Author: bugman
Date: Mon Feb 11 13:43:33 2008
New Revision: 4942
URL: http://svn.gna.org/viewcvs/relax?rev=4942&view=rev
Log:
Blocked revisions
4673-4693,4698-4701,4712-4717,4745,4748,4759,4778-4780,4785,4787,4792,4796,4799,4802,4804,4815-4819,4821-4834,4839,4841-4850,4854-4856,4858-4860,4886-4888,4898-4936
via svnmerge
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r4673 | bugman | 2008-01-13 12:48:43 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the model arg of the model_free.select_model() user function.
The testing of this arg started with and elif statement!!!
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r4674 | bugman | 2008-01-13 12:53:06 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fixes for the model-free user function arg unit tests.
Some args had to be supplied in the unit tests to prevent RelaxErrors from
reaching the correct arg.
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r4675 | bugman | 2008-01-13 12:57:32 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the params arg of the model_free.create_model() user function.
This arg is now properly checked.
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r4676 | bugman | 2008-01-13 13:01:10 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the Model_free_main.__init__() method and converted its docstring
to that of the class.
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r4677 | bugman | 2008-01-13 17:31:48 +0100 (Sun, 13 Jan 2008) | 5 lines
Renamed all the instantiated classes in specific_fns.__init__.
This is to avoid name clashes and the overwriting of the module names.
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r4678 | bugman | 2008-01-13 17:37:05 +0100 (Sun, 13 Jan 2008) | 3 lines
Imported the specific_fns.model_free_obj object.
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r4679 | bugman | 2008-01-13 18:19:08 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the create_model() model-free method to the new relax design.
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r4680 | bugman | 2008-01-13 18:22:22 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the model_setup() model-free method to the new relax design.
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r4681 | bugman | 2008-01-13 18:25:13 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the data_init() model-free method to the new relax design.
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r4682 | bugman | 2008-01-13 18:26:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Updated the docstring of the model_setup() model-free method to be in
epydoc format.
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r4683 | bugman | 2008-01-13 18:28:09 +0100 (Sun, 13 Jan 2008) | 5 lines
Added the missing import of the spin_loop.
The model 'm4' construction system test now passes.
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r4684 | bugman | 2008-01-13 18:29:44 +0100 (Sun, 13 Jan 2008) | 3 lines
Fixes for all the unit tests of the generic_fns.value.partition_params()
function.
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r4685 | bugman | 2008-01-13 18:32:16 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the select_model() model-free method to the new relax design.
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r4686 | bugman | 2008-01-13 18:39:35 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the overfit_deselect() model-free method to the new relax design.
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r4687 | bugman | 2008-01-13 18:43:26 +0100 (Sun, 13 Jan 2008) | 3 lines
Cleaned up the code of the overfit_deselect() model-free method.
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r4688 | bugman | 2008-01-13 19:00:31 +0100 (Sun, 13 Jan 2008) | 5 lines
Converted the grid_search() model-free method to the new relax design.
The grid_search_setup() method has been merged into this method.
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r4689 | bugman | 2008-01-13 19:03:55 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the system test of AIC model selection between two diffusion
tensors.
The diffusion tensor was not been properly set up.
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r4690 | bugman | 2008-01-13 19:16:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Shifted all of the model-free optimisation related methods into a separate
module.
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r4691 | bugman | 2008-01-13 19:16:32 +0100 (Sun, 13 Jan 2008) | 3 lines
Renamed the module to avoid a name clash.
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r4692 | bugman | 2008-01-13 19:50:36 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_names() model-free method to the new relax
design.
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r4693 | bugman | 2008-01-13 20:02:17 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_vector() model-free method to the new relax
design.
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r4698 | semor | 2008-01-14 02:26:39 +0100 (Mon, 14 Jan 2008) | 3 lines
Added comments to the imports.
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r4699 | semor | 2008-01-14 05:25:19 +0100 (Mon, 14 Jan 2008) | 3 lines
Added more comments to the imports.
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r4700 | semor | 2008-01-14 05:31:50 +0100 (Mon, 14 Jan 2008) | 3 lines
Added somemore comments to the imports.
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r4701 | semor | 2008-01-14 15:49:41 +0100 (Mon, 14 Jan 2008) | 3 lines
Added some comments to the imports and ordered imports alphabetically.
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r4712 | bugman | 2008-01-15 10:46:52 +0100 (Tue, 15 Jan 2008) | 3 lines
Removed the empty __init__() method and shifted its docstring to that of
the class.
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r4713 | bugman | 2008-01-15 10:47:09 +0100 (Tue, 15 Jan 2008) | 3 lines
Removed an orphaned comment.
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r4714 | bugman | 2008-01-15 10:50:04 +0100 (Tue, 15 Jan 2008) | 3 lines
Updated the base class method has_errors() to the new relax design.
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r4715 | bugman | 2008-01-15 10:52:45 +0100 (Tue, 15 Jan 2008) | 3 lines
Updated the return_data() and return_error() base class methods to the new
relax design.
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r4716 | bugman | 2008-01-15 10:54:47 +0100 (Tue, 15 Jan 2008) | 3 lines
Updated the base class method sim_return_selected() to the new relax design.
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r4717 | bugman | 2008-01-15 11:13:30 +0100 (Tue, 15 Jan 2008) | 5 lines
Added a dummy overfit_deselect() method to the base class.
This method does nothing.
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r4745 | bugman | 2008-01-15 14:40:06 +0100 (Tue, 15 Jan 2008) | 3 lines
Shifted the grid ops tests into the test_grid_ops() base class function.
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r4748 | bugman | 2008-01-15 14:52:49 +0100 (Tue, 15 Jan 2008) | 3 lines
Fixed a bug in the test_grid_ops() base class method which was preventing
relax from starting.
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r4759 | semor | 2008-01-15 19:11:09 +0100 (Tue, 15 Jan 2008) | 8 lines
Changed the precision for gX in the mfpar file for use of ModelFree with
the palmer.py script.
The change was from a three decimal precision (-2.713) to a four decimal
precision (-2.7126).
This was discussed in thread starting at:
https://mail.gna.org/public/relax-devel/2008-01/msg00040.html
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r4778 | bugman | 2008-01-16 11:30:55 +0100 (Wed, 16 Jan 2008) | 3 lines
Converted the maths_fns.chi2 module from Numeric to numpy.
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r4779 | bugman | 2008-01-16 12:00:28 +0100 (Wed, 16 Jan 2008) | 5 lines
Updated the docstrings of the chi-squared value, gradient, and Hessian
functions.
They are now in epydoc format.
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r4780 | bugman | 2008-01-16 12:04:34 +0100 (Wed, 16 Jan 2008) | 3 lines
Added a module docstring to the chi2 module.
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r4785 | semor | 2008-01-16 16:08:42 +0100 (Wed, 16 Jan 2008) | 5 lines
Corrected a function spacing so it has 2 preceding empty lines.
This was pointed by the 'code_validator' script.
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r4787 | bugman | 2008-01-16 16:37:07 +0100 (Wed, 16 Jan 2008) | 3 lines
Shifted all the dummy return_conversion_factor() methods which return 1
into the base class.
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r4792 | bugman | 2008-01-16 17:01:15 +0100 (Wed, 16 Jan 2008) | 3 lines
Temporarily shifted the model-free code from using the 'minimise' directory
to using minfx.
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r4796 | bugman | 2008-01-16 17:31:48 +0100 (Wed, 16 Jan 2008) | 3 lines
Shifted the model-free disassemble_param_vector() method as it is specific
to minimisation.
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r4799 | bugman | 2008-01-16 18:00:59 +0100 (Wed, 16 Jan 2008) | 3 lines
Converted the model-free code from Numeric to numpy.
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r4802 | semor | 2008-01-16 19:00:11 +0100 (Wed, 16 Jan 2008) | 3 lines
Removed a trailing whitespace.
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r4804 | bugman | 2008-01-17 10:19:47 +0100 (Thu, 17 Jan 2008) | 5 lines
Created a base class method num_instances() to check the sequence and
return the number of spins.
The J(w) mapping and relaxation curve fitting num_instances() methods have
been removed.
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r4815 | bugman | 2008-01-17 15:08:15 +0100 (Thu, 17 Jan 2008) | 8 lines
Updated the generic_fns.value module functions set() and partition_params()
to be more general.
The updating is not complete, but works for most of the current codebase.
The assumption of a data
analysis type having a diffusion or other tensor has been removed. This
has been replaced by the
concept that the params are now partitioned into those that are spin
specific and those that are
not. The diffusion tensor stuff will be moved into the model-free code.
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r4816 | bugman | 2008-01-17 15:18:56 +0100 (Thu, 17 Jan 2008) | 5 lines
Removed some useless code in the partition_params() function.
Because of the main if-else loop, this code will never be executed!
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r4817 | bugman | 2008-01-17 15:21:56 +0100 (Thu, 17 Jan 2008) | 3 lines
Fixed all of the unit tests of the generic_fns.value.partition_params()
function.
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r4818 | bugman | 2008-01-17 15:28:16 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed some debugging code which is now covered by the unit tests.
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r4819 | bugman | 2008-01-17 15:34:31 +0100 (Thu, 17 Jan 2008) | 5 lines
More fixes for the unit tests of the generic_fns.value.partition_params()
function.
The current data pipe needed to be changed back to a model-free pipe.
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r4821 | semor | 2008-01-17 15:57:43 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the maths_fns.jw_mapping module from Numeric to numpy.
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r4822 | bugman | 2008-01-17 16:07:22 +0100 (Thu, 17 Jan 2008) | 7 lines
Big refactorisation of the value setting code. Expect breakages as the
changes aren't complete!
The parameter setting set() base class method has been shifted from the
specific code to
the generic_fns.value module (and has been converted to a function). This
method simply sets spin
specific functions and hence has been renamed to the set_spin_params()
function.
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r4823 | bugman | 2008-01-17 16:11:21 +0100 (Thu, 17 Jan 2008) | 5 lines
Added a few more functions to be returned by get_specific_fn().
These include data_init(), default_value(), and set_update().
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r4824 | bugman | 2008-01-17 16:13:14 +0100 (Thu, 17 Jan 2008) | 3 lines
Shifted the RelaxParamSetError import to the generic_fns.value module.
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r4825 | bugman | 2008-01-17 16:19:55 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed the Numeric and Scientific packages from the relax prompt namespace.
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r4826 | bugman | 2008-01-17 16:23:02 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the data.diff_tensor code from Numeric to numpy.
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r4827 | semor | 2008-01-17 16:34:33 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted more maths_fns modules from Numeric to numpy.
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r4828 | semor | 2008-01-17 16:37:25 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted another maths_fns module from Numeric to numpy.
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r4829 | bugman | 2008-01-17 16:56:35 +0100 (Thu, 17 Jan 2008) | 3 lines
Removed the cdp aliases as they are not used very often.
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r4830 | bugman | 2008-01-17 17:02:50 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted the generic_fns.value code from Numeric to numpy.
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r4831 | bugman | 2008-01-17 17:10:28 +0100 (Thu, 17 Jan 2008) | 6 lines
Changed the call to diffusion_tensor.set() to the new specific function
set_nonspin_params().
The code for setting parameters that are non-spin specific is very much
dependent on the analysis
type, and hence this has been shifted into a call into specific_fns.
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r4832 | bugman | 2008-01-17 17:16:22 +0100 (Thu, 17 Jan 2008) | 5 lines
Implemented the base class method set_non_spin_params().
This throws a RelaxError if anything is sent into the function.
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r4833 | bugman | 2008-01-17 17:21:11 +0100 (Thu, 17 Jan 2008) | 5 lines
Wrote the model-free specific set_non_spin_params() method.
This simply calls the diffusion tensor setting code.
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r4834 | bugman | 2008-01-17 17:35:05 +0100 (Thu, 17 Jan 2008) | 5 lines
Big inheritance bug fix for the model-free code.
The base class methods were being used instead of the model-free methods!
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r4839 | bugman | 2008-01-17 18:20:36 +0100 (Thu, 17 Jan 2008) | 6 lines
Modified the partition_params() function to better handle when no parameter
name is supplied.
This situation is used for setting the parameter values of the model. The
function now returns the
model_values list to be used later on.
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r4841 | semor | 2008-01-17 21:50:18 +0100 (Thu, 17 Jan 2008) | 5 lines
Converted another maths_fns module from Numeric to numpy.
The Numeric.matrixmultiply module is deprecated and was thus replaced by
the numpy.dot module.
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r4842 | semor | 2008-01-17 21:53:51 +0100 (Thu, 17 Jan 2008) | 3 lines
Finished the conversion of maths_fns modules from Numeric to numpy.
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r4843 | semor | 2008-01-17 21:58:50 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted dx modules from Numeric to numpy.
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r4844 | semor | 2008-01-17 22:04:34 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted some sample scripts from Numeric to numpy.
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r4845 | semor | 2008-01-17 22:09:17 +0100 (Thu, 17 Jan 2008) | 3 lines
Converted test_suite modules from Numeric to numpy.
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r4846 | semor | 2008-01-17 22:13:26 +0100 (Thu, 17 Jan 2008) | 5 lines
Converted a specific_fns module from Numeric to numpy.
The Numeric.matrixmultiply module is deprecated and was thus replaced by
the numpy.dot module.
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r4847 | semor | 2008-01-17 22:15:32 +0100 (Thu, 17 Jan 2008) | 5 lines
Fully converted a specific_fns module from Numeric to numpy.
The Numeric.matrixmultiply to numpy.dot change had only been made in the
import and not the code.
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r4848 | semor | 2008-01-17 23:00:51 +0100 (Thu, 17 Jan 2008) | 8 lines
Converted generic_fns modules from Numeric to numpy.
As point in a post by Edward d'Auvergne (minfx-devel mailing list, see
below), the select_sim array
(which calls 'ones()') was specified as a integer array.
https://mail.gna.org/public/minfx-commits/2008-01/msg00004.html (Message-id:
<E1JF9Gs-000081-9c@xxxxxxxxxxxxxxxxxx>)
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r4849 | bugman | 2008-01-17 23:32:10 +0100 (Thu, 17 Jan 2008) | 5 lines
Initialise the model_values array in the partition_params() function.
This fixes a bug due to model_values not being defined.
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r4850 | bugman | 2008-01-17 23:33:55 +0100 (Thu, 17 Jan 2008) | 3 lines
Fixes for the unit tests of the partition_params() function.
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r4854 | bugman | 2008-01-18 15:42:02 +0100 (Fri, 18 Jan 2008) | 3 lines
Big refactorisation of the partition_params() and set() functions.
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r4855 | bugman | 2008-01-18 15:58:10 +0100 (Fri, 18 Jan 2008) | 3 lines
Changed the way the model parameters are set in the set() function.
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r4856 | bugman | 2008-01-18 16:01:28 +0100 (Fri, 18 Jan 2008) | 6 lines
Reverted r4850 as generic_fns.value.partition_params() has returned to its
previous behaviour.
The command used was:
svn merge -r4850:4849 .
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r4858 | semor | 2008-01-18 22:41:55 +0100 (Fri, 18 Jan 2008) | 3 lines
Uniformized the format of constants.
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r4859 | bugman | 2008-01-21 11:15:41 +0100 (Mon, 21 Jan 2008) | 5 lines
When None, the param variable is converted to a list of None with the
length equal to that of val.
This affects the generic_fns.value.set() function when no parameters are
supplied.
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r4860 | bugman | 2008-01-21 11:19:40 +0100 (Mon, 21 Jan 2008) | 6 lines
Reverted the last change as param needs to be passed to
set_non_spin_params() as None.
The command used was:
svn merge -r4859:4858 .
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r4886 | bugman | 2008-01-25 14:13:57 +0100 (Fri, 25 Jan 2008) | 9 lines
Bug fix for the generic_fns.value.set() function.
The differentiation between a spin specific parameter and a global
parameter was not working for
specific analyses with no spin specific parameters. The return_data_name()
function was being used
to differentiate, which makes no sense. So instead the is_spin_param()
function has been introduced
to allow the specific code to answer the question explicitly. Note that
this will temporarily break
many things.
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r4887 | bugman | 2008-01-25 15:31:19 +0100 (Fri, 25 Jan 2008) | 5 lines
Implemented the is_spin_param() base class method.
This function always returns true.
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r4888 | bugman | 2008-01-25 15:56:06 +0100 (Fri, 25 Jan 2008) | 3 lines
Implemented the model-free specific is_spin_param() method.
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r4898 | bugman | 2008-02-04 14:32:53 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed a junk comment.
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r4899 | bugman | 2008-02-04 14:38:37 +0100 (Mon, 04 Feb 2008) | 3 lines
Converted all methods in the Structure class into functions of the
generic_fns.structure module.
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r4900 | bugman | 2008-02-04 14:40:22 +0100 (Mon, 04 Feb 2008) | 3 lines
The args of the read_pdb() fn are no longer placed into self.
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r4901 | bugman | 2008-02-04 14:42:37 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed all references to 'self' from the generic_fns.structure module.
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r4902 | bugman | 2008-02-04 14:54:07 +0100 (Mon, 04 Feb 2008) | 3 lines
Updated all the tests of the read_pdb() function to the new relax design.
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r4903 | bugman | 2008-02-04 15:03:34 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed an unused import of SpecificData.
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r4904 | bugman | 2008-02-04 15:04:19 +0100 (Mon, 04 Feb 2008) | 3 lines
Changed the 3D structure data structure from a SpecificData class to the
Element class.
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r4905 | bugman | 2008-02-04 15:05:10 +0100 (Mon, 04 Feb 2008) | 3 lines
Deleted the SpecificData container as nothing now uses it.
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r4906 | bugman | 2008-02-04 16:07:25 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed the adding of the 'run' to the 3D structure data structure.
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r4907 | bugman | 2008-02-04 16:08:29 +0100 (Mon, 04 Feb 2008) | 3 lines
Replaced all 'relax_data_store.pdb[run]' with 'cdp.structure'.
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r4908 | bugman | 2008-02-04 16:19:41 +0100 (Mon, 04 Feb 2008) | 3 lines
Converted the load_structures() function to the new relax design.
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r4909 | bugman | 2008-02-04 16:22:14 +0100 (Mon, 04 Feb 2008) | 3 lines
Finished converting the read_pdb() function to the new relax design.
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r4910 | bugman | 2008-02-04 18:06:15 +0100 (Mon, 04 Feb 2008) | 6 lines
Huge redesign of the load_PDB_sequence() function (and converted it to the
new relax design).
This new function should give much more flexibility and abstraction in the
mapping from the
molecular structure to the relax mol-res-spin data structure.
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r4911 | bugman | 2008-02-07 10:33:14 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol 'command_history' structure into a module variable.
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r4912 | bugman | 2008-02-07 10:35:21 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted all the Molmol class methods into module functions.
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r4913 | bugman | 2008-02-07 10:36:42 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol command() function to the new relax design.
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r4914 | bugman | 2008-02-07 11:04:05 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol create_macro() function to the new relax design.
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r4915 | bugman | 2008-02-07 11:06:52 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol macro_exec() function to the new relax design.
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r4916 | bugman | 2008-02-07 11:08:02 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol open_pdb() function to the new relax design.
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[... 92 lines stripped ...]
r4942 - /1.2/