Add GDT and TM-score structural similarity metrics#189
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Add GDT and TM-score structural similarity metrics#189
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src/PDB/Kabsch.jl
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| return mean(values(scores)) | ||
| end | ||
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| tm_d0(L::Integer) = max(0.5, 1.24 * (L - 15)^(1 / 3) - 1.8) |
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tm_d0 currently computes 1.24 * (L - 15)^(1 / 3) - 1.8; when Ltarget is below 15 (short peptides), raising a negative base to the fractional exponent throws a DomainError before the max(0.5, …) guard can run. That means tm_score crashes instead of returning a score for small structures. Handle the Ltarget < 15 case explicitly (e.g., real cube root or early clamp) so short targets are supported.
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Summary
- Updated TM-score normalization to use a real cube root for
d0, avoiding DomainErrors for short targets while preserving the clamp behavior. src/PDB/Kabsch.jlL485
Testing
⚠️ not run (not requested)
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #189 +/- ##
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- Coverage 96.97% 96.96% -0.01%
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Files 64 64
Lines 4861 4948 +87
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+ Hits 4714 4798 +84
- Misses 147 150 +3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Benchmark Results (Julia v1)Time benchmarks
Memory benchmarks
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Summary
Testing
julia --project -e 'push!(LOAD_PATH,"test"); using MIToSTests; MIToSTests.retest("PDB"); MIToSTests.retest("Structure similarity (GDT/TM-score)")'Codex Task