Individual skill
complexa-target
Add, edit, inspect, or validate Proteina-Complexa target definitions for protein binders, ligand binders, and AME motif scaffolding. Use for target registries, chain/residue selectors, hotspots, ligand fields, and incomplete motif inputs. Covers direct YAML edits and complexa target/validate target commands; running a campaign with an already registered target belongs to complexa-design.
skills/bionemo-complexa-target/SKILL.md
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# 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.
## Instructions
`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.