Fix CE-Symm bug with short repeats#1101
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sbliven merged 5 commits intobiojava:masterfrom Sep 4, 2024
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Most are in docstrings. One misspelled public method has been deprecated.
[rcsb/symmetry#118](rcsb/symmetry#118) The problem was actually downstream from CE-Symm in the QuatSymmDetector code used for assigning a symmetry group. The code was re-aligning subunits using CE. This fails for short alignments of <15 residues (two AFP with default settings). Thus no atoms get aligned and an exception was thrown whenever an output format required information about the symmetry group. This fix re-uses the original CE-Symm alignment for the symmetry group detection. This might change CE-Symm and QuatSymm results for proteins with small subunits or borderline scores. Changes: - New `SubunitClustererMethod.MANUAL` enum value - Improve `SymmetryTools.getQuaternarySymmetry`
Better refinement now finds slightly larger helical rotation, moving it from R to H.
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This fixes rcsb/symmetry#118.
It switches the determination of the symmetry group and rotation axes to use the CESymm alignment directly. Before it was recomputed using QuatSymmDetector, which failed with short repeats.
A new CE-Symm version will be released after the next biojava release.