| name | complexa-setup |
| description | First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my environment file", "first-time setup", "what models do I have installed", "what's in my environment file", "download model weights", "download Complexa / AF2 / RF3 / ProteinMPNN / LigandMPNN / ESM2 / ESMFold checkpoints", "preflight my GPU", "verify environment", "complexa init", "complexa download", "complexa download --status", "complexa validate env", or any time a fresh checkout needs to be made runnable. This is the first skill to run on a new clone — it drives `complexa init`, `complexa download`, and `complexa validate env` end-to-end, edits the required `.env` keys, picks the right runtime (UV vs Docker), and emits a replayable setup artifact.
|
| compatibility | complexa CLI installed (pip install -e .); bash 4+; nvidia-smi optional |
| allowed-tools | Bash, Read, Write, AskUserQuestion |
Complexa Setup Skill
Drive the three steps a fresh Proteina-Complexa checkout needs before any
design run: create .env, fetch model weights, and sanity-check the env.
Probe the host for GPU / disk / tool binaries first so the user does not
discover a missing dependency mid-pipeline. End with a JSON setup artifact the
user (or a future agent) can re-read instead of re-deriving state.
CLI vs direct file-edit — pick the cheapest path per step
| Step | Preferred path | Why |
|---|
.env creation (Step 2) | File edit (copying the env template + 3 line swaps) or complexa init | complexa init is a thin wrapper around cp + 3 regex swaps (_swap_runtime_in_env in cli_runner.py). Either path works; pick CLI for new humans, direct edit for agents. |
.env value edits (Step 3) | File edit (StrReplace LOCAL_CODE_PATH=… etc.) | No CLI for this — the values are user-specific paths. |
| Download model weights (Step 4) | CLI (complexa download --…) | Dispatches to env/download_startup.sh (~1000 lines of bash with NGC URLs, retries, checksum-style skip-if-present). Don't try to replicate. |
| Validate env (Step 5) | CLI (complexa validate env) or test -f .env && test -d $DATA_PATH | CLI prints a nicer report; the manual check is one-liner-safe. |
| Validate full design config (after picking a pipeline) | CLI (complexa validate design CONFIG) | Non-trivial Hydra defaults traversal + ckpt + env-var checks; not worth replicating. |
What this skill enables
- A correctly-shaped
.env for either UV or Docker runtime.
- Model checkpoints (Complexa protein/ligand/AME plus community models) downloaded to known paths.
- A
preflight.json snapshot of the host (GPU, disk, .env, ckpts, tool binaries).
- A
run_manifest.json capturing exactly which complexa init + complexa download invocations were used (replay-friendly).
- A pass/fail report from
complexa validate env with clear next-step hints.
Step 1: Pre-flight check
Always run the shared preflight before touching the environment. It does not
require .env to exist — it falls back to defaults — and it tells you whether
the host can run Complexa at all.
bash .claude/skills/_shared/scripts/preflight.sh
The script writes ./complexa_setup/preflight.json. Read it and surface:
gpu.available — if false, design / evaluate steps will fail; warn the user.gpu.vram_gb — Complexa needs ≥40 GB (A100/H100/L40S).disk.free_gb at CKPT_PATH — minimum ~50 GB for the full Complexa + community model set.env.missing_required — anything listed here must be edited in .env before validation passes.tools.{foldseek,mmseqs,dssp,hbplus,sc}.exists — missing tools degrade evaluation but do not block generation.
Step 1b: Build the Python environment (only if .venv/ is missing)
The complexa CLI is installed inside the project's Python environment, not on
the system path by default. On a fresh clone, the .venv/ directory does
not yet exist and complexa init will fail with command not found. Build the
UV venv before anything else:
test -d .venv || ./env/build_uv_env.sh
source .venv/bin/activate
which complexa
Skip this step if which complexa already resolves — that means a previous
build is still good. The Docker runtime skips it entirely; the venv lives
inside the container image instead. If the user said "I just cloned" or you
see no .venv/ next to pyproject.toml, run the build script — complexa init
without a venv produces a confusing command not found rather than an obvious
"build the venv first" error.
Step 2: Create .env
Pick the runtime. UV is the default and faster to start; Docker is required on
Ubuntu 20.04 or systems with GLIBC mismatches.
Use AskUserQuestion if it is not obvious from context:
"Which runtime do you want to configure? uv (recommended, faster) or docker (use if you do not have a UV venv built locally)?"
Path A: file edit (preferred for agents)
complexa init only does three things — copy .env_example → .env and
swap the COMPLEXA_RUNTIME= line plus the UV_* ↔ DOCKER_* prefixes on the
tool/data/cache path block. You can do the same with cp + StrReplace and skip
the CLI:
cp .env_example .env
Skip the prefix swap entirely if you're staying on UV (the .env_example
already targets UV).
Path B: CLI
complexa init
complexa init --runtime docker
complexa init --force
If .env already exists and --force is not passed, only the runtime-dependent
lines are swapped — user edits in Step 3 are preserved across runtime flips.
Verify either way
test -f .env && echo "OK: .env present" || echo "MISSING"
grep -E '^COMPLEXA_RUNTIME=' .env
Step 3: Edit .env
No CLI for this — Step 2 only set the runtime; you still need to write your
machine-specific paths into .env by hand (StrReplace or your editor). The two
absolutely-required edits are:
LOCAL_CODE_PATH=/absolute/path/to/protein-foundation-models
LOCAL_DATA_PATH=/absolute/path/to/PFM_data
Everything else (cache, ckpts, community-model dirs, tool binaries) is derived
from LOCAL_CODE_PATH by default and only needs editing if you have a
non-standard layout. For the full table — every key, what it controls, what
fails if it is missing — see reference/env_keys.md.
Quick decision table for the four edits most users make:
| Key | Default | Set this if |
|---|
LOCAL_CODE_PATH | placeholder | Always — required |
LOCAL_DATA_PATH | /path/to/PFM_data | Always — required, points at target PDBs |
HF_TOKEN | placeholder | You need ESMFold or gated HF models |
WANDB_API_KEY | placeholder | You want training runs logged to W&B |
Step 4: Download checkpoints
Always use the CLI here. complexa download dispatches to
env/download_startup.sh (~1000 lines of bash with NGC URLs, retries, and
skip-if-present logic across ~6 community-model families). Rolling your own
wget loop is a recipe for partial downloads and wrong destination paths.
Ask which models the user actually needs — downloading everything is ~100+ GB.
Pick from the three Complexa variants and the community-model set. Each
Complexa variant unlocks exactly one complexa design pipeline; AF2 / RF3
inside the community-model set are what evaluate (and reward-guided search)
need at run time.
| Flag | What it downloads | Unlocks pipeline | Destination | Approx size |
|---|
--complexa | Complexa protein-binder model + AE (complexa.ckpt, complexa_ae.ckpt) | Protein binder (default) — configs/search_binder_local_pipeline.yaml | ./ckpts/ | ~3 GB |
--complexa-ligand | Ligand-binder model + AE (complexa_ligand.ckpt, complexa_ligand_ae.ckpt) | Ligand binder — configs/search_ligand_binder_local_pipeline.yaml | ./ckpts/ | ~3 GB |
--complexa-ame | AME motif-scaffolding model + AE (complexa_ame.ckpt, complexa_ame_ae.ckpt) | AME (enzyme) — configs/search_ame_local_pipeline.yaml | ./ckpts/ | ~3 GB |
--complexa-all | All three Complexa variants | All three pipelines | ./ckpts/ | ~9 GB |
--all | All community models (ProteinMPNN + LigandMPNN + AF2 + ESM2 + ESMFold + RF3) | Needed by evaluate / reward: AF2 (protein binder), RF3 (ligand binder + AME), MPNNs (inverse folding for every pipeline). | ./community_models/ | ~50 GB |
--everything | Complexa + community + optional (Boltz2 / Protenix) | Everything plus alternative refold backends | both | ~100+ GB |
--status | Show install state — does not download | (none) | (none) | n/a |
Minimum download per pipeline:
- Protein binder (default):
complexa download --complexa --all
- Ligand binder:
complexa download --complexa-ligand --all
- AME / enzyme:
complexa download --complexa-ame --all
- All three:
complexa download --everything
For the full per-model destination breakdown and per-flag NGC sources, see
reference/downloads.md.
Pick the smallest invocation that covers the user's goal, then run:
complexa download --complexa
complexa download --complexa-all
complexa download --all
complexa download --everything
Without arguments, complexa download launches an interactive wizard — prefer
explicit flags in agent mode.
Verify what landed:
complexa download --status
The status output groups by family (Complexa / community / optional) and prints
"Installed" or "Missing" per ckpt. Re-run the specific flag if a ckpt is
flagged missing.
Step 5: Validate
Final check that .env is loadable and the required paths resolve:
complexa validate env
validate env checks: (1) .env exists, (2) DATA_PATH is set and points at
an existing directory. It does not check ckpt files — those are checked by
complexa validate design <config> once you have a pipeline config picked.
Common failures and fixes:
| Symptom | Cause | Fix |
|---|
.env file: No .env file found | complexa init not run | Run complexa init first |
DATA_PATH: Not set in .env | Placeholder not edited | Edit LOCAL_DATA_PATH in .env |
DATA_PATH: Directory not found | Path edited but does not exist on disk | mkdir -p $LOCAL_DATA_PATH or copy target data there |
Hydra error InterpolationKeyError: AF2_DIR | Reward/eval config wants AF2 but .env does not define it | Download AF2 weights or remove AF2 from the config |
Step 6: Emit setup artifact
Drop a JSON manifest in ./complexa_setup/ so the user has a single file
describing the resulting state. The shared helper writes it for you:
mkdir -p ./complexa_setup
python .claude/skills/_shared/scripts/write_manifest.py \
--kind setup \
--runtime "$(grep -E '^COMPLEXA_RUNTIME=' .env | cut -d= -f2)" \
--preflight ./complexa_setup/preflight.json \
--out ./complexa_setup/run_manifest.json
Surface the resulting files to the user:
ls -la ./complexa_setup/
Expected contents:
complexa_setup/
├── preflight.json # GPU / disk / .env / ckpt / tool snapshot
└── run_manifest.json # init + download invocations + git SHA + runtime
Hardware requirements
| Resource | Minimum | Recommended |
|---|
| GPU | 1× CUDA GPU, ≥24 GB VRAM | A100 / H100 / L40S, 40–80 GB VRAM |
| CUDA | 12.0 | 12.4+ |
| Disk (CKPT_PATH) | 50 GB | 150 GB (covers --everything) |
| RAM | 16 GB | 64 GB+ |
| OS | Ubuntu 22.04+ (UV) | Ubuntu 22.04+ or Docker on any host |
Ubuntu 20.04 throws GLIBC errors with the UV runtime — use complexa init --runtime docker on those hosts. See .claude/skills/_shared/reference/hardware.md
for per-pipeline (binder vs ligand vs AME) requirements.
Troubleshooting
| Symptom | Cause | Fix |
|---|
complexa: command not found | Package not installed in active env | source .venv/bin/activate then pip install -e . |
complexa init says .env_example not found | Running outside repo root | cd to the project root (where .env_example lives) |
.env_example not found. Cannot initialize .env. | Not in project root | cd into protein-foundation-models/ and retry |
complexa download fails on NGC URL | Behind firewall / no internet | Configure a proxy for the download script, or download the model .ckpts manually from the NGC pages linked in the main README.md and drop them into ./ckpts/ |
complexa download --status shows ckpts present but validate fails | .env CKPT_PATH points elsewhere | Either move ckpts or edit LOCAL_CHECKPOINT_PATH in .env |
| GLIBC error on import | Ubuntu 20.04 with UV runtime | Re-run complexa init --runtime docker and use ./env/docker-ops.sh run |
For the full .env reference (every key, defaults, failure modes), see
reference/env_keys.md.
For the full download flag matrix, NGC URLs, and destination layout, see
reference/downloads.md.
