v2.10.0

Highlights

• Added --batch_size for Boltz-2 structure inference so multiple inputs can be processed per prediction batch.
• Added repeated-binder affinity support: requesting affinity for one copy of a repeated ligand entity now works, with one output per binder copy.
• Added summarized PAE fields to confidence_*.json: complex_pae, complex_ipae, chains_pae, and pair_chains_pae.

Details

• Batched Boltz-2 structure inference is now supported for structure prediction.
  Current limits: affinity prediction remains single-record, and guided inference (--use_potentials / contact guidance) stays restricted to --batch_size 1.
• Repeated-binder affinity requests now fan out over ligand copies during the affinity stage while keeping the structure prediction pass unchanged.
  Outputs are written per binder copy as affinity_<record>_<chain>.json.
• PAE summaries are now written into confidence_*.json, remain available with --no_write_full_pae, use contact-weighted aggregation like PDE, and serialize undefined values as null.
• Fixed a nested confidence aggregation bug in sequential mode that was breaking affinity GPU smoke tests after the PAE summary change.

Commits since v2.9.5

• ecf5067 Add contact-weighted PAE summaries to confidence JSON
• 1396534 Document PAE summary fix in README
• 992034e Add batched Boltz-2 structure inference
• 0895889 Support affinity prediction for repeated binders
• b025b6b Fix nested confidence aggregation in sequential mode
• d3832aa Bump version to 2.10.0