Feature Engineering second take with new addtions

[amruthesht]

Summary

Follow-up to the initial feature extraction PR. Completes Person 2 Tier 1:

• Add domain delta features — inter-helix distance/angle changes relative to curated reference structures (same refs as RMSD: 3F3E, 3F3A, 3F4J, 3USI)
• Add feature column manifest in docs/features.md (computed vs copied columns)
• Add tests for self-delta ≈ 0 and non-zero IF vs OF deltas
• Remove unused sort_by_resid helper

Example new features

domain_TM1_TM7_distance_delta_vs_3F3E domain_TM1_TM7_angle_delta_vs_3F3A domain_gate_TM1_TM6_distance_delta_vs_3F4J

Delta = query structure value − reference structure value.

Test plan

• pytest tests/test_features.py -v (8/8 passing)
• Self-delta for 3F3E vs 3F3E ≈ 0
• 3F3A vs 3F3E shows non-zero domain deltas
• Regenerate feature vectors locally if needed: python scripts/extract_feature_vectors.py

[orbeckst]

LGTM!

[orbeckst]

Try

ruff format .