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Relax 1.3.14

181 bytes added, 08:22, 20 September 2014
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* Added value.write user function calls to the J(w) mapping system test script.
* Added some value.write user functions to the J(w) mapping sample script.
* Modified the J(w) mapping test data to include relaxation values of None to trigger [https://gna.org/bugs/?19329 bug #19329].
* Speed up for the generic_fns.relax_re.search() function.
* More speed ups for the Selection.__contains_mol_res_spin_containers() method.
* Removal of a number of debugging print out statements.
* Significant speed ups of the return_spin() and return_residue() functions.
* Added a print out for the diffusion_tensor.init user function to inform the user of an angle unit change - this is in response to [https://gna.org/bugs/?19323 bug #19323 ] to make it clearer that a parameter conversion has occurred.
* Created a special specific API object called SPIN_PARAMS - this will be used to handle all operations to do with model parameters. The object Param_list has methods for parameter initialisation and handling (where all info is specified such as Grace string, units, default value, etc) and for determining if a parameter exists.
* Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data structures. The parameters are now all lowercase, for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow parameters are now converted throughout relax: 'bond_length' to 'r', 'CSA' to 'csa', 'heteronucleus' to 'heteronuc_type', 'proton' to 'proton_type'.
<section begin=bugfixes/>
* Fix for the title of the analysis selection wizard GUI element.
* Fix for the MemoryError during the "final" run of d'Auvergne Protocol[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] affecting 32-bit systems ([https://gna.org/bugs/?19528 bug #19528]).
* Epydoc docstring fixes for the API documentation.
* Bug fix for old numpy versions missing the float16 object.
* The relax data store __repr__() method now prints out all objects within the base object.
* Fix for a rare bug in the model-free analysis for when relaxation data of None is encountered.
* Fixes for the Dasha system test for the [https://gna.org/bugs/?19332 bug #19332 ] fix.
* Fixes for the Dasha use functions for file creation and data extraction - this should now handle relaxation data values of None, and also set the parameter values of deselected spins using the Dasha output files.
* Big bugfix for the value.read user function - the wrong spin ID string was being used to set the parameter value so that all spins have the same value set for the parameter([https://gna.org/bugs/?19332 bug #19332]).
* Bug fix for the consistency testing analysis for when relaxation data of None is encountered.
* The spin is now deselected if there is really less than three data points, excluding data points of None ([https://gna.org/bugs/?19329 bug #19329]).
* Bug fix for the arg_check.is_none() function - the RelaxNoneError was not imported!
* Fix for the numbering of the TER record and subsequence HETATM records in the PDB file creation. The structure.write_pdb user function now creates the correct TER record after the ATOM records, and the HETATM records are renumbered if needed.
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