/bionemo-complexa-target

name: complexa-target
description: >
  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.
allowed-tools: Bash, Read, Write, AskUserQuestion
metadata:
  author: Ohad Mosafi <omosafi@nvidia.com>

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.

Use the schema below and the selected registry; the CLI reference is needed only for CLI use. Finish with the saved entry, its consumer pipeline, the downstream `generation.task_name`, and the validation status.

| Step | Direct file edit (preferred) | CLI | |---|---|---| | Look at existing targets | Read `configs/targets/{,ligand_}targets_dict.yaml` (or `configs/design_tasks/ame_dict_v2.yaml` for AME) | `complexa target list` (protein/ligand only) | | Look at one target | Read the dict and grep for the key | `complexa target show NAME` | | Add a new target | Append a YAML block (Step 3a) | `complexa target add ...` (Step 3b) | | Verify configuration | Parse the saved YAML and compare the changed entry and untouched keys | `complexa target show NAME --dict PATH` | | Check runtime PDB-path resolution | Requires the full pipeline and environment | `complexa validate target CONFIG --target NAME` |

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.

| User intent | Pipeline | Targets dict file | This skill? | |---|---|---|---| | Bind a protein surface (PD-L1, IFNAR2, TNF-α, …) — **default** | `configs/search_binder_local_pipeline.yaml` | `configs/targets/targets_dict.yaml` | Yes — Step 2 (protein) | | Bind a small-molecule pocket (FAD, SAM, OQO, …) | `configs/search_ligand_binder_local_pipeline.yaml` | `configs/targets/ligand_targets_dict.yaml` | Yes — Step 2 (ligand) | | AME / enzyme scaffolding (motif + ligand, `M####_<pdb>` names) | `configs/search_ame_local_pipeline.yaml` | `configs/design_tasks/ame_dict_v2.yaml` | Partial — see "AME tasks" below |

AME tasks (enzyme pipeline)

AME tasks live under `motif_target_dict_cfg:` with `source`, `target_filename`, `ligand`, `contig_atoms`, `binder_length`, and `use_bonds_from_file`. The `contig_atoms` string contains curated chain/residue/atom selections. Existing entries illustrate the field structure, not the selections for a new motif. If motif atoms, ligand selection, or structure location are missing, list the missing inputs and write a separate, explicitly incomplete template if useful. Leave the registry unchanged until those scientific inputs are supplied. A task name or PDB ID alone does not determine them. In the missing-input handoff, explain that registration will be a direct edit under `motif_target_dict_cfg` once the curated selections are supplied; `complexa target add` cannot register AME tasks. Completed entries are selected with `++generation.task_name=<NAME>` and `configs/search_ame_local_pipeline.yaml`.

Step 2: Gather required info

Use the supplied values and ask only for missing required information. Required fields differ for protein, ligand, and AME definitions.

Protein target

| Field | Question | Example | Required | |---|---|---|---| | name | "Target name (used as the dict key and `task_name`)?" | `02_PDL1`, `MyTarget_v1` | yes | | source | "Source directory under `$DATA_PATH/target_data/`?" | `bindcraft_targets`, `custom_targets` | yes (or `target_path`) | | target_filename | "PDB filename (no `.pdb` extension)?" | `PD-L1`, `IFNAR2` | yes (or `target_path`) | | target_input | "Chain + residue range — see reference for grammar." | `A1-115`, `A1-50,B1-50` | yes | | hotspot_residues | "Hotspot residues (interface contact residues)?" | `["A33", "A95", "A102"]` | optional, recommended | | binder_length | "B