks the J(w) mapping change of r5742.
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r5919 | bugman | 2008-04-21 14:59:00 +0200 (Mon, 21 Apr 2008) | 5 lines
Improved the testing in the consistency testing calculate() method.
This mimicks the J(w) mapping changes of r5743 and r5744.
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r5920 | bugman | 2008-04-21 15:02:56 +0200 (Mon, 21 Apr 2008) | 5 lines
The proton type is now set in the consistency testing system test.
This mimicks the J(w) mapping changes of r5745.
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r5921 | bugman | 2008-04-21 15:05:20 +0200 (Mon, 21 Apr 2008) | 3 lines
mu0 and h_bar are now passed into Consistency().
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r5922 | bugman | 2008-04-21 15:11:15 +0200 (Mon, 21 Apr 2008) | 5 lines
Fix for the test_opendx_theta_phi_da() system test.
The structure.vectors() user function is no longer passed the heteronuc arg.
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r5923 | bugman | 2008-04-21 15:12:46 +0200 (Mon, 21 Apr 2008) | 3 lines
Added a missing RelaxError import.
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r5924 | bugman | 2008-04-21 15:38:46 +0200 (Mon, 21 Apr 2008) | 3 lines
Created the RelaxSpinsNotLoadedError class.
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r5925 | bugman | 2008-04-21 16:08:50 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the RelaxSequenceError class. The pipe arg is now optional.
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r5926 | bugman | 2008-04-21 16:21:04 +0200 (Mon, 21 Apr 2008) | 3 lines
Added a unit test to test that the Selection object has no memory of previous selections.
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r5927 | bugman | 2008-04-21 17:03:16 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixed a name clash of 'spin_id'.
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r5928 | bugman | 2008-04-21 17:08:26 +0200 (Mon, 21 Apr 2008) | 5 lines
Added a check for the spin number and name being set in the vectors() function.
This must be set for the XH vector to be isolated.
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r5929 | bugman | 2008-04-21 17:09:48 +0200 (Mon, 21 Apr 2008) | 5 lines
Fix for the test_opendx_theta_phi_da() system test.
The spin information is now loaded.
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r5930 | bugman | 2008-04-21 17:28:46 +0200 (Mon, 21 Apr 2008) | 3 lines
Modified the read() function to write out all the new spins.
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r5931 | bugman | 2008-04-21 17:30:57 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the calls to the functions of the generic_fns.diffusion_tensor module.
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r5932 | bugman | 2008-04-21 17:33:44 +0200 (Mon, 21 Apr 2008) | 3 lines
Updated the map_bounds() function to the new design.
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r5933 | bugman | 2008-04-21 17:34:10 +0200 (Mon, 21 Apr 2008) | 3 lines
Fixed the call to map_bounds().
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r5934 | bugman | 2008-04-21 17:38:28 +0200 (Mon, 21 Apr 2008) | 6 lines
Reverted r5933, as this change was incorrect.
The command used was:
svn merge -r5933:5932 .
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r5935 | bugman | 2008-04-21 17:38:55 +0200 (Mon, 21 Apr 2008) | 3 lines
Added the dummy spin_id keyword arg to the map_bounds() function.
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r5936 | bugman | 2008-04-21 17:41:30 +0200 (Mon, 21 Apr 2008) | 3 lines
Converted the return_conversion_factor() function to the new design.
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r5937 | bugman | 2008-04-21 17:43:43 +0200 (Mon, 21 Apr 2008) | 3 lines
Converted the return_units() function to the new relax design.
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r5938 | bugman | 2008-04-21 22:52:35 +0200 (Mon, 21 Apr 2008) | 3 lines
Loosened the checks in the angles calculation system test to allow 64 bit platforms to pass.
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r5939 | bugman | 2008-04-21 23:14:05 +0200 (Mon, 21 Apr 2008) | 6 lines
Renamed the test_read_results() system test to test_read_results_1_2().
This is because the results file is in the 1.2 line format. Hence the results file has been renamed
as well. The loading of the 1.2 program state has also been axed.
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r5940 | bugman | 2008-04-21 23:15:34 +0200 (Mon, 21 Apr 2008) | 3 lines
Deleted the relax 1.2 save state (used in the results file reading system test).
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r5941 | bugman | 2008-04-21 23:34:17 +0200 (Mon, 21 Apr 2008) | 3 lines
Wrote the PipeContainer.is_empty() method.
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r5942 | bugman | 2008-04-21 23:38:49 +0200 (Mon, 21 Apr 2008) | 3 lines
Added a unit test for the PipeContainer.is_empty() method.
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r5943 | bugman | 2008-04-21 23:40:57 +0200 (Mon, 21 Apr 2008) | 3 lines
Wrote the Element.is_empty() method.
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r5944 | bugman | 2008-04-21 23:43:57 +0200 (Mon, 21 Apr 2008) | 3 lines
Fix for the PipeContainer.is_empty() method.
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r5945 | bugman | 2008-04-21 23:46:18 +0200 (Mon, 21 Apr 2008) | 5 lines
Modified the unit test of the PipeContainer.is_empty() method.
The pipe type can be set in an empty pipe.
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r5946 | bugman | 2008-04-21 23:47:39 +0200 (Mon, 21 Apr 2008) | 3 lines
The pipe type of None is no longer checked for in the PipeContainer.is_empty() method.
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r5947 | bugman | 2008-04-22 00:13:52 +0200 (Tue, 22 Apr 2008) | 3 lines
Modified the API documentation construction so that most of the test suite is not present.
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r5948 | bugman | 2008-04-23 00:08:43 +0200 (Wed, 23 Apr 2008) | 3 lines
Started to convert the model-free read_columnar_results() method to the new relax design.
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r5949 | bugman | 2008-04-23 18:01:39 +0200 (Wed, 23 Apr 2008) | 3 lines
Added a directory for the structural data of the test suite and added a small molecule structure.
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r5950 | bugman | 2008-04-23 18:02:49 +0200 (Wed, 23 Apr 2008) | 3 lines
Renamed one of the test suite PDB files.
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r5951 | bugman | 2008-04-23 18:08:33 +0200 (Wed, 23 Apr 2008) | 3 lines
Fixed all the test suite tests pointing to the renamed 'test.pdb' file.
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r5952 | bugman | 2008-04-23 18:44:01 +0200 (Wed, 23 Apr 2008) | 5 lines
Added a system test for the loading of spins from a small molecule.
This uses the Scientific Python PDB data object.
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r5953 | bugman | 2008-04-23 22:44:33 +0200 (Wed, 23 Apr 2008) | 5 lines
Disabled the unit test for spin selections with parentheses.
This test can wait until someone tries to implement the feature.
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r5954 | bugman | 2008-04-23 22:58:27 +0200 (Wed, 23 Apr 2008) | 5 lines
Added two simple unit tests for printing out the contents of a data pipe.
This tests the PipeContainer.__repr__() method.
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r5955 | bugman | 2008-04-23 23:00:12 +0200 (Wed, 23 Apr 2008) | 5 lines
Fix for the PipeContainer.__repr__() method.
The is_empty() function is skipped.
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r5956 | bugman | 2008-04-23 23:02:29 +0200 (Wed, 23 Apr 2008) | 3 lines
Added a tearDown() clean up method for the unit tests of the PipeContainer.
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r5957 | bugman | 2008-04-23 23:05:19 +0200 (Wed, 23 Apr 2008) | 3 lines
The PipeContainer.__repr__() unit test are now stricter, checking for returned strings.
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r5958 | bugman | 2008-04-23 23:14:39 +0200 (Wed, 23 Apr 2008) | 5 lines
Fixed a unit test for the Scientific_data.atom_loop() method with the '@163' spin selection.
2 unit test functions had the same name, so only one was being run.
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r5959 | bugman | 2008-04-23 23:18:52 +0200 (Wed, 23 Apr 2008) | 3 lines
Fixes for the test_atom_loop_spin_selection1() unit test.
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r5960 | bugman | 2008-04-23 23:27:49 +0200 (Wed, 23 Apr 2008) | 3 lines
Wrote 7 unit tests for the Selection.contains_spin() method.
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r5961 | bugman | 2008-04-23 23:33:08 +0200 (Wed, 23 Apr 2008) | 3 lines
Wrote 6 unit tests for the Selection.contains_*() methods when regular expression is passed in.
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r5962 | bugman | 2008-04-23 23:37:52 +0200 (Wed, 23 Apr 2008) | 3 lines
The Selection.contains_*() methods now call the wildcard_match() function for comparisons.
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r5963 | bugman | 2008-04-23 23:44:31 +0200 (Wed, 23 Apr 2008) | 3 lines
Improved the wildcard_match() function to allow comparisons of the strings both ways.
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r5964 | bugman | 2008-04-24 00:12:24 +0200 (Thu, 24 Apr 2008) | 5 lines
Spun off half of the read() function into the new generate() function.
The new function will be very useful for other parts of relax.
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r5965 | bugman | 2008-04-24 00:23:20 +0200 (Thu, 24 Apr 2008) | 6 lines
Improvements for the add_item() methods of MolecularContainer, ResidueContainer, and SpinContainer.
The logic is much improved and split into 2 parts: replace the current empty container or append a
new container.
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r5966 | bugman | 2008-04-24 00:28:14 +0200 (Thu, 24 Apr 2008) | 3 lines
Removed some dodgy code from return_molecule().
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r5967 | bugman | 2008-04-24 00:31:16 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed a bug in the copy() fn uncovered by the fix of r5966.
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r5968 | bugman | 2008-04-24 10:17:34 +0200 (Thu, 24 Apr 2008) | 6 lines
Loosened the model-free optimisation tests as different numpy versions were affecting the precision.
The checks of the model-free params and chi2 use self.assertAlmostEqual() again, as numpy was
causing float differences at around the machine precision mark.
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