Boltz YAML Combiner¶
Combines molecular building blocks into a valid Boltz YAML configuration. It merges sequences (required) with optional constraints, templates, and properties, validates structure and chain ID uniqueness, and prepares auxiliary files (e.g., MSA and template PDB/CIF) referenced by filename in the YAML.
Usage¶
Use this after assembling lists with Boltz List Combiner. Connect the combined sequences (and optionally constraints, templates, and properties). The node outputs a Boltz YAML dictionary and a file-bundle dictionary that upstream prediction nodes consume.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| sequences | True | * | List of sequence objects (proteins, nucleic acids, or ligands). Typically created by Boltz Sequence Builder/Protein/Ligand nodes and merged by Boltz List Combiner. | [{"protein": {"id": "A", "sequence": "MSEQUENCE", "msa": "empty", "_sequence_name": "protA"}}, {"ligand": {"id": "L", "smiles": "C1=CC=CC=C1"}}] |
| constraints | False | * | Optional list of constraint objects (e.g., pocket, bond, contact) from Boltz Constraint Builder combined via Boltz List Combiner. | [{"pocket": {"binder": "L", "contacts": [["A", 10], ["A", 25]], "max_distance": 6.0}}] |
| templates | False | * | Optional list of template objects that include structure content (PDB/CIF). The node converts embedded content to filenames and adds them to the file bundle. | [{"pdb": " |
| properties | False | * | Optional list of property objects (e.g., affinity specifications) from Boltz Property Builder combined via Boltz List Combiner. | [{"affinity": {"binder": "L"}}] |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| boltz_yaml | BOLTZ_YAML | Validated Boltz YAML dictionary with sequences and any provided constraints, templates, and properties. Includes version and filename references to auxiliary files. | {"version": 1, "sequences": [{"protein": {"id": "A", "sequence": "MSEQUENCE", "msa": "msa_1.a3m"}}, {"ligand": {"id": "L", "smiles": "C1=CC=CC=C1"}}], "templates": [{"pdb": "template_2.pdb", "chain_id": "A"}], "properties": [{"affinity": {"binder": "L"}}]} |
| boltz_files | BOLTZ_FILES | Dictionary of auxiliary files referenced by the YAML (e.g., MSA files and template structures) keyed by generated filenames. | {"msa_1.a3m": " |
Important Notes¶
- Unique chain IDs: All chain IDs across all sequences must be unique; duplicates cause an error.
- Required sequence fields: Protein/DNA/RNA sequences must include "sequence"; ligands must include exactly one of "smiles" or "ccd".
- MSA handling: If a protein has an MSA that is not "empty", the content is written to a generated filename (msa_N.a3m) and the YAML references that filename.
- Shared MSA optimization: Proteins with identical sequence strings share the same MSA file; the YAML for those entries points to the same filename.
- Template handling: Template PDB/CIF content is moved to generated filenames (template_N.pdb or template_N.cif) and referenced from the YAML.
- Validation: The node enforces Boltz YAML structure, auto-sets version=1 if missing, and will error on invalid entity types or missing required fields.
- Input form: Each input can be a single object or a list; the node normalizes internally. Typically, use Boltz List Combiner to construct lists.
Troubleshooting¶
- Duplicate chain ID found: Ensure each chain ID appears only once across all sequences (including duplicated chains from multi-chain entries).
- Missing sequence field: For protein/dna/rna entries, include the "sequence" field. For ligand entries, include exactly one of "smiles" or "ccd".
- Both SMILES and CCD provided for ligand: Provide only one field for ligands; remove the extra field.
- No sequences provided: The sequences input is required and must contain at least one sequence object.
- Invalid template content: Template objects must include valid PDB/CIF content; the node generates filenames from non-empty contents only.
- Unexpected input type: If inputs are raw objects instead of lists, ensure they are combined with Boltz List Combiner or pass as lists; the node accepts both.