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→Bugfixes: Copied the bugfixes text from the CHANGES file.
<section begin=bugfixes/>
* Fix for two-point calculation of exponential curve with corrupted data. The two-point calculation is now also skipped, if the measured intensity is 0. This can happen for corrupted intensity files.
* Fix for the internal structural object get_model() method - it now actually returns the model.
* Fixes for the structure.add_atom user function to allow for list of lists for the atomic position. This allows different coordinates to be supplied for each model.
* Added safety checks for NaN values to the lib.structure.pdb_write module. This is within the _record_validate() function. The check prevents the creation of invalid PDB files.
* Fix for the experimental information data pipe object when converting to XML state and results files. This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions. The names and descriptions for the software, citation and script list objects were incorrectly set. These have been fixed so that the name of the data structure and the real description is present in the XML state or results file instead of <relax_list desc='relax list container'>.
* Fix for the experimental information data pipe object when converting to XML state and results files. This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions. The names and descriptions for the software, citation and script list objects were incorrectly set. These have been fixed so that the name of the data structure and the real description is present in the XML state or results file instead of <relax_list desc='relax list container'>.
* Fix for the cdp.exp_info.software data structure setup. This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions. The Element data container name was being replaced by the software name, making it impossible to restore from the XML.
* Implemented the cdp.exp_info.from_xml() method to correctly restore the experimental info structure. This fixes bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions. This custom ExpInfo.from_xml() method is required to properly recreate the software, script and citation list data structures of the cdp.exp_info data structure, as these are special RelaxListType objects populated by Element objects (both from data_store.data_classes).
* Bug fix for the structure.delete user function. When individual atoms are deleted, the bonded atom data structure is no correctly updated to remove the now non-existent atom.
* Another bug fix for the structure.delete user function when deleting individual atoms. The bonded atom data structure consisting of indices requires all indices after the deleted atom to be decremented by 1.
* Bug fix for the CONECT records created by the structure.write_pdb user function. The atom numbers inside the structural object were being used for the CONECT records rather than the atom numbers used within the PDB file.
* Fix for writing out point files, when only one point is used. The code was testing for > 1 points to be present, before writing out point files. Bug #22753 (https://gna.org/bugs/index.php?22753): dx.map does not work when only 1 point is used.
* Fix for bug #22563 (https://gna.org/bugs/?22563). This is the NS MMQ 2-site dispersion model running at 32-bit precision and not 64-bit as it should be. The numpy.complex64 32-bit types have been replaced by numpy.complex128 in the lib.dispersion.ns_mmq_2site module.
* Critical fix for k_AB not belonging to list of global parameters. k_AB was only changed to the spin of interest, but not for the rest of the cluster. When the parameter vector is assembled, "assemble_param_vector(spins=spins)" it takes the global parameter from spin 0. Bug #22754 (https://gna.org/bugs/index.php?22754): The minimise.calculate user function does not calculate chi2 value for clustered residues.
* Improvements for PDB creation in the relax library for out of bounds structural coordinates. The lib.structure.pdb_write module atom() and hetatm() functions will now more gracefully handle atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999]. When such coordinates are encountered, instead of producing a too long PDB line which does not pass the validation step, the functions will set the coordinates to the boundary value. This will at least allow a valid PDB file to be created, despite the warping of the coordinates.
* Expanded the list of global dispersion parameters in the set_param_values() API method. This is a quick expansion of Troels' fix for the k_AB parameter to allow for the release of relax 3.3.1. This is a small part of the discussion at http://thread.gmane.org/gmane.science.nmr.relax.scm/23948/focus=7188.
<section end=bugfixes/>