Boltz Ligand Sequence¶
Creates a ligand entry for Boltz YAML configurations. You choose whether to specify the ligand by SMILES or by a CCD code and assign it to one or more chain IDs. The node validates your choice and ensures only the appropriate field is set.
Usage¶
Use this node when you need to add a ligand to a Boltz modeling job. Select the input method (SMILES or CCD), provide the identifier, and set the chain ID(s). Feed the output into BoltzListCombinerNode and then into BoltzYAMLCombinerNode alongside protein/DNA/RNA sequences, constraints, and templates.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| chain_id | True | STRING | Primary chain identifier for this ligand. | L |
| ligand_type | True | ["smiles", "ccd"] | How the ligand is specified. Choose 'smiles' to input a SMILES string or 'ccd' to input a CCD code. | smiles |
| ligand_smiles | False | STRING | SMILES string for the ligand. Required if ligand_type is 'smiles'. | CC(=O)Oc1ccccc1C(=O)O |
| ligand_ccd | False | STRING | CCD (Chemical Component Dictionary) code for the ligand. Required if ligand_type is 'ccd'. | ATP |
| multiple_chains | False | STRING | Comma-separated additional chain IDs to duplicate this ligand across multiple chains. If provided, the 'id' field becomes a list. | M,N |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| ligand_sequence | * | A list containing a single ligand mapping suitable for Boltz YAML assembly. Example structure: [{"ligand": {"id": "L" or ["L","M",...], "smiles": "..."}] or with "ccd" instead of "smiles". | [{"ligand": {"id": "L", "smiles": "CCO"}}] |
Important Notes¶
- Single specification rule: Provide either a SMILES string or a CCD code based on ligand_type; not both.
- Required fields by type: If ligand_type='smiles', 'ligand_smiles' must be non-empty; if ligand_type='ccd', 'ligand_ccd' must be non-empty.
- Multiple chains: Supplying comma-separated IDs in 'multiple_chains' turns the 'id' field into a list to replicate the same ligand across those chains.
- Downstream uniqueness: Ensure chain IDs are unique across all sequences when later combined into a Boltz YAML.
- Return shape: Output is a list containing one ligand object; this is designed to feed directly into list-combining and YAML-combining nodes.
Troubleshooting¶
- Error: SMILES string is required when ligand_type is 'smiles': Enter a valid SMILES in 'ligand_smiles' or change ligand_type.
- Error: CCD code is required when ligand_type is 'ccd': Enter a valid CCD code in 'ligand_ccd' or change ligand_type.
- Error: Invalid ligand type: Ensure 'ligand_type' is set to either 'smiles' or 'ccd'.
- Duplicate chain ID warnings/errors downstream: When assembling YAML, make sure no other sequence uses the same chain ID(s) as this ligand.
- Multiple chains not applied: Verify 'multiple_chains' is a comma-separated list without spaces-only entries (e.g., "M,N").