complexa-evaluate-pdbs

Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use this skill whenever the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute i_pLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score binder candidates", "designability of this folder", "scRMSD for designs", "motif RMSD for these PDBs", "complexa analysis", "complexa evaluate from a PDB directory", "evaluate from pdb dir", or score third-party outputs (BindCraft, AlphaProteo, RFdiffusion, hand-curated decoys). It picks the correct evaluate_*.yaml config, wires ++dataset.pdb_dir and the folding backend, runs complexa analysis (the evaluate → analyze chain), parses the result CSV, reports pass-rates against the right result_type thresholds, and emits a replayable eval_manifest.json. Reach for this skill before hand-rolling refolding scripts.