## Stop

`$ boltz-api small-molecule:design stop`

**post** `/compute/v1/small-molecule/design/{id}/stop`

Stop an in-progress design run early

### Parameters

- `--id: string`

  Design run ID

### Returns

- `SmallMoleculeDesignStopResponse: object { id, completed_at, created_at, 12 more }`

  A small molecule design engine run that generates novel molecules

  - `id: string`

    Unique SmDesignRun identifier

  - `completed_at: string`

  - `created_at: string`

  - `data_deleted_at: string`

    When the input, output, and result data was permanently deleted. Null if data has not been deleted.

  - `engine: "boltz-sm-design"`

    Engine used for small molecule design

    - `"boltz-sm-design"`

  - `engine_version: string`

    Engine version used for small molecule design

  - `error: object { code, message, details }`

    - `code: string`

      Machine-readable error code

    - `message: string`

      Human-readable error message

    - `details: optional unknown`

      Additional field-level error details keyed by input path, when available.

  - `input: object { num_molecules, target, chemical_space, 3 more }`

    Pipeline input (null if data deleted)

    - `num_molecules: number`

      Number of molecules to generate. Must be between 10 and 1,000,000.

    - `target: object { entities, bonds, constraints, 2 more }`

      Target protein with binding pocket for small molecule design or screening

      - `entities: array of object { chain_ids, type, value, 2 more }`

        Protein entities defining the target structure. Each entity represents a protein chain.

        - `chain_ids: array of string`

          Chain IDs for this entity

        - `type: "protein"`

          - `"protein"`

        - `value: string`

          Amino acid sequence (one-letter codes)

        - `cyclic: optional boolean`

          Whether the sequence is cyclic

        - `modifications: optional array of object { residue_index, type, value }  or object { residue_index, type, value }`

          Post-translational modifications. Optional; defaults to an empty list when omitted.

          - `CCDModificationResponse: object { residue_index, type, value }`

            - `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: object { residue_index, type, value }`

            - `residue_index: number`

              0-based index of the residue to modify

            - `type: "smiles"`

              - `"smiles"`

            - `value: string`

              SMILES string for the modification

      - `bonds: optional array of object { atom1, atom2 }`

        Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.

        - `atom1: object { atom_name, chain_id, type }  or object { atom_name, chain_id, residue_index, type }`

          Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

          - `LigandAtomResponse: object { atom_name, chain_id, type }`

            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: object { atom_name, chain_id, residue_index, type }`

            - `atom_name: string`

              Standardized atom name (verifiable in CIF file on RCSB)

            - `chain_id: string`

              Chain ID containing the atom

            - `residue_index: number`

              0-based residue index

            - `type: "polymer_atom"`

              - `"polymer_atom"`

        - `atom2: object { atom_name, chain_id, type }  or object { atom_name, chain_id, residue_index, type }`

          Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

          - `LigandAtomResponse: object { atom_name, chain_id, type }`

            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: object { atom_name, chain_id, residue_index, type }`

            - `atom_name: string`

              Standardized atom name (verifiable in CIF file on RCSB)

            - `chain_id: string`

              Chain ID containing the atom

            - `residue_index: number`

              0-based residue index

            - `type: "polymer_atom"`

              - `"polymer_atom"`

      - `constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more }  or object { max_distance_angstrom, token1, token2, 2 more }`

        Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.

        - `PocketConstraintResponse: object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more }`

          Constrains the binder to interact with specific pocket residues on the target.

          - `binder_chain_id: string`

            Chain ID of the binder molecule

          - `contact_residues: map[array of number]`

            Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. "A") and the value is an array of 0-indexed residue indices that define the pocket on that chain.

          - `max_distance_angstrom: number`

            Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A.

          - `type: "pocket"`

            - `"pocket"`

          - `force: optional boolean`

            Whether to force the constraint

        - `ContactConstraintResponse: object { max_distance_angstrom, token1, token2, 2 more }`

          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: object { chain_id, residue_index, type }  or object { atom_name, chain_id, type }`

            Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

            - `PolymerContactTokenResponse: object { chain_id, residue_index, type }`

              - `chain_id: string`

                Chain ID

              - `residue_index: number`

                0-based residue index

              - `type: "polymer_contact"`

                - `"polymer_contact"`

            - `LigandContactTokenResponse: object { atom_name, chain_id, type }`

              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: object { chain_id, residue_index, type }  or object { atom_name, chain_id, type }`

            Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.

            - `PolymerContactTokenResponse: object { chain_id, residue_index, type }`

              - `chain_id: string`

                Chain ID

              - `residue_index: number`

                0-based residue index

              - `type: "polymer_contact"`

                - `"polymer_contact"`

            - `LigandContactTokenResponse: object { atom_name, chain_id, type }`

              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: optional boolean`

            Whether to force the constraint

      - `pocket_residues: optional map[array of number]`

        Binding pocket residues, keyed by chain ID. Each key is a chain ID (e.g. "A") and the value is an array of 0-indexed residue indices that define the binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket.

      - `reference_ligands: optional array of string`

        Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection.

    - `chemical_space: optional "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: optional string`

      Client-provided key to prevent duplicate submissions on retries

    - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }`

      Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.

      - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"`

        Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied.

        - `"recommended"`

        - `"extra"`

        - `"aggressive"`

        - `"disabled"`

      - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more }  or object { type, fraction_csp3, mol_logp, 8 more }  or object { patterns, type }  or 2 more`

        Custom filters to apply. Molecules must pass all filters (AND logic).

        - `LipinskiFilterResponse: object { max_hba, max_hbd, max_logp, 3 more }`

          Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors.

          - `max_hba: number`

            Maximum number of hydrogen bond acceptors. Lipinski threshold: 10

          - `max_hbd: number`

            Maximum number of hydrogen bond donors. Lipinski threshold: 5

          - `max_logp: number`

            Maximum LogP. Lipinski threshold: 5

          - `max_mw: number`

            Maximum molecular weight (Da). Lipinski threshold: 500

          - `type: "lipinski_filter"`

            - `"lipinski_filter"`

          - `allow_single_violation: optional boolean`

            If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass).

        - `RdkitDescriptorFilterResponse: object { type, fraction_csp3, mol_logp, 8 more }`

          Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained.

          - `type: "rdkit_descriptor_filter"`

            - `"rdkit_descriptor_filter"`

          - `fraction_csp3: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `mol_logp: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `mol_wt: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_aromatic_rings: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_h_acceptors: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_h_donors: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_heteroatoms: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_rings: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `num_rotatable_bonds: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

          - `tpsa: optional object { max, min }`

            Min/max range constraint for an RDKit molecular descriptor

            - `max: optional number`

              Maximum allowed value (inclusive)

            - `min: optional number`

              Minimum allowed value (inclusive)

        - `SmartsCustomFilterResponse: object { patterns, type }`

          Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.

          - `patterns: array of string`

            SMARTS patterns. Molecules matching any pattern are rejected.

          - `type: "smarts_custom_filter"`

            - `"smarts_custom_filter"`

        - `SmartsCatalogFilterResponse: object { catalog, type }`

          Filter molecules using a predefined SMARTS catalog of structural alerts.

          - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more`

            Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures.

            - `"PAINS"`

            - `"PAINS_A"`

            - `"PAINS_B"`

            - `"PAINS_C"`

            - `"BRENK"`

            - `"CHEMBL"`

            - `"CHEMBL_BMS"`

            - `"CHEMBL_Dundee"`

            - `"CHEMBL_Glaxo"`

            - `"CHEMBL_Inpharmatica"`

            - `"CHEMBL_LINT"`

            - `"CHEMBL_MLSMR"`

            - `"CHEMBL_SureChEMBL"`

            - `"NIH"`

          - `type: "smarts_catalog_filter"`

            - `"smarts_catalog_filter"`

        - `SmilesRegexFilterResponse: object { patterns, type }`

          Filter molecules by regex patterns on their SMILES representation.

          - `patterns: array of string`

            Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected.

          - `type: "smiles_regex_filter"`

            - `"smiles_regex_filter"`

    - `workspace_id: optional string`

      Target workspace ID (admin keys only; ignored for workspace keys)

  - `livemode: boolean`

    Whether this resource was created with a live API key.

  - `progress: object { num_molecules_generated, total_molecules_to_generate, latest_result_id }`

    - `num_molecules_generated: number`

      Number of molecules generated so far

    - `total_molecules_to_generate: number`

      Total number of molecules requested

    - `latest_result_id: optional string`

      ID of the most recently generated result

  - `started_at: string`

  - `status: "pending" or "running" or "succeeded" or 2 more`

    - `"pending"`

    - `"running"`

    - `"succeeded"`

    - `"failed"`

    - `"stopped"`

  - `stopped_at: string`

  - `workspace_id: string`

    Workspace ID

  - `idempotency_key: optional string`

    Client-provided idempotency key

### Example

```cli
boltz-api small-molecule:design stop \
  --id id
```