Add GDT and TM-score structural similarity metrics

[diegozea]

Summary

• add fragment-based GDT (TS/HA) and TM-score calculations built on MIToS PDB superimposition utilities
• expose the new structure similarity functions through the PDB API and test them on representative alignments

Testing

• julia --project -e 'push!(LOAD_PATH,"test"); using MIToSTests; MIToSTests.retest("PDB"); MIToSTests.retest("Structure similarity (GDT/TM-score)")'

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Avoid DomainError in tm_score for short targets

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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[codecov]

Codecov Report

❌ Patch coverage is 96.55172% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.96%. Comparing base (4a26a3d) to head (51d5577).

Files with missing lines	Patch %	Lines
src/PDB/Kabsch.jl	96.55%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #189      +/-   ##
==========================================
- Coverage   96.97%   96.96%   -0.01%     
==========================================
  Files          64       64              
  Lines        4861     4948      +87     
==========================================
+ Hits         4714     4798      +84     
- Misses        147      150       +3     

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[coveralls]

coverage: 97.145% (-0.01%) from 97.156%
when pulling 51d5577 on codex/implement-gdt-and-tm-score-functions
into 4a26a3d on master.