relax SVN archive

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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@...>)
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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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r4917 | bugman | 2008-02-07 11:09:56 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the test_binary() method into a module function.
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r4918 | bugman | 2008-02-07 11:11:17 +0100 (Thu, 07 Feb 2008) | 3 lines

Updated the generic_fns.molmol module to import the relevent functions from the relax_io module.
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r4919 | bugman | 2008-02-07 11:13:02 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol pipe_open() function to the new relax design.
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r4920 | bugman | 2008-02-07 11:15:04 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol pipe_open_test() function to the new relax design.
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r4921 | bugman | 2008-02-07 11:27:46 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol pipe_write() function to the new relax design.
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r4922 | bugman | 2008-02-07 11:28:36 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol ribbon() function to the new relax design.
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r4923 | bugman | 2008-02-07 11:30:01 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol tensor_pdb() function to the new relax design.
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r4924 | bugman | 2008-02-07 11:30:29 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol view() function to the new relax design.
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r4925 | bugman | 2008-02-07 11:34:37 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the Molmol write() function to the new relax design.
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r4926 | bugman | 2008-02-07 11:36:08 +0100 (Thu, 07 Feb 2008) | 3 lines

Updated the calls to the create_macro() function.
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r4927 | bugman | 2008-02-07 11:43:09 +0100 (Thu, 07 Feb 2008) | 3 lines

Shifted the core of the angles system test into a relax script.
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r4928 | bugman | 2008-02-07 13:34:48 +0100 (Thu, 07 Feb 2008) | 3 lines

Converted the generic_fns.structure.vectors() function to the new relax design.
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r4929 | bugman | 2008-02-07 13:38:09 +0100 (Thu, 07 Feb 2008) | 3 lines

Replaced all calls to count_spins() with exists_mol_res_spin_data().
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r4930 | bugman | 2008-02-07 13:40:04 +0100 (Thu, 07 Feb 2008) | 3 lines

Updated the RelaxPdbError class to not require the pipe argument.
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r4931 | bugman | 2008-02-07 13:41:23 +0100 (Thu, 07 Feb 2008) | 5 lines

Bug fix for the generic_fns.structure.vectors() function.

The test for the structure was back to front.
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r4932 | bugman | 2008-02-07 13:42:25 +0100 (Thu, 07 Feb 2008) | 3 lines

Removed the tests for the res_num and res_name args as they no longer exist.
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r4933 | bugman | 2008-02-07 13:48:15 +0100 (Thu, 07 Feb 2008) | 3 lines

Added the verbosity argument to the structure.vectors() user function.
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r4934 | bugman | 2008-02-07 13:49:35 +0100 (Thu, 07 Feb 2008) | 3 lines

Added the verbosity argument to the generic_fns.structure.vectors() function.
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r4935 | bugman | 2008-02-07 13:50:37 +0100 (Thu, 07 Feb 2008) | 5 lines

Bug fix for the generic_fns.structure.xh_vector() function.

The 'cdp' was not being aliased.
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r4936 | bugman | 2008-02-07 13:53:32 +0100 (Thu, 07 Feb 2008) | 5 lines

Bug fix for the generic_fns.structure.vectors() function.

There was a problem with the new numpy arrays (which has no problems as Numeric arrays).
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