Replaces old v2 rescore script with the paper's canonical v5-S2 3-seed ensemble pipeline (seeds 1024/5555/789). Fixes:
1. Adds second Kabsch (holo->apo) on binder coords so the binder sits next to the apo receptor slot; previously Q_apo=0 for every design because 1CFD sits ~34 A from 3CLN in world frame.
2. Sequence-anchored ordinal Kabsch instead of residue-ID intersection — the ID intersection paired the wrong CAs whenever chain A was renumbered from 1 (PXDesign, Protenix, Proteina).
3. HETATM-safe receptor extraction — PXDesign writes chain A as HETATM and get_residues(only_standard=True) dropped every one.
4. 3-seed ensemble (seeds 1024/5555/789) with per-seed and mean scores.
5. Accepts .cif in addition to .pdb.
6. --design_dir / --target CLI args instead of hardcoded internal paths.
