relax SVN archive

svn+ssh://bugman@.../svn/relax/trunk

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r26746 | bugman | 2014-11-26 11:12:30 +0100 (Wed, 26 Nov 2014) | 8 lines

Fixes for the links at the bottom of all HTML manual pages.

This is for the automatically generated documentation at http://www.nmr-relax.com/manual/index.html,
created using latex2html. The links all require double quotes, and some a trailing '/'. The links
fixed are http://www.nmr-relax.com, http://www.nmr-relax.com/manual/ and
http://download.gna.org/relax/manual/relax.pdf.
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r26747 | bugman | 2014-11-26 11:21:53 +0100 (Wed, 26 Nov 2014) | 7 lines

Removed the repository backup file text from the relax manual.

This is for http://www.nmr-relax.com/manual/Latest_sources_the_relax_repositories.html. The gzipped
repository dump file has not been created by Gna! for many, many years. The problem was identified
by the W3C link checker (http://validator.w3.org/checklink).
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r26760 | bugman | 2014-11-26 14:22:47 +0100 (Wed, 26 Nov 2014) | 5 lines

Updated all of the http://www.nmr-relax.com/manual/ links in the lib.dispersion package.

This is for all of the individual model pages in the HTML manual.
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r26768 | bugman | 2014-11-26 18:35:06 +0100 (Wed, 26 Nov 2014) | 3 lines

Improved the description for the relax_fit.select_model user function.
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r26769 | bugman | 2014-11-26 19:29:54 +0100 (Wed, 26 Nov 2014) | 12 lines

A small code rearrangement to create the new target_functions.relax_fit_wrapper module.

This follows from the idea at https://gna.org/task/?7415#comment6. The *func_wrapper() functions of
the specific_analyses.relax_fit.optimisation module have been shifted out and converted to class
methods to create the target_functions.relax_fit_wrapper module. This will be used to abstract away
all of the C code, and will form the infrastructure to allow new exponential curves to be quickly
supported.

The modules of the specific_analyses.relax_fit and specific_analyses.relax_disp packages now import
the target_functions.relax_fit_wrapper.Relax_fit_opt target function class and use that instead.
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r26770 | bugman | 2014-11-26 19:42:20 +0100 (Wed, 26 Nov 2014) | 8 lines

Shifted the C code Jacobian functions into the new target_functions.relax_fit_wrapper module.

This shifts all of the relaxation curve-fitting C code access into the
target_functions.relax_fit_wrapper module so that the rest of relax does not need to handle the C
code. This will allow for new models to be very easily supported, as they would all be set up in
this target function module.
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r26771 | bugman | 2014-11-27 09:45:09 +0100 (Thu, 27 Nov 2014) | 3 lines

Updated the formula in the description of the relax_fit.select_model user function.
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r26782 | bugman | 2014-11-27 15:16:48 +0100 (Thu, 27 Nov 2014) | 8 lines

Modified the printouts from the structure.write_pdb user function if models are present.

Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each model, the header 'MODEL
records' is printed followed by a single '.' character for each model. For structures with many models,
this results in a huge speed up of the user function which is strongly limited by how fast the
terminal can display text.
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r26791 | bugman | 2014-11-27 19:11:38 +0100 (Thu, 27 Nov 2014) | 11 lines

Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository.

These files were created by Andras Boeszoermenyi <Andras_Boeszoermenyi att hms dott harvard dot
edu>. They are attached to the task at http://gna.org/task/?7415 as the Relax_sym.tar.gz file at
http://gna.org/task/download.php?file_id=22989. They were created for the formula I0*(1 -
exp(−R1*t)) where I0 = 1000000000000000.00 and R1 = 0.5. These files and the associated
relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of
a basic system test. This system test could then be used to implement the saturation-recovery
experiment equations in relax.
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