Add metal/cofactor handling to the Boltz-2 YAML as CCD ligand entries -
the modes classical docking couldn't model:
- HDAC2 + catalytic Zn (vorinostat chelates it)
- PKR + FBP + Mg (allosteric activator + metal)
- hemoglobin + heme
Same cofactors present when co-folding negatives into a target (fair test).
build_boltz_yaml() gains a cofactor_ccds arg (emits `ligand: {ccd: ...}`
entries); TARGETS carries per-target cofactors; cofold()/main() thread them
through. Verified locally: YAML builds correctly with Zn / FBP+Mg.
Honest limitation noted: Hb's voxelotor site is at the tetramer centre and
covalent (Schiff base), so single-chain+heme only approximates it - HDAC2
(Zn) and PKR (cofactor) are the real co-folding tests. Ready for
`modal run gpu/modal_app.py`.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Junior B.
07705a5884