Boltz Ligand Sequence¶
Builds a ligand entry for Boltz YAML. You choose how to specify the ligand (SMILES string or CCD code) and assign one or multiple chain IDs. The node validates inputs and outputs a standardized ligand sequence object ready to be combined into a full Boltz configuration.
Usage¶
Use this node when you need to add a ligand definition to a Boltz run. Select the ligand specification type (SMILES or CCD), provide the corresponding value, and set one or more chain IDs. Feed its output into a list combiner and then into the Boltz YAML combiner alongside proteins, constraints, templates, and properties.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| chain_id | True | STRING | Primary chain ID to assign to this ligand. | L |
| ligand_type | True | ENUM['smiles','ccd'] | How the ligand is specified: 'smiles' to provide a SMILES string, or 'ccd' to provide a PDB CCD code. | smiles |
| ligand_smiles | False | STRING | Ligand SMILES string. Required when ligand_type is 'smiles'. | CC(=O)Oc1ccccc1C(=O)O |
| ligand_ccd | False | STRING | Ligand CCD (Chemical Component Dictionary) three-letter code. Required when ligand_type is 'ccd'. | ATP |
| multiple_chains | False | STRING | Comma-separated list of additional chain IDs if you want multiple identical ligand copies. | M,N |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| ligand_sequence | * | A list containing one ligand sequence object in Boltz format. Example structure: [{'ligand': {'id': 'L' or ['L','M',...], 'smiles': '...' OR 'ccd': '...'}}]. | [{'ligand': {'id': ['L','M'], 'smiles': 'CC(=O)Oc1ccccc1C(=O)O'}}] |
Important Notes¶
- You must provide exactly one ligand specification matching ligand_type: 'smiles' requires ligand_smiles; 'ccd' requires ligand_ccd.
- If ligand_type is 'smiles' and ligand_smiles is empty, or ligand_type is 'ccd' and ligand_ccd is empty, the node will raise an error.
- chain_id defaults to 'L'. Use multiple_chains to duplicate the same ligand across additional chains (e.g., 'M,N').
- The output is a list containing a single mapping; it is designed to be combined with other sequences via a list combiner and then assembled into YAML with the Boltz YAML combiner.
Troubleshooting¶
- Error: "SMILES string is required when ligand_type is 'smiles'" — Provide a non-empty ligand_smiles value or switch ligand_type to 'ccd' with a CCD code.
- Error: "CCD code is required when ligand_type is 'ccd'" — Provide a non-empty ligand_ccd value or switch ligand_type to 'smiles' with a SMILES string.
- Error: "Invalid ligand type:
" — Set ligand_type to either 'smiles' or 'ccd'. - Unexpected result format downstream — Ensure you pass this node's output through the List Combiner and then into the YAML Combiner to create a valid Boltz YAML and files set.