relax SVN archive

Updated all the tests of the read_pdb() function to the new relax design.

Removed all references to 'self' from the generic_fns.structure module.

The args of the read_pdb() fn are no longer placed into self.

Converted all methods in the Structure class into functions of the generic_fns.structure module.

Removed a junk comment.

Merged revisions 4854-4856,4858-4860,4886-4888 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3

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r4854 | bugman | 2008-01-18 09:42:02 -0500 (Fri, 18 Jan 2008) | 3 lines

Big refactorisation of the partition_params() and set() functions.
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r4855 | bugman | 2008-01-18 09:58:10 -0500 (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 10:01:28 -0500 (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 16:41:55 -0500 (Fri, 18 Jan 2008) | 3 lines

Uniformized the format of constants.
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r4859 | bugman | 2008-01-21 05:15:41 -0500 (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 05:19:40 -0500 (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 08:13:57 -0500 (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 09:31:19 -0500 (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 09:56:06 -0500 (Fri, 25 Jan 2008) | 3 lines

Implemented the model-free specific is_spin_param() method.
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Updated the 5-state xz plane system test to check the optimised parameter values.

Clean up of the 5-state xz system test now that everything works.

Bug fix for the 5-state xz system test.

One of the input tensors was incorrect because of an integer division rather than float division!!!

Bug fix for the change to the numpy.sum() function.

In Numeric the axis keyword argument defaults to 0. In numpy it defaults to None!