Shared helper to resolve the indexing (alternative-indexing / reindexing) ambiguity that
arises when the lattice symmetry is higher than the crystal Laue symmetry (merohedral /
pseudo-merohedral): a crystal can be validly indexed in several ways related by reindexing
operators, and the right one is chosen by agreement with a reference (reference-MTZ
intensities, or later a model) - so no reference-free ambigator (cosym) is needed.
ReindexAmbiguity.{h,cpp}:
- ReindexAmbiguityOperators() = gemmi::find_twin_laws() = the coset operators (empty for a
holohedral crystal, i.e. no ambiguity);
- ReindexReflections() applies an operator to a copy of the merged reflections;
- ChooseReindex() picks identity or the twin law that maximizes a caller-supplied score;
- ReferenceIntensityCC() is a ready scorer (Pearson CC vs a reference, matched by Laue-ASU key).
This does NOT touch the screw-axis / enantiomorph ambiguity (P4_1 vs P4_3), which leaves the
merged intensities unchanged and is adopted from the reference/model rather than scored.
Tests: holohedral -> no operators, merohedral (P4) -> operators present, a misindexed dataset
is recovered by reference CC (score >0.99), a correctly indexed one keeps identity.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8
d00f4303c8