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* Delete docs/docs/plugin/superposition.md * Add TM-align structure alignment algorithm Implement TM-align for structure-based protein alignment, providing an alternative to sequence-based superposition methods. TM-align finds optimal structural alignments regardless of sequence similarity using TM-score. New features: - Core TM-align algorithm (src/mol-math/linear-algebra/3d/tm-align.ts) - TM-score calculation with length-independent normalization - Dynamic programming for optimal alignment - Gapless threading and fragment-based initialization - Multiple refinement passes for accuracy (~97.7% of US-align reference) - High-level wrapper (src/mol-model/structure/structure/util/tm-align.ts) - tmAlign() function accepting StructureElement.Loci inputs - Returns transformation matrix, TM-scores, RMSD, and alignment - BasicWrapper API (src/examples/basic-wrapper/) - tmAlign(pdbId1, chain1, pdbId2, chain2, color1?, color2?) - sequenceAlign() - sequence-based superposition - loadStructures() - load without alignment - Example HTML pages demonstrating usage - UI integration (src/mol-plugin-ui/structure/superposition.tsx) - TM-align option in superposition panel References: Zhang Y, Skolnick J. Nucl Acids Res 33, 2302-9 (2005) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Delete src/examples/basic-wrapper/index.html * changing reference test case * Restoring src/examples/basic-wrapper/index.html * Addressing comments in pull request * Authorship added --------- Co-authored-by: Diego del Alamo <diego.delalamo@gmail.com> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Mol* Developer Documentation
Contributions to the documentations are highly welcome! Please make a pull request with your changes.
Requires Python 3.x to build. From this directory:
pip install mkdocs-material
mkdocs serve