Author: bugman
Date: Thu Apr 24 14:24:01 2008
New Revision: 5972
URL: http://svn.gna.org/viewcvs/relax?rev=5972&view=rev
Log:
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@63&@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
[... 246 lines stripped ...]
r5972 - /1.2/