ProteinDJ v2.2.0 - Paired sweeping parameters

What's Changed

Paired Parameters for Bindsweeper

Paired parameters allow you to sweep multiple parameters in lock-step, rather than as a Cartesian product. This is useful when parameters are inherently linked — for example, each target PDB has a corresponding MSA file or specific hotspot residues.

sweep_params:
  uncropped_target_pdb:
    values:
      - "input/protein1.pdb"
      - "input/protein2.pdb"
      - "input/protein3.pdb"
    paired_with:
      boltz_msa_path:
        - "input/msas/protein1.a3m"
        - "input/msas/protein2.a3m"
        - "input/msas/protein3.a3m"

Bug Fixes:

• Fix BindCraft advanced parameters helper in main.nf by @nskirk in #36
• ipSAE filename matching
• Validation of design length ignored when providing rfd_contigs
• Ranking now uses integers for file name matching and only outputs top N designs in ranked_designs.csv
• Changed ProteinMPNN to use a batch_id instead of task_id (which can change on resume)

New Contributors

• @nskirk made their first contribution in #36

Full Changelog: v2.1.1...v2.2.0