complexa-target

name	complexa-target
description	Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new target for binder design", "register a hotspot", "set up a PDL1 binder target", "ligand binder pocket", "SMILES target", "AME task", "enzyme motif", "M0024_1nzy", "M0096_1chm", "complexa target add", "complexa target show", "configure target X", "what targets are available", "where do hotspots live", "what does target_input mean", "chain-spec syntax", "binder length range", "contig_atoms", or any question about `configs/targets/{,ligand_}targets_dict.yaml` and `configs/design_tasks/ame_dict_v2.yaml`. Also covers `complexa validate target`. This is the only skill that touches the three targets dict files.
allowed-tools	Bash, Read, Write, AskUserQuestion

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 a different schema (contig_atoms plus 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:

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 the PDB resolves on disk	— (no shortcut, this checks Hydra defaults)	complexa validate target CONFIG --target NAME

complexa target only sees the two protein-style dicts (targets_dict.yaml and ligand_targets_dict.yaml). For AME tasks (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.
• Add a new AME task (motif + ligand, M####_<pdb>) in configs/design_tasks/ame_dict_v2.yaml — 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.

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 — file edit only (see below)

AME tasks (enzyme pipeline)

Not added via complexa target add — 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. See reference/target_schema.md "AME task names" section.

Step 2: Gather required info

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

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	"Binder length range [min, max] or single [length]?"	[80, 150], [100]	optional (default [60, 120])
pdb_id	"Reference PDB ID (optional, metadata only)?"	"2lag"	optional

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

Field	Question	Example	Required
ligand	"3-letter PDB ligand residue code?"	FAD, OQO, SAM	yes (presence marks target as ligand)
smiles	"SMILES string for the ligand?"	"O=C2C3=Nc1cc(c(...)..."	recommended
ligand_only	"Generate pocket around ligand only (no protein-protein interface)?"	true / false	optional (default true)
use_bonds_from_file	"Use bond info from the input PDB/CIF?"	true / false	optional (default true)
target_input	not required for ligand targets	—	no

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)

Flag	Type	Applies to	Notes
name (positional)	str	both	dict key
--dict PATH	path	both	override target dict path
-i, --interactive	flag	both	open $EDITOR
-e, --editor NAME	str	both	code, nano, vim, cursor, ...
--source NAME	str	both	directory under $DATA_PATH/target_data/
--target-filename NAME	str	both	PDB stem (no .pdb)
--target-path PATH	str	both	full path; overrides source+filename
--target-input SPEC	str	protein	chain/residue range, e.g. A1-115
--hotspot-residues R [R ...]	list	both	e.g. A33 A95
--binder-length N [N ...]	int list	both	[min, max] or [length]
--pdb-id ID	str	both	metadata only
--ligand CODE	str	ligand	presence marks ligand target
--ligand-only	flag	ligand	pocket-only mode
--smiles STR	str	ligand	SMILES for the ligand
--use-bonds-from-file	flag	ligand	use PDB bonds
-f, --force	flag	both	overwrite existing without prompt

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.

complexa target add does NOT validate the biology of what you give it. It writes whatever you pass straight into the dict: a --target-input that references non-existent residues/chains, a DNA/RNA sequence, an antibody sequence, a SMILES string in the protein --target-input slot, or plain garbage are all accepted silently. The failure only surfaces later, mid-design. When you (an agent) drive this interactively you should sanity-check inputs first — confirm the chain/residue spec against the actual PDB, route SMILES to the ligand dict (--smiles + --ligand, never --target-input), and refuse non-protein/non-ligand inputs. Scripted callers (the complexa-sweep bash glue, CI, any non-interactive caller) get no such protection — they must validate inputs before calling complexa target add, then verify the result with complexa target show <name> and complexa validate target <config> --target <name> (Step 4).

Step 4: Verify

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

# 1. Confirm the entry landed and looks right. This is the AUTHORITATIVE
#    existence check — a 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.
#    Pass a REAL pipeline config (this file must exist) AND --target.
complexa validate target configs/search_binder_local_pipeline.yaml --target 02_PDL1

complexa validate target (from src/proteinfoundation/cli/validate.py::validate_target) checks, only when given a config path that exists:

• DATA_PATH is set and target_data/ exists.
• The target name resolves in target_dict_cfg (reports "Target not found … (N targets available)" if absent).
• 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.

Two gotchas that make validate target silently useless — both apply here:

• No config, no dict check. complexa validate target --target X without a config path skips the dict-membership check entirely (it only checks DATA_PATH/target_data/) and returns green for any X, including garbage. Always pass a real config, as in command 2 above.
• Wrong config name = no check. If the config file does not exist, the CLI aborts with "Config file not found" before checking anything. There is no search_protein_local_pipeline.yaml — the protein config is search_binder_local_pipeline.yaml. Use the real name (see configs/search_*_local_pipeline.yaml).

So treat command 1 (complexa target show / rg the dict) as the real existence check; validate target is a path/field sanity check on top of it.

For ligand targets, point --target at a ligand pipeline config (configs/search_ligand_binder_local_pipeline.yaml); for AME, configs/search_ame_local_pipeline.yaml.

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

Symptom	Cause	Fix
Target PDB file: File not found from validate target	<source>/<target_filename>.pdb does not exist under $DATA_PATH/target_data/	Confirm the PDB stem and source dir. Use --target-path /full/path.pdb if the file lives outside target_data/.
"Target 'X' already exists! Overwrite? (y/N)"	Name collision in dict	Either pick a new name, or pass -f / --force to overwrite.
Hotspot residue not in PDB	Wrong chain or residue number	Open the PDB, re-check chain letters (case-sensitive) and residue indices. Hotspots use the format <CHAIN><RESNUM> — see reference.
Chain not found	target_input references a chain that does not exist in the PDB	Inspect the PDB with grep "^ATOM" target.pdb | awk '{print $5}' | sort -u.
Ligand code missing from PDB	The 3-letter ligand code does not appear as a HETATM residue name in the file	Open the PDB and check HETATM lines; you may need a _ligand_centered variant of the PDB.
SMILES parse failure downstream	Bad SMILES string	Validate with rdkit.Chem.MolFromSmiles(smiles) before adding. Quote SMILES in shell to escape brackets and parens.
Target name with leading digit breaks Hydra interpolation	YAML treats 02_PDL1 as a string fine; some override syntaxes need quoting	Use ++generation.task_name=02_PDL1; quote if the shell strips characters.
target_input appears ignored for a ligand target	By design — ligand targets do not use target_input; pocket is defined by the ligand	Leave it unset for ligand targets.

Reference

• reference/target_schema.md — every field, chain-spec grammar, AME task schema, 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).
• 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.