Complexa Target

complexa-target

Add or edit a design target in Proteina-Complexa. Targets live in three YAML files, one per complexa design pipeline:

• configs/targets/targets_dict.yaml — protein binder (default pipeline)
• configs/targets/ligand_targets_dict.yaml — ligand binder
• configs/design_tasks/ame_dict_v2.yaml — AME / enzyme scaffolding

The complexa target CLI only manages the first two. AME tasks use an extended schema (the same core fields as ligand targets plus contig_atoms for hand-curated per-residue motif atom selections) and are file-edit-only.

Preferred path: edit the YAML directly

complexa target add is a thin wrapper around "load YAML → build dict → append a block" (see src/proteinfoundation/cli/target_manager.py:add_target_cli and append_target_to_dict). For agentic use, just edit the targets dict directly — the schema is short, the existing entries are great copy templates, and you skip 14 CLI flags / SMILES shell-escaping. Use the CLI only if you explicitly want its YAML auto-quoter or its overwrite-prompt safety.

The skill therefore presents both paths:

complexa target only sees the two protein-style dicts (targets_dict.yaml and ligand_targets_dict.yaml). For AME tasks (which use a different schema), file-edit is the only path — see Step 1 below.

What this skill enables

• Register a protein target (chain + residue range + hotspots) in configs/targets/targets_dict.yaml.
• Register a ligand target (PDB pocket + 3-letter code + SMILES) in configs/targets/ligand_targets_dict.yaml.
• Resolve the right AME task name (e.g. M0024_1nzy, M0096_1chm) for the AME pipeline — these are not added via complexa target add (see Step 1).
• Verify a target resolves to a real PDB on disk with complexa validate target.
• Emit a replayable artifact (target_definition.yaml) for downstream design runs.

Step 1: Decide the target type

Targets live in three different files, one per complexa design pipeline. Pick the file by working out which pipeline the user will run, then add the entry to that file. Each file is consumed by exactly one pipeline.

AME tasks (enzyme pipeline)

Similar story — AME tasks live in configs/design_tasks/ame_dict_v2.yaml under motif_target_dict_cfg: with their own schema (source, target_filename, ligand, contig_atoms, binder_length, use_bonds_from_file). The contig_atoms string encodes per-residue motif atom selections like "A64: [O, C]; A86: [CB, CA, N, C]; ..." — these are hand-curated, so adding a new AME task is a file edit, not a CLI invocation. Browse the file, copy a similar entry as a template, and pass ++generation.task_name=<NAME> to complexa design configs/search_ame_local_pipeline.yaml.

Step 2: Gather required info

Use AskUserQuestion to collect — do not guess these. Required fields differ for protein vs ligand.

Protein target

Ligand target — protein fields above (minus target_input), plus:

Check for name collisions by reading the dict (rg '^ NEW_NAME:' configs/targets/targets_dict.yaml) or running complexa target list -v --ligand / --protein.

Step 3a: Append the YAML block directly (preferred)

Open configs/targets/targets_dict.yaml (or ligand_targets_dict.yaml for ligand targets), find a similar existing entry as a style template, and append the new block under target_dict_cfg:. Two-space indent, single blank line between entries.

Protein template

  02_PDL1:
    source: bindcraft_targets
    target_filename: PD-L1
    target_input: "A1-115"
    hotspot_residues: ["A37", "A39", "A49", "A98"]
    binder_length: [64, 155]
    pdb_id: "4z18"

Rules to match the existing file style (mirrors what complexa target add would emit):

• Quote chain/residue ranges ("A1-115", "A33") and any SMILES — flow-style strings get tripped up by : and brackets otherwise.
• Use flow-style lists (["A33", "A95"], [64, 155]) — that's what the on-disk dump produces.
• target_input, source, target_filename are required for protein. target_path (absolute path) can replace source + target_filename if the PDB lives outside $DATA_PATH/target_data/.

Ligand template

  41_7BKC_LIGAND:
    source: ligand_targets
    target_filename: 7BKC_ligand_centered
    hotspot_residues: [null]
    binder_length: [100]
    pdb_id: 7BKC
    ligand: 'FAD'
    ligand_only: True
    SMILES: "O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C"
    use_bonds_from_file: True

The presence of the ligand: key flips the target into ligand mode — there is no separate is_ligand flag. target_input is not required for ligands.

After saving, skip to Step 4 to verify.

Step 3b: CLI alternative (complexa target add)

Use the CLI when you want its automatic chain/residue quoting, the overwrite-confirm prompt, or to wire target creation into a non-Python script. Prefer non-interactive mode for agentic use (-i / --editor opens an editor and blocks).

Confirmed flags (from src/proteinfoundation/cli/target_cli.py)

Protein example

complexa target add 02_PDL1 \
  --source bindcraft_targets \
  --target-filename PD-L1 \
  --target-input A1-115 \
  --hotspot-residues A37 A39 A49 A98 \
  --binder-length 64 155 \
  --pdb-id 4z18

Ligand example

complexa target add 41_7BKC_LIGAND \
  --source ligand_targets \
  --target-filename 7BKC_ligand_centered \
  --pdb-id 7BKC \
  --ligand FAD \
  --ligand-only \
  --use-bonds-from-file \
  --smiles "O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C" \
  --binder-length 100

Why these defaults: --source defaults to custom_targets (protein) or ligand_targets (ligand) and --target-filename defaults to name, so be explicit when the PDB stem differs from the target name. The dict gets ligand_only: true and use_bonds_from_file: true by default for ligand targets — pass the flags to be explicit, or omit to accept defaults.

Step 4: Verify

Run two checks, in order. Stop and fix on the first failure.

# 1. Confirm the entry landed and looks right.
#    Direct read works just as well: `rg -A 7 '^  02_PDL1:' configs/targets/targets_dict.yaml`
complexa target show 02_PDL1

# 2. Resolve the PDB path and validate it exists on disk.
#    No shortcut for this — it traverses Hydra defaults to find the target dict.
complexa validate target configs/search_protein_local_pipeline.yaml --target 02_PDL1

complexa validate target (from src/proteinfoundation/cli/validate.py::validate_target) checks:

• DATA_PATH is set and target_data/ exists.
• The target name resolves in target_dict_cfg.
• Either target_path exists, or $DATA_PATH/target_data/<source>/<target_filename>.pdb exists.
• target_input, hotspot_residues, binder_length are reported back so a human can sanity-check them.

For ligand targets, point --target at a ligand pipeline config (e.g. a ligand binder search config).

Step 5: Emit artifact

Save a replayable record under ./target_<name>/:

mkdir -p target_02_PDL1
complexa target show 02_PDL1 > target_02_PDL1/target_show.txt

Then write the appended YAML snippet (the lines complexa target add wrote under target_dict_cfg:) to target_02_PDL1/target_definition.yaml using the Write tool. The artifact lets the user diff target definitions across runs and re-create the entry on another checkout via complexa target add ... --force.

Hardware requirements

None for target definition — this is a YAML edit, not a training/inference step. Disk impact is a few KB appended to the targets dict (plus an automatic .yaml.bak backup written by save_targets_dict).

For the downstream design / evaluate runs that consume the target, defer to complexa-design and _shared/reference/hardware.md.

Troubleshooting

Reference

• reference/target_schema.md — every field, chain-spec grammar, AME task-name grammar, three worked examples.
• configs/targets/targets_dict.yaml — live protein entries (copy a known-good one as a template).
• configs/targets/ligand_targets_dict.yaml — live ligand entries.
• configs/design_tasks/ame_dict_v2.yaml — AME task definitions (file-edit only, not exposed via complexa target CLI).
• src/proteinfoundation/cli/target_cli.py — argparse source of truth.
• src/proteinfoundation/cli/target_manager.py — add_target_cli, list_targets, show_target, schema in TARGET_FIELDS.
• src/proteinfoundation/cli/validate.py — validate_target implementation.