# Complexa Evaluate Pdbs

Agent runbook for evaluating an existing PDB directory through the separately installed...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Design
- License: Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add NVIDIA/skills --skill complexa-evaluate-pdbs -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill complexa-evaluate-pdbs -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill complexa-evaluate-pdbs -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill complexa-evaluate-pdbs -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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
bash scripts/preflight.sh
```

Surface from `preflight.json`:

- `gpu.available` and `gpu.vram_gb`, colabdesign/RF3 need ≥40 GB; ESMFold tolerates ≥24 GB.
- `env.missing_required`, must include the keys for the chosen folding backend:
  - `colabdesign` → `AF2_DIR`
  - `rf3_latest` → `RF3_CKPT_PATH`, `RF3_EXEC_PATH`
  - `esmfold` → ESMFold weights resolvable
- `tools.{foldseek,mmseqs}`, required by `aggregation.compute_diversity` / `compute_mmseqs_diversity` (both default `true`).

If any required key is missing, route the user to the `complexa-setup` skill.

## Step 2: Identify the design type

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-complexa-evaluate-pdbs/SKILL.md