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complexa-evaluate-pdbs

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Agent runbook for evaluating an existing PDB directory through the separately installed first-party Proteina-Complexa CLI. Use to refold or score designs, compute interface pAE, i_pLDDT, scRMSD, motif RMSD, or designability, run complexa analysis, or assess third-party BindCraft, AlphaProteo, or RFdiffusion outputs. SKILL.md selects and invokes the evaluation configuration; bundled executables only inspect local readiness and write a run manifest.

skills/bionemo-complexa-evaluate-pdbs/SKILL.md

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# 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