Boltz YAML Combiner¶
Combines sequences, constraints, templates, and properties into a single Boltz YAML configuration and a companion files bundle. It validates structure, enforces unique chain IDs, and automatically converts embedded MSA/template content into referenced filenames while emitting those contents in the files bundle. Also ensures ligand fields are valid and sets a default YAML version.
Usage¶
Use this node after assembling inputs with the Boltz Sequence/Constraint/Template/Property builders and (optionally) Boltz List Combiner. Connect the combined sequences (required), and optionally constraints, templates, and properties. Feed this node’s outputs (boltz_yaml and boltz_files) directly into downstream Boltz execution nodes (e.g., prediction).
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| sequences | True | * | List of sequence objects produced by Boltz Sequence Builder nodes (often aggregated with Boltz List Combiner). Each item is a mapping like {'protein'\|'dna'\|'rna'\|'ligand': {...}} including 'id' and content fields. | [{"protein": {"id": "A", "sequence": "MKT...", "msa": "...a3m content...", "_msa_format": "a3m"}}, {"ligand": {"id": "L", "smiles": "CCO"}}] |
| constraints | False | * | Optional list of constraint objects from Boltz Constraint Builder (e.g., pocket, contact, bond constraints). | [{"pocket": {"binder": "L", "contacts": [["A", 10], ["A", 25]], "max_distance": 6.0}}] |
| templates | False | * | Optional list of template objects from Boltz Template Builder. Accepts PDB or CIF content that will be converted into referenced filenames. | [{"pdb": "HEADER...\nATOM ...\nEND"} ] |
| properties | False | * | Optional list of property objects from Boltz Property Builder (e.g., affinity with a binder chain). | [{"affinity": {"binder": "L"}}] |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| boltz_yaml | BOLTZ_YAML | Validated Boltz YAML configuration containing sequences (and optional constraints/templates/properties). References MSAs/templates by generated filenames. | {"version": 1, "sequences": [{"protein": {"id": "A", "sequence": "MKT...", "msa": "msa_1.a3m"}}, {"ligand": {"id": "L", "smiles": "CCO"}}], "templates": [{"pdb": "template_2.pdb"}], "constraints": [{"pocket": {"binder": "L", "contacts": [["A", 10], ["A", 25]], "max_distance": 6.0}}]} |
| boltz_files | BOLTZ_FILES | Auxiliary files dictionary containing emitted MSA and template file contents keyed by the filenames referenced in boltz_yaml. | {"msa_1.a3m": "...a3m content...", "template_2.pdb": "HEADER...\nATOM ...\nEND"} |
Important Notes¶
- Sequences are required; constraints, templates, and properties are optional.
- All chain IDs across all sequences (including multiple copies) must be unique; duplicates cause validation errors.
- For ligands, provide either 'smiles' or 'ccd' (but not both).
- Protein MSAs may be supplied inline; the node will generate filenames (e.g., msa_1.a3m) and move contents into boltz_files. Identical protein sequences will automatically share the same MSA file reference.
- Templates supplied as PDB or CIF content are converted to filenames (template_X.pdb or template_X.cif) and stored in boltz_files.
- The node sets 'version' to 1 if not specified.
Troubleshooting¶
- Duplicate chain ID found: Ensure every chain ID across all sequences is unique (including additional copies defined via multiple chains).
- Missing sequence field: For protein/dna/rna entries, include a non-empty 'sequence'.
- Invalid ligand specification: Provide exactly one of 'smiles' or 'ccd' for ligand entries.
- No sequences provided: Supply at least one sequence object via the sequences input (commonly a list from Boltz List Combiner).
- Template or MSA not appearing in files: Confirm content is non-empty; the node only emits file entries for provided contents.
- MSA/sequence mismatch warnings: If identical sequences are present, the node reuses a single MSA file reference to satisfy tool requirements. Review your configuration if unexpected sharing occurs.