Trusted, Bureaucrats
4,223
edits
Changes
Jump to navigation
Jump to search
→Features: Updated the feature list, copying from the CHANGES file.
<section begin=features/>
* The Needleman-Wunsch sequence alignment algorithm now calculates an alignment score.
* Implementation of the central star multiple sequence alignment (MSA) algorithm.
* Implementation of a reside number based multiple sequence alignment (MSA) algorithm.
* Large speed up of the molecule, residue, and spin selection object, affecting all parts of relax.
* Sequence alignments are now saved in the relax data store.
* Important formatting improvement for the description in the GUI user function windows, removing excess empty lines after lists.
* Creation of the structure.sequence_alignment user function. The MSA algorithm can be set to either 'Central Star' or 'residue number', the pairwise sequence alignment algorithm to 'NW70' for the Needleman-Wunsch algorithm, and the substitution matrix to one of 'BLOSUM62', 'PAM250', or 'NUC 4.4'.
* More advanced support for different numpy number types in the lib.xml relax library module. This allows numpy int16, int32, float32, and float64 objects to be saved in the relax data store and retrieved from relax XML save and results files.
* Merger of structure.align into the structure.superimpose user function.
* The assembly of common atomic coordinates by the structure user functions now takes sequence alignments into account. The logic is to first use a sequence alignment from the relax data store if present, use no sequence alignment if coordinates only come from structural models, or fall back to a residue number based alignment. This affects the structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and structure.web_of_motion user functions.
* Large improvements in the memory management for all parts of the GUI.
<section end=features/>
