Claude/debug ni complex shape ewrvu#96
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The Kabsch algorithm minimizes RMSD but CShM uses overlap maximization. For near-perfect matches (CShM < 1), this subtle difference caused a ~16% discrepancy between Q-Shape (0.228) and SHAPE v2.1 (0.197) for octahedral complexes. Added local refinement after Kabsch in exhaustivePermutationSearch() that performs gradient-free optimization to maximize overlap. This closes the gap and achieves perfect parity with SHAPE for all tested CN=6 geometries. https://claude.ai/code/session_019kQeTerQbpoMJGtNGCMfju
Additional test files created during the investigation of the OC-6 CShM discrepancy. These tests help verify normalization, overlap calculations, and rotation optimization for octahedral complexes. https://claude.ai/code/session_019kQeTerQbpoMJGtNGCMfju
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