boltz-api 0.45.0 → 0.46.0

package/src/resources/predictions/structure-and-binding.ts

@@ -131,40 +131,6 @@ export class StructureAndBinding extends APIResource {
   ): APIPromise<StructureAndBindingStartResponse> {
     return this._client.post('/compute/v1/predictions/structure-and-binding', { body, ...options });
   }
-
-  /**
-   * Returns the total token count for a prospective Boltz2 complex along with the
-   * maximum token count the caller's compute config will accept. Pure introspection
-   * — never rejects when the complex is too large; still rejects on malformed inputs
-   * the model could not interpret. Use the sandbox prediction endpoint if you need
-   * the cap enforced.
-   *
-   * @example
-   * ```ts
-   * const response =
-   *   await client.predictions.structureAndBinding.tokenCount({
-   *     input: {
-   *       entities: [
-   *         {
-   *           chain_ids: ['string'],
-   *           type: 'protein',
-   *           value: 'value',
-   *         },
-   *       ],
-   *     },
-   *     model: 'boltz-2.1',
-   *   });
-   * ```
-   */
-  tokenCount(
-    body: StructureAndBindingTokenCountParams,
-    options?: RequestOptions,
-  ): APIPromise<StructureAndBindingTokenCountResponse> {
-    return this._client.post('/compute/v1/predictions/structure-and-binding/token-count', {
-      body,
-      ...options,
-    });
-  }
 }
 
 export type StructureAndBindingListResponsesCursorPage = CursorPage<StructureAndBindingListResponse>;
@@ -2091,20 +2057,6 @@ export namespace StructureAndBindingStartResponse {
   }
 }
 
-export interface StructureAndBindingTokenCountResponse {
-  /**
-   * Maximum token count the caller's compute config will accept for a sandbox
-   * prediction.
-   */
-  max_token_count: number;
-
-  /**
-   * Total token count for the complex, after applying the affinity model's internal
-   * crop when relevant.
-   */
-  total_token_count: number;
-}
-
 export interface StructureAndBindingRetrieveParams {
   /**
    * Workspace ID. Only used with admin API keys. Ignored (or validated) for
@@ -3372,631 +3324,6 @@ export namespace StructureAndBindingStartParams {
   }
 }
 
-export interface StructureAndBindingTokenCountParams {
-  input: StructureAndBindingTokenCountParams.Input;
-
-  /**
-   * Model to use for prediction
-   */
-  model: 'boltz-2.1';
-
-  /**
-   * Client-provided key to prevent duplicate submissions on retries
-   */
-  idempotency_key?: string;
-
-  /**
-   * Target workspace ID (admin keys only; ignored for workspace keys)
-   */
-  workspace_id?: string;
-}
-
-export namespace StructureAndBindingTokenCountParams {
-  export interface Input {
-    /**
-     * Entities (proteins, RNA, DNA, ligands) forming the complex to predict. Order
-     * determines chain assignment.
-     */
-    entities: Array<
-      | Input.Boltz2ProteinEntity
-      | Input.RnaEntity
-      | Input.DnaEntity
-      | Input.LigandCcdEntity
-      | Input.LigandSmilesEntity
-    >;
-
-    binding?: Input.LigandProteinBinding | Input.ProteinProteinBinding;
-
-    /**
-     * Bond constraints between atoms. Atom-level ligand references currently support
-     * ligand_ccd only; ligand_smiles is unsupported.
-     */
-    bonds?: Array<Input.Bond>;
-
-    /**
-     * Structural constraints (pocket and contact). Atom-level ligand references
-     * currently support ligand_ccd only; ligand_smiles is unsupported.
-     */
-    constraints?: Array<Input.PocketConstraint | Input.ContactConstraint>;
-
-    model_options?: Input.ModelOptions;
-
-    /**
-     * Number of structure samples to generate
-     */
-    num_samples?: number;
-
-    /**
-     * Template structure files to guide protein-chain prediction. Supports up to 4 CIF
-     * or PDB templates from HTTPS URLs or base64 uploads. Use template_chains to map
-     * request chains to template-file chains.
-     */
-    templates?: Array<Input.Template>;
-  }
-
-  export namespace Input {
-    export interface Boltz2ProteinEntity {
-      /**
-       * Chain IDs for this entity
-       */
-      chain_ids: Array<string>;
-
-      type: 'protein';
-
-      /**
-       * Amino acid sequence (one-letter codes)
-       */
-      value: string;
-
-      /**
-       * Whether the sequence is cyclic
-       */
-      cyclic?: boolean;
-
-      /**
-       * CCD post-translational modifications. Optional; defaults to an empty list when
-       * omitted. SMILES modifications are not supported.
-       */
-      modifications?: Array<Boltz2ProteinEntity.Modification>;
-
-      /**
-       * Optional protein MSA control. Omit msa on all protein entities to use automatic
-       * MSA generation. Use custom for user-provided A3M/CSV files, or empty for
-       * single-sequence mode. Custom MSA and automatic MSA cannot be mixed in one
-       * request.
-       */
-      msa?: Boltz2ProteinEntity.Boltz2CustomMsa | Boltz2ProteinEntity.Boltz2EmptyMsa;
-    }
-
-    export namespace Boltz2ProteinEntity {
-      /**
-       * Polymer residue modification. Only CCD codes are supported; SMILES modifications
-       * are not accepted.
-       */
-      export interface Modification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        /**
-         * Modification format. Only CCD polymer modifications are supported.
-         */
-        type: 'ccd';
-
-        /**
-         * CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for
-         * phosphoserine)
-         */
-        value: string;
-      }
-
-      /**
-       * Use a user-provided MSA for this protein entity. If any protein entity uses a
-       * custom MSA, every other protein entity must use either custom or empty MSA;
-       * automatic MSA generation cannot be mixed with custom MSAs in the same request.
-       */
-      export interface Boltz2CustomMsa {
-        /**
-         * Custom MSA file format. Base64 uploads must use media_type text/x-a3m for A3M or
-         * text/csv for CSV.
-         */
-        format: 'a3m' | 'csv';
-
-        /**
-         * How to provide a file to the API
-         */
-        source: Boltz2CustomMsa.URLSource | Boltz2CustomMsa.Base64Source;
-
-        type: 'custom';
-      }
-
-      export namespace Boltz2CustomMsa {
-        export interface URLSource {
-          type: 'url';
-
-          url: string;
-        }
-
-        export interface Base64Source {
-          /**
-           * Base64-encoded file contents
-           */
-          data: string;
-
-          /**
-           * MIME type (e.g., text/csv)
-           */
-          media_type: string;
-
-          type: 'base64';
-        }
-      }
-
-      /**
-       * Run this protein entity in single-sequence mode without an MSA. Use this for
-       * chains that should not use automatic MSA generation, including non-homologous
-       * chains in a request that also includes custom MSAs.
-       */
-      export interface Boltz2EmptyMsa {
-        type: 'empty';
-      }
-    }
-
-    export interface RnaEntity {
-      /**
-       * Chain IDs for this entity
-       */
-      chain_ids: Array<string>;
-
-      type: 'rna';
-
-      /**
-       * RNA nucleotide sequence (A, C, G, U, N)
-       */
-      value: string;
-
-      /**
-       * Whether the sequence is cyclic
-       */
-      cyclic?: boolean;
-
-      /**
-       * CCD chemical modifications. Optional; defaults to an empty list when omitted.
-       * SMILES modifications are not supported.
-       */
-      modifications?: Array<RnaEntity.Modification>;
-    }
-
-    export namespace RnaEntity {
-      /**
-       * Polymer residue modification. Only CCD codes are supported; SMILES modifications
-       * are not accepted.
-       */
-      export interface Modification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        /**
-         * Modification format. Only CCD polymer modifications are supported.
-         */
-        type: 'ccd';
-
-        /**
-         * CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for
-         * phosphoserine)
-         */
-        value: string;
-      }
-    }
-
-    export interface DnaEntity {
-      /**
-       * Chain IDs for this entity
-       */
-      chain_ids: Array<string>;
-
-      type: 'dna';
-
-      /**
-       * DNA nucleotide sequence (A, C, G, T, N)
-       */
-      value: string;
-
-      /**
-       * Whether the sequence is cyclic
-       */
-      cyclic?: boolean;
-
-      /**
-       * CCD chemical modifications. Optional; defaults to an empty list when omitted.
-       * SMILES modifications are not supported.
-       */
-      modifications?: Array<DnaEntity.Modification>;
-    }
-
-    export namespace DnaEntity {
-      /**
-       * Polymer residue modification. Only CCD codes are supported; SMILES modifications
-       * are not accepted.
-       */
-      export interface Modification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        /**
-         * Modification format. Only CCD polymer modifications are supported.
-         */
-        type: 'ccd';
-
-        /**
-         * CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for
-         * phosphoserine)
-         */
-        value: string;
-      }
-    }
-
-    export interface LigandCcdEntity {
-      /**
-       * Chain IDs for this ligand
-       */
-      chain_ids: Array<string>;
-
-      type: 'ligand_ccd';
-
-      /**
-       * CCD code (e.g., ATP, ADP)
-       */
-      value: string;
-    }
-
-    export interface LigandSmilesEntity {
-      /**
-       * Chain IDs for this ligand
-       */
-      chain_ids: Array<string>;
-
-      type: 'ligand_smiles';
-
-      /**
-       * SMILES string representing the ligand
-       */
-      value: string;
-    }
-
-    export interface LigandProteinBinding {
-      /**
-       * Chain ID of the ligand binder (must have exactly 1 copy, <50 atoms, and only
-       * ligands+proteins in entities)
-       */
-      binder_chain_id: string;
-
-      type: 'ligand_protein_binding';
-    }
-
-    export interface ProteinProteinBinding {
-      /**
-       * Chain IDs of the protein binders
-       */
-      binder_chain_ids: Array<string>;
-
-      type: 'protein_protein_binding';
-    }
-
-    /**
-     * Bond between two atoms. Atom-level ligand references currently support
-     * ligand_ccd entities only; ligand_smiles is unsupported.
-     */
-    export interface Bond {
-      /**
-       * Ligand atom reference. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      atom1: Bond.LigandAtom | Bond.PolymerAtom;
-
-      /**
-       * Ligand atom reference. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      atom2: Bond.LigandAtom | Bond.PolymerAtom;
-    }
-
-    export namespace Bond {
-      /**
-       * Ligand atom reference. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      export interface LigandAtom {
-        /**
-         * Standardized atom name (verifiable in CIF file on RCSB). Atom-level references
-         * to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID containing the atom
-         */
-        chain_id: string;
-
-        type: 'ligand_atom';
-      }
-
-      export interface PolymerAtom {
-        /**
-         * Standardized atom name (verifiable in CIF file on RCSB)
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID containing the atom
-         */
-        chain_id: string;
-
-        /**
-         * 0-based residue index
-         */
-        residue_index: number;
-
-        type: 'polymer_atom';
-      }
-
-      /**
-       * Ligand atom reference. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      export interface LigandAtom {
-        /**
-         * Standardized atom name (verifiable in CIF file on RCSB). Atom-level references
-         * to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID containing the atom
-         */
-        chain_id: string;
-
-        type: 'ligand_atom';
-      }
-
-      export interface PolymerAtom {
-        /**
-         * Standardized atom name (verifiable in CIF file on RCSB)
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID containing the atom
-         */
-        chain_id: string;
-
-        /**
-         * 0-based residue index
-         */
-        residue_index: number;
-
-        type: 'polymer_atom';
-      }
-    }
-
-    /**
-     * Constrains the binder to interact with specific pocket residues on the target.
-     */
-    export interface PocketConstraint {
-      /**
-       * Chain ID of the binder molecule
-       */
-      binder_chain_id: string;
-
-      /**
-       * 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.
-       */
-      contact_residues: { [key: string]: Array<number> };
-
-      /**
-       * Maximum allowed distance in Angstroms between binder and pocket residues.
-       * Typical range: 4-8 A.
-       */
-      max_distance_angstrom: number;
-
-      type: 'pocket';
-
-      /**
-       * Whether to force the constraint
-       */
-      force?: boolean;
-    }
-
-    /**
-     * Contact constraint between two tokens. Atom-level ligand references currently
-     * support ligand_ccd entities only; ligand_smiles is unsupported.
-     */
-    export interface ContactConstraint {
-      /**
-       * Maximum distance in Angstroms
-       */
-      max_distance_angstrom: number;
-
-      /**
-       * Ligand contact token. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      token1: ContactConstraint.PolymerContactToken | ContactConstraint.LigandContactToken;
-
-      /**
-       * Ligand contact token. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      token2: ContactConstraint.PolymerContactToken | ContactConstraint.LigandContactToken;
-
-      type: 'contact';
-
-      /**
-       * Whether to force the constraint
-       */
-      force?: boolean;
-    }
-
-    export namespace ContactConstraint {
-      export interface PolymerContactToken {
-        /**
-         * Chain ID
-         */
-        chain_id: string;
-
-        /**
-         * 0-based residue index
-         */
-        residue_index: number;
-
-        type: 'polymer_contact';
-      }
-
-      /**
-       * Ligand contact token. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      export interface LigandContactToken {
-        /**
-         * Atom name. Atom-level references to ligand_smiles entities are currently
-         * unsupported; use ligand_ccd instead.
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID
-         */
-        chain_id: string;
-
-        type: 'ligand_contact';
-      }
-
-      export interface PolymerContactToken {
-        /**
-         * Chain ID
-         */
-        chain_id: string;
-
-        /**
-         * 0-based residue index
-         */
-        residue_index: number;
-
-        type: 'polymer_contact';
-      }
-
-      /**
-       * Ligand contact token. Atom-level ligand references currently support ligand_ccd
-       * entities only; ligand_smiles is unsupported.
-       */
-      export interface LigandContactToken {
-        /**
-         * Atom name. Atom-level references to ligand_smiles entities are currently
-         * unsupported; use ligand_ccd instead.
-         */
-        atom_name: string;
-
-        /**
-         * Chain ID
-         */
-        chain_id: string;
-
-        type: 'ligand_contact';
-      }
-    }
-
-    export interface ModelOptions {
-      /**
-       * The number of recycling steps to use for prediction. Default is 3.
-       */
-      recycling_steps?: number;
-
-      /**
-       * The number of sampling steps to use for prediction. Default is 200.
-       */
-      sampling_steps?: number;
-
-      /**
-       * Diffusion step scale (temperature). Controls sampling diversity — higher values
-       * produce more varied structures. Default is 1.638.
-       */
-      step_scale?: number;
-    }
-
-    /**
-     * Template structure used as an inference-time guide for Boltz-2.1 protein-chain
-     * geometry. Provide a CIF or PDB file from an HTTPS URL or base64 upload.
-     */
-    export interface Template {
-      /**
-       * Request-to-template chain mappings. Each input_chain_id and template_chain_id
-       * must be unique within this template.
-       */
-      template_chains: Array<Template.TemplateChain>;
-
-      /**
-       * How to provide a template structure file. URLs must point to a CIF or PDB file;
-       * base64 uploads must use chemical/x-cif or chemical/x-pdb.
-       */
-      template_structure: Template.URLSource | Template.TemplateStructureBase64Source;
-
-      /**
-       * Force the template reference potential with this distance threshold in
-       * angstroms. Omit to use the template without force.
-       */
-      force_threshold_angstroms?: number;
-    }
-
-    export namespace Template {
-      /**
-       * Mapping from one request chain to the corresponding chain in the template
-       * structure file.
-       */
-      export interface TemplateChain {
-        /**
-         * Chain ID in this prediction request
-         */
-        input_chain_id: string;
-
-        /**
-         * Corresponding chain ID in the template structure file
-         */
-        template_chain_id: string;
-      }
-
-      export interface URLSource {
-        type: 'url';
-
-        url: string;
-      }
-
-      export interface TemplateStructureBase64Source {
-        /**
-         * Base64-encoded template structure file contents
-         */
-        data: string;
-
-        /**
-         * Template structure MIME type
-         *
-         * - `chemical/x-cif` - CIF template structure
-         * - `chemical/x-pdb` - PDB template structure
-         */
-        media_type: 'chemical/x-cif' | 'chemical/x-pdb';
-
-        type: 'base64';
-      }
-    }
-  }
-}
-
 export declare namespace StructureAndBinding {
   export {
     type StructureAndBindingRetrieveResponse as StructureAndBindingRetrieveResponse,
@@ -4004,12 +3331,10 @@ export declare namespace StructureAndBinding {
     type StructureAndBindingDeleteDataResponse as StructureAndBindingDeleteDataResponse,
     type StructureAndBindingEstimateCostResponse as StructureAndBindingEstimateCostResponse,
     type StructureAndBindingStartResponse as StructureAndBindingStartResponse,
-    type StructureAndBindingTokenCountResponse as StructureAndBindingTokenCountResponse,
     type StructureAndBindingListResponsesCursorPage as StructureAndBindingListResponsesCursorPage,
     type StructureAndBindingRetrieveParams as StructureAndBindingRetrieveParams,
     type StructureAndBindingListParams as StructureAndBindingListParams,
     type StructureAndBindingEstimateCostParams as StructureAndBindingEstimateCostParams,
     type StructureAndBindingStartParams as StructureAndBindingStartParams,
-    type StructureAndBindingTokenCountParams as StructureAndBindingTokenCountParams,
   };
 }

package/src/resources/small-molecule/design.ts

@@ -66,8 +66,8 @@ export class Design extends APIResource {
 
   /**
    * 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.
+   * resource or consuming GPU. Includes generation charges implied by the scheduler
+   * iteration cap plus structure-scoring charges for each requested molecule.
    *
    * @example
    * ```ts

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = '0.45.0'; // x-release-please-version
+export const VERSION = '0.46.0'; // x-release-please-version