Complexa Evaluate-PDBs Skill

Score a directory of pre-existing PDB files against the same metrics Proteina-Complexa uses internally. Wraps complexa analysis <evaluate_config> ++sample_storage_path=<dir>: the CLI runs the evaluate step (refold + interface metrics + monomer metrics) and then the analyze step (success thresholds, diversity, pass-rate CSVs). Do not run complexa generate here — the inputs already exist.

What this skill enables

• Re-fold a directory of designed PDBs with AF2 (colabdesign), RF3 (rf3_latest), ESMFold (esmfold), or Boltz2 (boltz2_default).
• Compute binder interface metrics: i_pAE, min_ipAE, i_pTM, pLDDT, binder/complex scRMSD.
• Compute monomer designability (ProteinMPNN-redesigned scRMSD) and codesignability (original sequence refold scRMSD).
• For motif inputs: motif RMSD (CA + all-atom), motif-region designability/codesignability, sequence recovery.
• Aggregate into per-PDB CSVs plus pass-rate summaries using the default thresholds for the result_type.

Step 1: Pre-flight

Always check GPU / disk / tool binaries before launching a refold job. RF3 and ColabDesign-AF2 are large.

bash .claude/skills/_shared/scripts/preflight.sh