# Small Molecule # Design ## Start `client.smallMolecule.design.start(DesignStartParamsbody, RequestOptionsoptions?): DesignStartResponse` **post** `/compute/v1/small-molecule/design` Create a new design run that generates novel small molecule candidates for a protein target ### Parameters - `body: DesignStartParams` - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `atom2: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraint` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `chemical_space?: "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilter` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilter` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `DesignStartResponse` A small molecule design engine run that generates novel molecules - `id: string` Unique SmDesignRun identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `chemical_space?: "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id?: string` ID of the most recently generated result - `started_at: string | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.design.start({ num_molecules: 10, target: { entities: [ { chain_ids: ['string'], type: 'protein', value: 'value', }, ], }, }); console.log(response.id); ``` ## List `client.smallMolecule.design.list(DesignListParamsquery?, RequestOptionsoptions?): CursorPage` **get** `/compute/v1/small-molecule/design` List small molecule design runs, optionally filtered by workspace ### Parameters - `query: DesignListParams` - `after_id?: string` Return results after this ID - `before_id?: string` Return results before this ID - `limit?: number` Max items to return. Defaults to 100. - `workspace_id?: string` Filter by workspace ID. Only used with admin API keys. If not provided, defaults to the workspace associated with the API key, or the default workspace for admin keys. ### Returns - `DesignListResponse` Summary of a small molecule design engine run (excludes input) - `id: string` Unique SmDesignRunSummary identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id?: string` ID of the most recently generated result - `started_at: string | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); // Automatically fetches more pages as needed. for await (const designListResponse of client.smallMolecule.design.list()) { console.log(designListResponse.id); } ``` ## Retrieve `client.smallMolecule.design.retrieve(stringid, DesignRetrieveParamsquery?, RequestOptionsoptions?): DesignRetrieveResponse` **get** `/compute/v1/small-molecule/design/{id}` Retrieve a design run by ID, including progress and status ### Parameters - `id: string` - `query: DesignRetrieveParams` - `workspace_id?: string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `DesignRetrieveResponse` A small molecule design engine run that generates novel molecules - `id: string` Unique SmDesignRun identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `chemical_space?: "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id?: string` ID of the most recently generated result - `started_at: string | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const design = await client.smallMolecule.design.retrieve('id'); console.log(design.id); ``` ## List Results `client.smallMolecule.design.listResults(stringid, DesignListResultsParamsquery?, RequestOptionsoptions?): CursorPage` **get** `/compute/v1/small-molecule/design/{id}/results` Retrieve paginated results from a design run ### Parameters - `id: string` - `query: DesignListResultsParams` - `after_id?: string` Return results after this ID - `before_id?: string` Return results before this ID - `limit?: number` Max results to return. Defaults to 100. - `workspace_id?: string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `DesignListResultsResponse` A single designed small molecule result - `id: string` Unique result ID - `artifacts: Artifacts` - `archive: Archive` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `structure: Structure` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `created_at: string` - `metrics: Metrics` Scoring metrics for a designed small molecule - `binding_confidence: number` Confidence that the molecule binds the target (0-1). Primary metric for hit discovery. - `complex_iplddt: number` Interface pLDDT for the complex (0-1 float). Confidence at the binding interface. - `complex_plddt: number` pLDDT for the full complex (0-1 float). - `iptm: number` Interface predicted TM score (0-1). Confidence in relative positioning of ligand and protein. - `optimization_score: number` Binding strength ranking score for lead optimization. Higher values indicate stronger predicted binding. - `ptm: number` Predicted TM score (0-1). Global structure quality metric. - `structure_confidence: number` Confidence in the predicted 3D structure (0-1). - `smiles: string` SMILES string of the designed molecule - `warnings?: Array` Warnings about potential quality issues with this result. - `code: string` Machine-readable warning code (e.g. "low_confidence", "unusual_geometry") - `message: string` Human-readable description of the warning ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); // Automatically fetches more pages as needed. for await (const designListResultsResponse of client.smallMolecule.design.listResults('id')) { console.log(designListResultsResponse.id); } ``` ## Stop `client.smallMolecule.design.stop(stringid, RequestOptionsoptions?): DesignStopResponse` **post** `/compute/v1/small-molecule/design/{id}/stop` Stop an in-progress design run early ### Parameters - `id: string` ### Returns - `DesignStopResponse` A small molecule design engine run that generates novel molecules - `id: string` Unique SmDesignRun identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `chemical_space?: "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id?: string` ID of the most recently generated result - `started_at: string | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.design.stop('id'); console.log(response.id); ``` ## Delete Data `client.smallMolecule.design.deleteData(stringid, RequestOptionsoptions?): DesignDeleteDataResponse` **post** `/compute/v1/small-molecule/design/{id}/delete-data` Permanently delete the input, output, and result data associated with this design run. The design run record itself is retained with a `data_deleted_at` timestamp. This action is irreversible. ### Parameters - `id: string` ### Returns - `DesignDeleteDataResponse` - `id: string` ID of the resource whose data was deleted - `data_deleted: true` - `true` - `data_deleted_at: string` When the data was deleted ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.design.deleteData('id'); console.log(response.id); ``` ## Estimate Cost `client.smallMolecule.design.estimateCost(DesignEstimateCostParamsbody, RequestOptionsoptions?): DesignEstimateCostResponse` **post** `/compute/v1/small-molecule/design/estimate-cost` Estimate the billed cost of a small molecule design run without creating any resource or consuming GPU. Includes the SynFlowNet generation charges implied by the scheduler iteration cap plus Boltz2 scoring for each requested molecule. ### Parameters - `body: DesignEstimateCostParams` - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `atom2: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraint` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `chemical_space?: "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilter` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilter` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `DesignEstimateCostResponse` Estimate response with monetary values encoded as decimal strings to preserve precision. - `breakdown: Breakdown` Cost breakdown for the billed application. - `application: "structure_and_binding" | "small_molecule_design" | "small_molecule_library_screen" | 3 more` - `"structure_and_binding"` - `"small_molecule_design"` - `"small_molecule_library_screen"` - `"protein_design"` - `"protein_library_screen"` - `"adme"` - `cost_per_unit_usd: string` Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total. - `num_units: number` Number of units shown for the estimate. For structure-and-binding, this is the requested number of samples. For protein and small-molecule design/screen endpoints, this is the requested number of proteins or molecules. - `disclaimer: string` - `estimated_cost_usd: string` Estimated total cost as a decimal string ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.design.estimateCost({ num_molecules: 10, target: { entities: [ { chain_ids: ['string'], type: 'protein', value: 'value', }, ], }, }); console.log(response.breakdown); ``` # Library Screen ## Start `client.smallMolecule.libraryScreen.start(LibraryScreenStartParamsbody, RequestOptionsoptions?): LibraryScreenStartResponse` **post** `/compute/v1/small-molecule/library-screen` Screen a set of small molecule candidates against a protein target ### Parameters - `body: LibraryScreenStartParams` - `molecules: Array` List of small molecules to screen. - `smiles: string` SMILES string of the molecule - `id?: string` Optional identifier for this molecule - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `atom2: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraint` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilter` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilter` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `LibraryScreenStartResponse` A small molecule library screening engine run - `id: string` Unique SmScreen identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-screen"` Engine used for small molecule library screen - `"boltz-sm-screen"` - `engine_version: string` Engine version used for small molecule library screen - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `molecules: Molecules` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `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?: string` ID of the most recently screened result - `rejection_summary?: RejectionSummary` - `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 | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.libraryScreen.start({ molecules: [{ smiles: 'smiles' }], target: { entities: [ { chain_ids: ['string'], type: 'protein', value: 'value', }, ], }, }); console.log(response.id); ``` ## List `client.smallMolecule.libraryScreen.list(LibraryScreenListParamsquery?, RequestOptionsoptions?): CursorPage` **get** `/compute/v1/small-molecule/library-screen` List small molecule library screens, optionally filtered by workspace ### Parameters - `query: LibraryScreenListParams` - `after_id?: string` Return results after this ID - `before_id?: string` Return results before this ID - `limit?: number` Max items to return. Defaults to 100. - `workspace_id?: string` Filter by workspace ID. Only used with admin API keys. If not provided, defaults to the workspace associated with the API key, or the default workspace for admin keys. ### Returns - `LibraryScreenListResponse` Summary of a small molecule library screening engine run (excludes input) - `id: string` Unique SmScreenSummary identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-screen"` Engine used for small molecule library screen - `"boltz-sm-screen"` - `engine_version: string` Engine version used for small molecule library screen - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `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?: string` ID of the most recently screened result - `rejection_summary?: RejectionSummary` - `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 | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); // Automatically fetches more pages as needed. for await (const libraryScreenListResponse of client.smallMolecule.libraryScreen.list()) { console.log(libraryScreenListResponse.id); } ``` ## Retrieve `client.smallMolecule.libraryScreen.retrieve(stringid, LibraryScreenRetrieveParamsquery?, RequestOptionsoptions?): LibraryScreenRetrieveResponse` **get** `/compute/v1/small-molecule/library-screen/{id}` Retrieve a library screen by ID, including progress and status ### Parameters - `id: string` - `query: LibraryScreenRetrieveParams` - `workspace_id?: string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `LibraryScreenRetrieveResponse` A small molecule library screening engine run - `id: string` Unique SmScreen identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-screen"` Engine used for small molecule library screen - `"boltz-sm-screen"` - `engine_version: string` Engine version used for small molecule library screen - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `molecules: Molecules` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `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?: string` ID of the most recently screened result - `rejection_summary?: RejectionSummary` - `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 | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const libraryScreen = await client.smallMolecule.libraryScreen.retrieve('id'); console.log(libraryScreen.id); ``` ## List Results `client.smallMolecule.libraryScreen.listResults(stringid, LibraryScreenListResultsParamsquery?, RequestOptionsoptions?): CursorPage` **get** `/compute/v1/small-molecule/library-screen/{id}/results` Retrieve paginated results from a library screen ### Parameters - `id: string` - `query: LibraryScreenListResultsParams` - `after_id?: string` Return results after this ID - `before_id?: string` Return results before this ID - `limit?: number` Max results to return. Defaults to 100. - `workspace_id?: string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `LibraryScreenListResultsResponse` Result for a single screened small molecule - `id: string` Unique result ID - `artifacts: Artifacts` - `archive: Archive` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `structure: Structure` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `created_at: string` - `metrics: Metrics` Scoring metrics for a screened small molecule - `binding_confidence: number` Confidence that the molecule binds the target (0-1). Primary metric for hit discovery. - `complex_iplddt: number` Interface pLDDT for the complex (0-1 float). Confidence at the binding interface. - `complex_plddt: number` pLDDT for the full complex (0-1 float). - `iptm: number` Interface predicted TM score (0-1). Confidence in relative positioning of ligand and protein. - `optimization_score: number` Binding strength ranking score for lead optimization. Higher values indicate stronger predicted binding. - `ptm: number` Predicted TM score (0-1). Global structure quality metric. - `structure_confidence: number` Confidence in the predicted 3D structure (0-1). - `smiles: string` SMILES string of the screened molecule - `external_id?: string` Client-provided identifier for this molecule, if provided - `warnings?: Array` Warnings about potential quality issues with this result. - `code: string` Machine-readable warning code (e.g. "low_confidence", "unusual_geometry") - `message: string` Human-readable description of the warning ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); // Automatically fetches more pages as needed. for await (const libraryScreenListResultsResponse of client.smallMolecule.libraryScreen.listResults( 'id', )) { console.log(libraryScreenListResultsResponse.id); } ``` ## Stop `client.smallMolecule.libraryScreen.stop(stringid, RequestOptionsoptions?): LibraryScreenStopResponse` **post** `/compute/v1/small-molecule/library-screen/{id}/stop` Stop an in-progress library screen early ### Parameters - `id: string` ### Returns - `LibraryScreenStopResponse` A small molecule library screening engine run - `id: string` Unique SmScreen identifier - `completed_at: string | null` - `created_at: string` - `data_deleted_at: string | null` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-screen"` Engine used for small molecule library screen - `"boltz-sm-screen"` - `engine_version: string` Engine version used for small molecule library screen - `error: Error | null` - `code: string` Machine-readable error code - `message: string` Human-readable error message - `details?: unknown` Additional field-level error details keyed by input path, when available. - `input: Input | null` Pipeline input (null if data deleted) - `molecules: Molecules` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `atom2: LigandAtomResponse | PolymerAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtomResponse` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraintResponse` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraintResponse` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactTokenResponse | LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `livemode: boolean` Whether this resource was created with a live API key. - `progress: Progress | null` - `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?: string` ID of the most recently screened result - `rejection_summary?: RejectionSummary` - `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 | null` - `status: "pending" | "running" | "succeeded" | 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string | null` - `workspace_id: string` Workspace ID - `idempotency_key?: string` Client-provided idempotency key ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.libraryScreen.stop('id'); console.log(response.id); ``` ## Delete Data `client.smallMolecule.libraryScreen.deleteData(stringid, RequestOptionsoptions?): LibraryScreenDeleteDataResponse` **post** `/compute/v1/small-molecule/library-screen/{id}/delete-data` Permanently delete the input, output, and result data associated with this library screen. The library screen record itself is retained with a `data_deleted_at` timestamp. This action is irreversible. ### Parameters - `id: string` ### Returns - `LibraryScreenDeleteDataResponse` - `id: string` ID of the resource whose data was deleted - `data_deleted: true` - `true` - `data_deleted_at: string` When the data was deleted ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.libraryScreen.deleteData('id'); console.log(response.id); ``` ## Estimate Cost `client.smallMolecule.libraryScreen.estimateCost(LibraryScreenEstimateCostParamsbody, RequestOptionsoptions?): LibraryScreenEstimateCostResponse` **post** `/compute/v1/small-molecule/library-screen/estimate-cost` Estimate the cost of a small molecule library screen without creating any resource or consuming GPU. ### Parameters - `body: LibraryScreenEstimateCostParams` - `molecules: Array` List of small molecules to screen. - `smiles: string` SMILES string of the molecule - `id?: string` Optional identifier for this molecule - `target: Target` Target protein with binding pocket for small molecule design or screening - `entities: Array` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: Array` Chain IDs for this entity - `type: "protein"` - `"protein"` - `value: string` Amino acid sequence (one-letter codes) - `cyclic?: boolean` Whether the sequence is cyclic - `modifications?: Array` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds?: Array` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `atom2: LigandAtom | PolymerAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom` - `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"` - `"polymer_atom"` - `constraints?: Array` Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint` Constrains the binder to interact with specific pocket residues on the target. - `binder_chain_id: string` Chain ID of the binder molecule - `contact_residues: Record>` 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"` - `"pocket"` - `force?: boolean` Whether to force the constraint - `ContactConstraint` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `max_distance_angstrom: number` Maximum distance in Angstroms - `token1: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: PolymerContactToken | LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force?: boolean` Whether to force the constraint - `pocket_residues?: Record>` 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?: Array` 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. - `idempotency_key?: string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters?: MoleculeFilters` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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?: Array` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter` 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"` - `"lipinski_filter"` - `allow_single_violation?: boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter` 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"` - `"rdkit_descriptor_filter"` - `fraction_csp3?: FractionCsp3` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_logp?: MolLogp` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `mol_wt?: MolWt` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_aromatic_rings?: NumAromaticRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_acceptors?: NumHAcceptors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_h_donors?: NumHDonors` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_heteroatoms?: NumHeteroatoms` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rings?: NumRings` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `num_rotatable_bonds?: NumRotatableBonds` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `tpsa?: Tpsa` Min/max range constraint for an RDKit molecular descriptor - `max?: number` Maximum allowed value (inclusive) - `min?: number` Minimum allowed value (inclusive) - `SmartsCustomFilter` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: Array` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" | "PAINS_A" | "PAINS_B" | 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"` - `"smarts_catalog_filter"` - `SmilesRegexFilter` Filter molecules by regex patterns on their SMILES representation. - `patterns: Array` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id?: string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `LibraryScreenEstimateCostResponse` Estimate response with monetary values encoded as decimal strings to preserve precision. - `breakdown: Breakdown` Cost breakdown for the billed application. - `application: "structure_and_binding" | "small_molecule_design" | "small_molecule_library_screen" | 3 more` - `"structure_and_binding"` - `"small_molecule_design"` - `"small_molecule_library_screen"` - `"protein_design"` - `"protein_library_screen"` - `"adme"` - `cost_per_unit_usd: string` Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total. - `num_units: number` Number of units shown for the estimate. For structure-and-binding, this is the requested number of samples. For protein and small-molecule design/screen endpoints, this is the requested number of proteins or molecules. - `disclaimer: string` - `estimated_cost_usd: string` Estimated total cost as a decimal string ### Example ```typescript import Boltz from 'boltz-api'; const client = new Boltz({ apiKey: process.env['BOLTZ_API_KEY'], // This is the default and can be omitted }); const response = await client.smallMolecule.libraryScreen.estimateCost({ molecules: [{ smiles: 'smiles' }], target: { entities: [ { chain_ids: ['string'], type: 'protein', value: 'value', }, ], }, }); console.log(response.breakdown); ```