Imported from NVIDIA-BioNeMo/Proteina-Complexa (skills/complexa-design/SKILL.md). Install upstream with npx skills add NVIDIA-BioNeMo/Proteina-Complexa --skill complexa-design. Copyright stays with the author.

Complexa Design Skill

Drive the full four-stage complexa design pipeline: generate (flow matching + search), filter (top-N by reward), evaluate (refold with AF2 or RF3), then analyze (success rate and sequence-structure 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

Always run the shared preflight before launching a design — generation needs the GPU and the right checkpoint, evaluation needs AF2 or RF3 weights and tool binaries. Bail early if the host cannot run the chosen pipeline.

Set SKILL_DIR to the directory containing this manifest, then run:

bash "$SKILL_DIR"/scripts/preflight.sh

Read the JSON report emitted by preflight and bail if any of these are missing for the chosen pipeline:

• gpu.available: false -> all pipelines fail.
• gpu.vram_gb < 40 -> generation OOMs at default batch_size: 16; lower to 8.
• ckpts.complexa[.ckpt] -> required for protein binder.
• ckpts.complexa_ligand[.ckpt] -> required for ligand binder.
• ckpts.complexa_ame[.ckpt] -> required for AME.
• env.AF2_DIR missing -> protein binder default eval (colabdesign) fails.
• env.RF3_CKPT_PATH or env.RF3_EXEC_PATH missing -> ligand binder / AME default eval (rf3_latest) fails.

If a ckpt is missing, point at complexa-setup and have the user run complexa download --complexa-<variant> first.

Step 2: Pick the pipeline

Select the pipeline YAML that matches the requested target. Each YAML pins the corresponding checkpoint, target dictionary, reward, and refold backend.

Protein binder is the default when the user does not identify a ligand or motif. Do not remove the lora: block in ligand or AME pipeline YAMLs; those released checkpoints require it. AME defaults to single-pass; enable a reward model before selecting a reward-guided search algorithm. Use the exact pipeline command in the bundled Pipeline Reference at "$SKILL_DIR"/references/pipelines.md; it also lists checkpoints, target dictionaries, and thresholds.

Step 3: Gather parameters

Use AskUserQuestion to fill in the four parameters that vary every run. Default to sensible production settings if the user has no preference.

• Target name — must be a key in the matching protein, ligand, or AME target dictionary documented in the bundled Pipeline Reference. If the user names a target that is not present, hand off to complexa-target to add it first.
• Run name — a short identifier appended to the output dir (e.g. pdl1_v1).
• Search algorithm — default to beam-search with beam_width=8 and n_branch=4 for production. Use single-pass for a quick smoke test.
• Evaluation refold backend — protein binder defaults to colabdesign (AF2); ligand and AME default to rf3_latest. Use esmfold for fast iteration (worse but seconds per sample).

Step 4: Validate

Validate before running. This is cheap (seconds) and catches missing ckpts, missing env vars, unknown override keys, and missing target entries — all of which would otherwise abort the pipeline mid-evaluation after hours of generation.

Run complexa validate design with the selected pipeline command and the chosen target override. The bundled Inference Guide at "$SKILL_DIR"/references/INFERENCE.md has exact validation examples. The validator returns non-zero on failure and prints a status report. Re-run it with the suggested overrides until it returns clean.

Step 5: Run the pipeline

complexa design is the right tool for the full 4-stage run — it orchestrates generate → filter → evaluate → analyze as sequential subprocesses with a shared run name, log directory, and multi-GPU split. Re-implementing that manually loses the per-stage log routing and progress prints.

Use ++ (forced) Hydra overrides; they apply to all stages. Start from the matching production command in the bundled Pipeline Reference and add the run name, target, search algorithm, beam width, and refold backend selected above. For ligand binder and AME, select the matching pipeline and target; the common overrides can otherwise be reused.

Add --verbose to stream logs to the terminal. The skill does not poll progress — the user re-invokes if they want a status; point them at complexa status and the run's log directory.

Debugging a single stage

For debugger or profiler use, call the matching proteinfoundation module directly with the same resolved pipeline configuration. Prefer the CLI for ordinary runs because it preserves logs and parallel-job routing; the individual-stage command patterns are in the bundled Inference Guide.

For AME inputs evaluated with RF3, ensure the ligand is represented as L:0 before refolding; otherwise RF3 can complete CCD atoms and corrupt RMSD calculation. This does not apply to AF2 with ColabDesign or non-AME runs.

Wall-clock at default (nsteps=400, beam_width=8, batch_size=16, 100 designs, colabdesign eval) is about 30–120 minutes on a single A100 or H100.

Step 6: Collect results

Outputs land in generation and evaluation directories. Surface both, using the paths printed by the CLI:

Caution: These paths are relative to the current directory. Runs can consume tens of GB, and the manifest path below is overwritten on repeated use. Choose an empty run directory or back up existing results first.

Read the combined results CSV and summarize the success-rate, per-design, and diversity CSVs described in the bundled Evaluation Metrics Guide. Report top-N designs by i_pAE for protein binders or min_ipAE for ligand binders.

Step 7: Emit manifest

Drop a JSON manifest beside the results so the run is replayable. The shared helper captures the command, config, git SHA, and pointers to the result CSVs.

python3 "$SKILL_DIR"/scripts/write_manifest.py \
    --output-dir <results-directory> \
    --command "<exact-complexa-command-that-was-run>" \
    --skill complexa-design \
    --out <manifest-file>

Surface the manifest path and the result CSV to the user.

Most-common overrides

The 10 overrides that cover ~90% of runs. Full reference (every key, type, default) is in the bundled Overrides Reference.

Hardware requirements

Typical wall-clock for 100 designs, beam_width=8, default nsteps=400:

• Protein binder + colabdesign refold: ~60–120 min on one A100 or H100.
• Ligand binder + RF3 refold: ~90–180 min (RF3 dominates).
• AME + RF3 refold: ~120–240 min.
• Any pipeline + ESMFold refold: ~30–60 min (fast iteration).

Bumping gen_njobs=2 and eval_njobs=2 halves wall-clock on a 2-GPU host. See the bundled Hardware Reference for per-pipeline VRAM tables.

Troubleshooting (common cases)

For detailed troubleshooting, see the bundled Troubleshooting Reference.