Complexa Design Skill

Drive the full four-stage complexa design pipeline: generate (flow matching + search) -> filter (top-N by reward) -> evaluate (refold with AF2/RF3) -> analyze (success rate, FoldSeek/MMseqs diversity). Pick the right pipeline config for the design intent, validate the run upfront so the user does not discover a missing ckpt mid-folding, run it, and emit a replayable manifest + per-design success CSV.

What this skill enables

• Protein binder design for protein targets (AF2 reward + ColabDesign refold).
• Ligand binder design for small-molecule targets (RF3 reward + RF3 refold).
• AME motif scaffolding with ligand context (motif + ligand features, RF3).
• Search-based optimization: single-pass, best-of-n, beam-search, fk-steering, mcts.
• Refold backends: ColabDesign (AF2), RF3, Boltz2, ESMFold (fast iteration).
• Pass-rate + diversity analysis with per-result_type thresholds.

Step 1: Pre-flight