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Implement structural superimposition and TM-score #705

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merged 5 commits into from
Jan 6, 2025

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This PR implements the tm_score() function to compute the TM score on two given protein structures (monomeric or multimeric).

In addition superimpose_structural_homology() takes inspiration from TM-align to find corresponding CA atoms (required as input to tm_score()) and to transform the mobile structure minimizing the TM-score.

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codspeed-hq bot commented Nov 20, 2024

CodSpeed Performance Report

Merging #705 will not alter performance

Comparing padix-key:structural-superimpose (803f61b) with main (e76eb24)

Summary

✅ 47 untouched benchmarks
🆕 4 new benchmarks

Benchmarks breakdown

Benchmark main padix-key:structural-superimpose Change
🆕 benchmark_superimpose[superimpose] N/A 2.7 ms N/A
🆕 benchmark_superimpose[superimpose_homologs] N/A 101.7 ms N/A
🆕 benchmark_superimpose[superimpose_structural_homologs] N/A 41.3 ms N/A
🆕 benchmark_superimpose[superimpose_without_outliers] N/A 16.5 ms N/A

@padix-key padix-key force-pushed the structural-superimpose branch from 5bf6cd2 to 803f61b Compare January 6, 2025 13:32
@padix-key padix-key merged commit aecc27d into biotite-dev:main Jan 6, 2025
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