## Resume a stopped small molecule library screen `$ boltz-api small-molecule:library-screen resume` **post** `/compute/v1/small-molecule/library-screen/{id}/resume` Resume a stopped small molecule library screen from its last checkpoint ### Parameters - `--id: string` Library screen ID ### Returns - `SmallMoleculeLibraryScreenResumeResponse: object { id, completed_at, created_at, 14 more }` A small molecule library screening pipeline run - `id: string` Unique SmScreen 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: "boltzmol"` 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 { molecules, target, molecule_filters }` Pipeline input (null if data deleted) - `molecules: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: object { entities, bonds, constraints, 3 more }` Target protein sequences for small molecule design or screening. - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `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) - `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 - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `type: optional "no_template"` Target is defined directly by protein sequences rather than a structure template. - `"no_template"` - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse: object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse: object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse: object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `SmartsCatalogFilterResponse: object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `SmilesRegexFilterResponse: object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `livemode: boolean` Whether this resource was created with a live API key. - `pipeline: "boltzmol"` Pipeline used for small molecule library screen - `pipeline_version: "1.0"` Pipeline version used for small molecule library screen - `progress: object { num_molecules_failed, num_molecules_screened, total_molecules_to_screen, 2 more }` - `num_molecules_failed: number` Number of accepted molecules that reached terminal failure during screening. - `num_molecules_screened: number` Number of accepted molecules that produced usable screening results. - `total_molecules_to_screen: number` Total number of molecules accepted into screening after server-side validation and filtering. - `latest_result_id: optional string` ID of the most recently screened result - `rejection_summary: optional object { filtered_count, invalid_count }` - `filtered_count: number` Number of submitted molecules removed by server-side filtering rules. - `invalid_count: number` Number of submitted molecules rejected as invalid input. - `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 small-molecule: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": "boltzmol", "engine_version": "1.0", "error": { "code": "code", "message": "message", "details": {} }, "input": { "molecules": { "url": "https://example.com", "url_expires_at": "2019-12-27T18:11:19.117Z" }, "target": { "entities": [ { "chain_ids": [ "string" ], "type": "protein", "value": "value", "cyclic": true, "modifications": [ { "residue_index": 0, "type": "ccd", "value": "value" } ] } ], "bonds": [ { "atom1": { "atom_name": "atom_name", "chain_id": "chain_id", "type": "ligand_atom" }, "atom2": { "atom_name": "atom_name", "chain_id": "chain_id", "type": "ligand_atom" } } ], "constraints": [ { "binder_chain_id": "binder_chain_id", "contact_residues": { "A": [ 42, 43, 44, 67, 68, 69 ] }, "max_distance_angstrom": 0, "type": "pocket", "force": true } ], "pocket_residues": { "A": [ 42, 43, 44, 67, 68, 69 ] }, "reference_ligands": [ "string" ], "type": "no_template" }, "molecule_filters": { "boltz_smarts_catalog_filter_level": "recommended", "custom_filters": [ { "max_hba": 0, "max_hbd": 0, "max_logp": 0, "max_mw": 0, "type": "lipinski_filter", "allow_single_violation": true } ] } }, "livemode": true, "pipeline": "boltzmol", "pipeline_version": "1.0", "progress": { "num_molecules_failed": 0, "num_molecules_screened": 0, "total_molecules_to_screen": 0, "latest_result_id": "latest_result_id", "rejection_summary": { "filtered_count": 0, "invalid_count": 0 } }, "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" } ```