Author: bugman
Date: Wed Apr 16 21:39:13 2008
New Revision: 5794
URL: http://svn.gna.org/viewcvs/relax?rev=5794&view=rev
Log:
Blocked revisions
5625-5627,5629-5662,5664-5707,5709,5721-5725,5727-5728,5730-5791 via svnmerge
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r5625 | bugman | 2008-04-13 16:23:26 +0200 (Sun, 13 Apr 2008) | 6 lines
Fix for the test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149() system test.
After the fix of r5622, this optimisation now works correctly!!! So the
optimisation stats have
been updated in the test.
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r5626 | bugman | 2008-04-13 16:25:36 +0200 (Sun, 13 Apr 2008) | 6 lines
Fix for the test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149() system
test.
The optimisation stats hard coded into the test are now correct.
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r5627 | bugman | 2008-04-13 16:27:56 +0200 (Sun, 13 Apr 2008) | 5 lines
Fix for the test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149() system
test.
The optimisation stats hard coded into the test are now correct.
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r5629 | bugman | 2008-04-13 18:52:45 +0200 (Sun, 13 Apr 2008) | 3 lines
Epytext fixes for the docstring of the structural API write_pdb_file() stub
method.
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r5630 | bugman | 2008-04-13 18:58:44 +0200 (Sun, 13 Apr 2008) | 3 lines
Renamed the class 'Str_object' to 'Base_struct_API'.
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r5631 | bugman | 2008-04-13 19:01:28 +0200 (Sun, 13 Apr 2008) | 3 lines
Epytext fixes for the __get_chemical_name() docstring.
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r5632 | bugman | 2008-04-13 19:12:03 +0200 (Sun, 13 Apr 2008) | 3 lines
Epytext fix for the Internal_PDB class docstring.
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r5633 | bugman | 2008-04-13 19:13:20 +0200 (Sun, 13 Apr 2008) | 3 lines
Epytext fixes for the write_pdb_file() docstring.
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r5634 | bugman | 2008-04-13 19:17:54 +0200 (Sun, 13 Apr 2008) | 3 lines
Shifted some class variables into the __init__() method as these are
supposed to change.
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r5635 | bugman | 2008-04-13 19:26:05 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the model-free back_calc() method to the new relax design.
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r5636 | bugman | 2008-04-13 19:44:55 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the model-free calculate() method to the new relax design.
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r5637 | bugman | 2008-04-13 19:50:50 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the model-free are_mf_params_set() method to the new relax design.
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r5638 | bugman | 2008-04-13 19:51:12 +0200 (Sun, 13 Apr 2008) | 3 lines
Fix for the call to are_mf_params_set().
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r5639 | bugman | 2008-04-13 19:52:13 +0200 (Sun, 13 Apr 2008) | 3 lines
Fixed a few misnamed variables in the model-free calculate() method.
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r5640 | bugman | 2008-04-13 19:53:01 +0200 (Sun, 13 Apr 2008) | 3 lines
Fixed the call to assemble_param_vector().
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r5641 | bugman | 2008-04-13 19:55:43 +0200 (Sun, 13 Apr 2008) | 3 lines
Changed all refs to 'cdp.diff' to 'cdp.diff_tensor'.
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r5642 | bugman | 2008-04-13 19:57:35 +0200 (Sun, 13 Apr 2008) | 3 lines
Spelling correction in a comment.
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r5643 | bugman | 2008-04-13 20:02:52 +0200 (Sun, 13 Apr 2008) | 3 lines
Modified the assemble_param_vector() method to allow the parameter set to
be given as an arg.
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r5644 | bugman | 2008-04-13 20:03:12 +0200 (Sun, 13 Apr 2008) | 3 lines
Comment fix.
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r5645 | bugman | 2008-04-13 20:03:45 +0200 (Sun, 13 Apr 2008) | 3 lines
Fixed the call to assemble_param_vector().
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r5646 | bugman | 2008-04-13 20:08:10 +0200 (Sun, 13 Apr 2008) | 3 lines
Fix for the initialisation of the maths_fns.mf.Mf class.
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r5647 | bugman | 2008-04-13 20:09:49 +0200 (Sun, 13 Apr 2008) | 3 lines
Fixes for the gyromagnetic ratio setup.
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r5648 | bugman | 2008-04-13 20:20:42 +0200 (Sun, 13 Apr 2008) | 5 lines
Converted the model_selection() user function to the new relax design.
The back end code still needs to be converted.
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r5649 | bugman | 2008-04-13 20:39:58 +0200 (Sun, 13 Apr 2008) | 3 lines
Removed the check of the recently deleted modsel_run arg.
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r5650 | bugman | 2008-04-13 20:42:20 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted all the model_selection methods into module functions.
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r5651 | bugman | 2008-04-13 20:43:13 +0200 (Sun, 13 Apr 2008) | 3 lines
Alphabetical ordering of functions.
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r5652 | bugman | 2008-04-13 20:45:48 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the aic() docstring to epydoc format.
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r5653 | bugman | 2008-04-13 20:46:37 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the aicc() docstring to epydoc format.
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r5654 | bugman | 2008-04-13 20:47:12 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the bic() docstring to epydoc format.
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r5655 | bugman | 2008-04-13 21:20:13 +0200 (Sun, 13 Apr 2008) | 3 lines
Fixed the module docstring.
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r5656 | bugman | 2008-04-13 21:25:29 +0200 (Sun, 13 Apr 2008) | 3 lines
Removed the word 'run' from the copy() docstring.
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r5657 | bugman | 2008-04-13 21:29:19 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the whole of the select() function to the new relax design.
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r5658 | bugman | 2008-04-13 22:17:48 +0200 (Sun, 13 Apr 2008) | 3 lines
Converted the default flag arg vals to bools in the minimise() method.
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r5659 | bugman | 2008-04-13 22:58:51 +0200 (Sun, 13 Apr 2008) | 5 lines
Some changes to the tests() function.
This code has to be completely redone though.
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r5660 | bugman | 2008-04-13 23:25:59 +0200 (Sun, 13 Apr 2008) | 3 lines
Created the same_sequence() function to test if two pipes have the same
sequence.
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r5661 | bugman | 2008-04-13 23:33:35 +0200 (Sun, 13 Apr 2008) | 3 lines
Deleted the tests() function and instead called same_sequence().
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r5662 | bugman | 2008-04-13 23:42:55 +0200 (Sun, 13 Apr 2008) | 3 lines
Bug fix for the same_sequence() function.
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r5664 | bugman | 2008-04-14 14:15:49 +0200 (Mon, 14 Apr 2008) | 3 lines
Added a ton of platform information to the model-free optimisation system
tests debugging string.
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r5665 | bugman | 2008-04-14 14:16:16 +0200 (Mon, 14 Apr 2008) | 3 lines
Small change to the debugging printout.
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r5666 | bugman | 2008-04-14 14:18:27 +0200 (Mon, 14 Apr 2008) | 3 lines
Shifted the system information into module variables, rather than
re-fetching these each time.
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r5667 | bugman | 2008-04-14 14:20:05 +0200 (Mon, 14 Apr 2008) | 3 lines
Catch MS Windows!
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r5668 | bugman | 2008-04-14 14:27:19 +0200 (Mon, 14 Apr 2008) | 3 lines
Made the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() test
pass on 32 bit Linux.
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r5669 | bugman | 2008-04-14 14:32:01 +0200 (Mon, 14 Apr 2008) | 3 lines
Spun off the value testing code into the new value_test() method.
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r5670 | bugman | 2008-04-14 14:33:11 +0200 (Mon, 14 Apr 2008) | 3 lines
For differences in optimisation, only the parameters which are different
are changed.
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r5671 | bugman | 2008-04-14 14:36:54 +0200 (Mon, 14 Apr 2008) | 3 lines
The test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149() system test now
passes on 32 bit Linux.
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r5672 | bugman | 2008-04-14 14:39:06 +0200 (Mon, 14 Apr 2008) | 3 lines
The test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149() system test now
passes on 32 bit Linux.
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r5673 | bugman | 2008-04-14 14:41:36 +0200 (Mon, 14 Apr 2008) | 3 lines
The test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149() system test now
passes on 32 bit Linux.
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r5674 | bugman | 2008-04-14 14:46:40 +0200 (Mon, 14 Apr 2008) | 3 lines
Converted all the remaining model-free optimisation system tests to use
value_test().
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r5675 | bugman | 2008-04-14 14:57:45 +0200 (Mon, 14 Apr 2008) | 3 lines
Tightened up the S2 test.
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r5676 | bugman | 2008-04-14 15:04:47 +0200 (Mon, 14 Apr 2008) | 3 lines
Made the S2 test exact!
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r5677 | bugman | 2008-04-14 15:09:14 +0200 (Mon, 14 Apr 2008) | 3 lines
Made the te test exact!
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r5678 | bugman | 2008-04-14 15:16:50 +0200 (Mon, 14 Apr 2008) | 3 lines
Made the Rex test exact! The Rex conversion factor has been shifted into
value_test().
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r5679 | bugman | 2008-04-14 15:20:08 +0200 (Mon, 14 Apr 2008) | 3 lines
The te conversion factor has been shifted into value_test().
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r5680 | bugman | 2008-04-14 15:24:46 +0200 (Mon, 14 Apr 2008) | 3 lines
Made the chi-squared test exact.
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r5681 | bugman | 2008-04-14 15:32:07 +0200 (Mon, 14 Apr 2008) | 3 lines
Created a unit test for testing the proper operation of the spin loop with
wildcard spin selection.
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r5682 | bugman | 2008-04-14 15:36:30 +0200 (Mon, 14 Apr 2008) | 3 lines
Created a unit test for the proper operation of the spin loop with spin
selection '@NH|@N5'.
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r5683 | bugman | 2008-04-14 15:37:09 +0200 (Mon, 14 Apr 2008) | 3 lines
Updated the docstring of test_spin_loop_wildcard().
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r5684 | bugman | 2008-04-14 15:38:45 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote a unit test for testing the generic_fns.selection.tokenise() function
on the string '@N*'.
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r5685 | bugman | 2008-04-14 15:46:39 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote a unit test for testing generic_fns.selection.parse_token() function
on the string 'N*'.
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r5686 | bugman | 2008-04-14 16:10:53 +0200 (Mon, 14 Apr 2008) | 3 lines
Created the Selection.match() method to add regular expression capabilities
to spin id strings.
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r5687 | bugman | 2008-04-14 16:12:39 +0200 (Mon, 14 Apr 2008) | 3 lines
The molecule and residue name checking now use the new Selection.match()
method.
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r5688 | bugman | 2008-04-14 16:13:26 +0200 (Mon, 14 Apr 2008) | 3 lines
Renamed Selection.match() to Selection.wildcard_match()
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r5689 | bugman | 2008-04-14 16:18:54 +0200 (Mon, 14 Apr 2008) | 3 lines
Converted all numbers to strings for the Selection.wildcard_match() method.
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r5690 | bugman | 2008-04-14 16:30:49 +0200 (Mon, 14 Apr 2008) | 5 lines
'*' is replaced with '+' ion the Selection.wildcard_match() method.
This is to convert from relax re format the python re format.
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r5691 | bugman | 2008-04-14 16:33:38 +0200 (Mon, 14 Apr 2008) | 3 lines
Bug fix: None, str, or number is now accepted in
Selection.wildcard_match().
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r5692 | bugman | 2008-04-14 16:39:36 +0200 (Mon, 14 Apr 2008) | 3 lines
'*' shouldn't be replaced by '+', it should be replaced by '.*'!
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r5693 | bugman | 2008-04-14 16:50:04 +0200 (Mon, 14 Apr 2008) | 3 lines
Renamed 'string' to 'id' in the Selection.wildcard_match() method.
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r5694 | bugman | 2008-04-14 16:51:28 +0200 (Mon, 14 Apr 2008) | 3 lines
Converted the Selection.wildcard_match() method into a module function.
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r5695 | bugman | 2008-04-14 16:54:33 +0200 (Mon, 14 Apr 2008) | 3 lines
The Scientific Python data object now uses the wildcard_match() method to
handle regular expression.
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r5696 | bugman | 2008-04-14 16:57:29 +0200 (Mon, 14 Apr 2008) | 3 lines
The identifier is now bracketed by '^' and '$' in wildcard_match().
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r5697 | bugman | 2008-04-14 17:31:59 +0200 (Mon, 14 Apr 2008) | 3 lines
The element type is added to the SpinContainer in the load_spins() function.
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r5698 | bugman | 2008-04-14 17:33:29 +0200 (Mon, 14 Apr 2008) | 3 lines
A few minor changes to the Selection object.
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r5699 | bugman | 2008-04-14 17:43:17 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote a unit test for the Selection object for complex boolean mol-res-spin
selections.
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r5700 | bugman | 2008-04-14 17:56:40 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote a unit test for the Selection object for boolean '&' mol-res-spin
selections.
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r5701 | bugman | 2008-04-14 17:58:26 +0200 (Mon, 14 Apr 2008) | 3 lines
Code rearrangment in the test_Selection_boolean_and() unit test.
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r5702 | bugman | 2008-04-14 18:03:12 +0200 (Mon, 14 Apr 2008) | 3 lines
Expanded and completed the test_Selection_complex_boolean() unit test of
"#Ap4Aase:4 & :Pro | #RNA".
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r5703 | bugman | 2008-04-14 18:13:20 +0200 (Mon, 14 Apr 2008) | 3 lines
Fixes for the test_Selection_complex_boolean() unit test.
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r5704 | bugman | 2008-04-14 18:20:37 +0200 (Mon, 14 Apr 2008) | 3 lines
A few changes to the test_boolean_complex_selection() unit test.
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r5705 | bugman | 2008-04-14 18:35:44 +0200 (Mon, 14 Apr 2008) | 5 lines
Converted test_boolean_or_selection() to test_Selection_boolean_or().
The Selection object is being fully probed.
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r5706 | bugman | 2008-04-14 18:47:01 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote the test_spin_loop_single_spin() unit test.
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r5707 | bugman | 2008-04-14 18:52:50 +0200 (Mon, 14 Apr 2008) | 3 lines
Wrote the unit test test_spin_loop_boolean_or().
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r5709 | bugman | 2008-04-14 21:15:06 +0200 (Mon, 14 Apr 2008) | 3 lines
Removed the svnmerged-integrated property. Don't know how this got here.
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r5721 | bugman | 2008-04-14 22:39:19 +0200 (Mon, 14 Apr 2008) | 3 lines
Fixes for the test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149() system
test on 64 bit Linux.
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r5722 | bugman | 2008-04-14 22:50:50 +0200 (Mon, 14 Apr 2008) | 3 lines
Fixes for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149()
system test for 64 bit Linux.
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r5723 | bugman | 2008-04-14 22:52:44 +0200 (Mon, 14 Apr 2008) | 3 lines
Modified the mesg_opt_debug() method to print only opt info rather than
everything in the spin cont.
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r5724 | bugman | 2008-04-14 22:58:00 +0200 (Mon, 14 Apr 2008) | 3 lines
Fixed all the model-free optimisation system tests for 64 bit Linux.
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r5725 | bugman | 2008-04-14 23:37:56 +0200 (Mon, 14 Apr 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-5710" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
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r5727 | bugman | 2008-04-14 23:42:15 +0200 (Mon, 14 Apr 2008) | 52 lines
Merged revisions 5711,5713-5725 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
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r5711 | bugman | 2008-04-14 21:20:26 +0200 (Mon, 14 Apr 2008) | 12 lines
Ok, lets try this again! Created a branch for some nasty breakages and
testing new ideas.
The command used was:
svn cp svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
The spin_loop and its siblings cannot currently handle the branching tree
formed by the Selection
object (nested within Selection._union and Selection._intersect). For
example if there are two
molecules loaded into the data store, 'Ap4Aase' and 'RNA', the spin_loop
with the spin id string
'#Ap4Aase:Glu | #RNA@C8' loops over all spins of both molecules!!!
Therefore all the usages of the
Selection object need to be redesigned, and possibly the Selection object
itself.
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r5713 | bugman | 2008-04-14 21:26:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Modified the spin_loop to check the tuple of (mol, res, spin) against the
selection object.
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r5714 | bugman | 2008-04-14 21:49:20 +0200 (Mon, 14 Apr 2008) | 5 lines
Redesigned the selection object method Selection.__contains__().
Now multiple MoleculeContainer, ResidueContainer, or SpinContainer
instances can be compared.
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r5715 | bugman | 2008-04-14 21:54:34 +0200 (Mon, 14 Apr 2008) | 3 lines
Some fixes for the Selection.__contains__() method.
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r5716 | bugman | 2008-04-14 21:59:10 +0200 (Mon, 14 Apr 2008) | 3 lines
Changed the spin_index_loop() function to use the same form as
spin_loop().
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r5717 | bugman | 2008-04-14 22:00:39 +0200 (Mon, 14 Apr 2008) | 3 lines
Updated the residue_loop() function.
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r5718 | bugman | 2008-04-14 22:03:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Updated all the other comparisons to the selection object.
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r5719 | bugman | 2008-04-14 22:17:11 +0200 (Mon, 14 Apr 2008) | 3 lines
The Selection.__contains__() method now is complete and all the relevant
unit tests pass again.
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r5720 | bugman | 2008-04-14 22:22:08 +0200 (Mon, 14 Apr 2008) | 3 lines
Small docstring updates.
........
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r5728 | bugman | 2008-04-14 23:43:05 +0200 (Mon, 14 Apr 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spin_loop_bool
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r5730 | bugman | 2008-04-15 22:12:42 +0200 (Tue, 15 Apr 2008) | 3 lines
Updated the model-free num_instances() method to the new relax design.
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r5731 | bugman | 2008-04-15 22:14:24 +0200 (Tue, 15 Apr 2008) | 3 lines
Fixed the calls to count_num_instances() in the select() function.
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r5732 | bugman | 2008-04-15 22:16:59 +0200 (Tue, 15 Apr 2008) | 3 lines
Fixed a self.assert_() call in the system test for AIC model selection
between diffusion tensors.
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r5733 | bugman | 2008-04-15 22:17:49 +0200 (Tue, 15 Apr 2008) | 5 lines
Renamed the system test method for AIC model selection between two
diffusion tensors.
The old name was test_diff(), whereas the new is
test_aic_mod_sel_diff_tensor().
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r5734 | bugman | 2008-04-15 22:20:42 +0200 (Tue, 15 Apr 2008) | 3 lines
Another fix for the checks in the test_aic_mod_sel_diff_tensor() system
test.
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r5735 | bugman | 2008-04-15 22:28:37 +0200 (Tue, 15 Apr 2008) | 3 lines
Some fixes for the model selection select() function - pipe switching was
necessary.
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r5736 | bugman | 2008-04-15 22:43:02 +0200 (Tue, 15 Apr 2008) | 3 lines
Converted the model-free model_statistics() method to the new relax design.
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r5737 | bugman | 2008-04-15 22:44:59 +0200 (Tue, 15 Apr 2008) | 6 lines
Modified the test_aic_mod_sel_diff_tensor() system test.
The model selection pipe will be created by the model_selection() use
function, it doesn't need to
be precreated!
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r5738 | bugman | 2008-04-15 22:53:16 +0200 (Tue, 15 Apr 2008) | 3 lines
Reintroduced the modsel_pipe arg to the model_selection() user function
(the deleted modsel_run).
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r5739 | bugman | 2008-04-15 22:55:51 +0200 (Tue, 15 Apr 2008) | 3 lines
Reintroduced the modsel_pipe arg to the select() function.
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r5740 | bugman | 2008-04-15 22:56:08 +0200 (Tue, 15 Apr 2008) | 3 lines
Removed some debugging code.
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r5741 | bugman | 2008-04-15 23:11:13 +0200 (Tue, 15 Apr 2008) | 3 lines
Converted the select() method docstring to epydoc format.
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r5742 | bugman | 2008-04-15 23:12:20 +0200 (Tue, 15 Apr 2008) | 3 lines
Fixed the setup of the maths_fns.jw_mapping.Mapping object.
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[... 210 lines stripped ...]
r5794 - /1.2/