## Resume a stopped protein library screen `$ boltz-api protein:library-screen resume` **post** `/compute/v1/protein/library-screen/{id}/resume` Resume a stopped protein library screen from its last checkpoint ### Parameters - `--id: string` Library screen ID ### Returns - `ProteinLibraryScreenResumeResponse: object { id, completed_at, created_at, 14 more }` A protein library screening pipeline run - `id: string` Unique ProteinLibraryScreen identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltzprot"` Deprecated. Use pipeline instead. - `engine_version: "1.0"` Deprecated. Use pipeline_version instead. - `error: object { code, message, details }` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details: optional unknown` Additional field-level error details keyed by input path, when available. - `input: object { proteins, target }` Pipeline input (null if data deleted) - `proteins: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more }` Target specification (structure template or template-free) - `StructureTemplateTargetResponse: object { chain_selection, structure, type }` Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used. - `chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]` Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible. - `StructureTemplateTargetPolymerChainSpec: object { chain_type, crop_residues, epitope_residues, 2 more }` Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target. - `chain_type: "polymer"` - `crop_residues: array of number or "all"` 0-indexed residue indices to retain from this chain, or 'all' to keep all residues. Residues not listed are excluded from the pipeline run. - `union_member_0: array of number` 0-indexed residue indices to keep - `union_member_1: "all"` - `epitope_residues: optional array of number` 0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues. - `flexible_residues: optional array of number` 0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues. - `non_binding_residues: optional array of number` 0-indexed residue indices where binder contact should be discouraged. All indices must be present in crop_residues and must not overlap epitope_residues. - `StructureTemplateTargetLigandChainSpec: object { chain_type }` Per-chain specification for a ligand chain in a structure template target. The full ligand is always included. - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `type: "structure_template"` - `NoTemplateTargetResponse: object { entities, type, bonds, 4 more }` Target defined by sequences only, without a 3D structure template - `entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 more` Entities (proteins, RNA, DNA, ligands) defining the target complex. - `ProteinEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `RNAEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "rna"` - `value: string` RNA nucleotide sequence (A, C, G, U, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `DNAEntityResponse: object { chain_ids, type, value, 2 more }` - `chain_ids: array of string` Chain IDs for this entity - `type: "dna"` - `value: string` DNA nucleotide sequence (A, C, G, T, N) - `cyclic: optional boolean` Whether the sequence is cyclic - `modifications: optional array of object { residue_index, type, value }` CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported. - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` Modification format. Only CCD polymer modifications are supported. - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `LigandCCDEntityResponse: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_ccd"` - `value: string` CCD code (e.g., ATP, ADP) - `LigandSmilesEntityResponse: object { chain_ids, type, value }` - `chain_ids: array of string` Chain IDs for this ligand - `type: "ligand_smiles"` - `value: string` SMILES string representing the ligand - `type: "no_template"` - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom. - `LigandAtomResponse: object { atom_name, chain_id, type }` Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom. - `atom_name: string` Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `PolymerAtomResponse: object { atom_name, chain_id, residue_index, type }` - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB) - `chain_id: string` Chain ID containing the atom - `residue_index: number` 0-based residue index - `type: "polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom. - `LigandAtomResponse: object { atom_name, chain_id, type }` Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom. - `atom_name: string` Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `PolymerAtomResponse: object { atom_name, chain_id, residue_index, type }` - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB) - `chain_id: string` Chain ID containing the atom - `residue_index: number` 0-based residue index - `type: "polymer_atom"` - `constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more }` Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms. - `PocketConstraintResponse: object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more }` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: map[array of number]` Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. "A") and the value is an array of 0-indexed residue indices that define the pocket on that chain. - `max_distance_angstrom: number` Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A. - `type: "pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraintResponse: object { max_distance_angstrom, token1, token2, 2 more }` Maximum-distance contact constraint between two polymer residues or ligand atoms. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom. - `PolymerContactTokenResponse: object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `LigandContactTokenResponse: object { atom_name, chain_id, type }` Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom. - `atom_name: string` Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom. - `PolymerContactTokenResponse: object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `LigandContactTokenResponse: object { atom_name, chain_id, type }` Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom. - `atom_name: string` Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `type: "contact"` - `force: optional boolean` Whether to force the constraint - `epitope_ligand_chains: optional array of string` Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection). - `epitope_residues: optional map[array of number]` Polymer chain residues where binder contact is desired (the epitope). Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. Residues must not overlap non_binding_residues on the same chain. - `non_binding_residues: optional map[array of number]` Polymer chain residues where binder contact should be discouraged. Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. Residues must not overlap epitope_residues on the same chain. - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltzprot"` Pipeline used for protein library screen - `pipeline_version: "1.0"` Pipeline version used for protein library screen - `progress: object { num_proteins_failed, num_proteins_screened, total_proteins_to_screen, latest_result_id }` - `num_proteins_failed: number` Number of accepted proteins that reached terminal failure during screening. - `num_proteins_screened: number` Number of accepted proteins that produced usable screening results. - `total_proteins_to_screen: number` Total number of proteins accepted into the screening run. - `latest_result_id: optional string` ID of the latest result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```cli boltz-api protein:library-screen resume \ --api-key 'My API Key' \ --id id ``` #### Response ```json { "id": "id", "completed_at": "2019-12-27T18:11:19.117Z", "created_at": "2019-12-27T18:11:19.117Z", "data_deleted_at": "2019-12-27T18:11:19.117Z", "engine": "boltzprot", "engine_version": "1.0", "error": { "code": "code", "message": "message", "details": {} }, "input": { "proteins": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "target": { "chain_selection": { "A": { "chain_type": "polymer", "crop_residues": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 ], "epitope_residues": [ 10, 11, 12 ], "flexible_residues": [ 5, 6, 7 ], "non_binding_residues": [ 0, 1, 2 ] } }, "structure": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "type": "structure_template" } }, "livemode": true, "pipeline": "boltzprot", "pipeline_version": "1.0", "progress": { "num_proteins_failed": 0, "num_proteins_screened": 0, "total_proteins_to_screen": 1, "latest_result_id": "latest_result_id" }, "started_at": "2019-12-27T18:11:19.117Z", "status": "pending", "stopped_at": "2019-12-27T18:11:19.117Z", "workspace_id": "workspace_id", "idempotency_key": "idempotency_key" } ```