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Pull request overview
This PR tunes dreid-pack packing/scoring parameters to improve side-chain recovery metrics (DB379) and runtime, and updates documentation to reflect the new defaults and benchmark results.
Changes:
- Increased the default self-energy pruning window from 15.0 → 30.0 kcal/mol (config default + CLI default + README).
- Updated core scoring constants: hydrogen-bond exponent (
HBOND_N2 → 4), rotamer bias cap (5.0 → 8.0), and residue-specific rotamer weights (×3). - Refreshed README benchmark tables and the pipeline diagram to match the new parameters.
Reviewed changes
Copilot reviewed 3 out of 4 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| README.md | Updates CLI default display, benchmark numbers, and Mermaid diagram thresholds/caps. |
| crates/dreid-pack/src/pack/constant.rs | Adjusts H-bond exponent and rotamer-bias parameters/weights used during scoring. |
| crates/dreid-pack/src/pack/config.rs | Updates the library default for self_energy_threshold. |
| crates/dreid-pack/src/bin/dpack/args.rs | Updates the CLI default for --self-energy / -E. |
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Summary:
Tuned packing parameters to improve χ recovery on DB379: χ1-4@20° 68.9% → 71.5% (+2.6 pp), RMSD 0.758 → 0.728 Å, pack time −25%.
Changes:
config.rs,args.rs): 15.0 → 30.0 kcal/mol (-E).constant.rs):HBOND_N2 → 4 (standard DREIDING perdreid-kerneldocs).constant.rs):ROTAMER_BIAS_CAP5.0 → 8.0 kcal/mol.constant.rs): all weights ×3 (dominant contributor, +1.7 pp).README.md): updated benchmark table and Mermaid diagram.