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.

For an offline edit, work on the supplied registry or requested output copy. When a copy is requested, create its parent directory and copy into an absent destination. If the destination already exists, inspect and preserve it: reuse it when it is the intended working copy, otherwise report the path conflict. Do not delete the output tree to restart a configuration edit. An installed Complexa runtime, GPU, or target structure is not required to write the configuration. Use the field schema below, preserve unrelated entries, and read back the saved block. Coordinate validation remains pending when the structure is absent; finish the configuration task without installing a runtime. With Read/Edit tools, read the destination copy before editing it; reading the original input path does not satisfy Edit's requirement for the output path.