boltz-api 0.43.0 → 0.44.1

package/resources/predictions/structure-and-binding.d.mts

@@ -93,6 +93,31 @@ export declare class StructureAndBinding extends APIResource {
      * ```
      */
     start(body: StructureAndBindingStartParams, options?: RequestOptions): APIPromise<StructureAndBindingStartResponse>;
+    /**
+     * 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>;
 }
 export type StructureAndBindingListResponsesCursorPage = CursorPage<StructureAndBindingListResponse>;
 export interface StructureAndBindingRetrieveResponse {
@@ -661,6 +686,7 @@ export declare namespace StructureAndBindingRetrieveResponse {
         interface AllSampleResult {
             metrics: AllSampleResult.Metrics;
             structure: AllSampleResult.Structure;
+            ligand_structure?: AllSampleResult.LigandStructure;
         }
         namespace AllSampleResult {
             interface Metrics {
@@ -711,10 +737,21 @@ export declare namespace StructureAndBindingRetrieveResponse {
                  */
                 url_expires_at: string;
             }
+            interface LigandStructure {
+                /**
+                 * URL to download the file
+                 */
+                url: string;
+                /**
+                 * When the presigned URL expires
+                 */
+                url_expires_at: string;
+            }
         }
         interface BestSample {
             metrics: BestSample.Metrics;
             structure: BestSample.Structure;
+            ligand_structure?: BestSample.LigandStructure;
         }
         namespace BestSample {
             interface Metrics {
@@ -765,6 +802,16 @@ export declare namespace StructureAndBindingRetrieveResponse {
                  */
                 url_expires_at: string;
             }
+            interface LigandStructure {
+                /**
+                 * URL to download the file
+                 */
+                url: string;
+                /**
+                 * When the presigned URL expires
+                 */
+                url_expires_at: string;
+            }
         }
         interface Archive {
             /**
@@ -1471,6 +1518,7 @@ export declare namespace StructureAndBindingStartResponse {
         interface AllSampleResult {
             metrics: AllSampleResult.Metrics;
             structure: AllSampleResult.Structure;
+            ligand_structure?: AllSampleResult.LigandStructure;
         }
         namespace AllSampleResult {
             interface Metrics {
@@ -1521,10 +1569,21 @@ export declare namespace StructureAndBindingStartResponse {
                  */
                 url_expires_at: string;
             }
+            interface LigandStructure {
+                /**
+                 * URL to download the file
+                 */
+                url: string;
+                /**
+                 * When the presigned URL expires
+                 */
+                url_expires_at: string;
+            }
         }
         interface BestSample {
             metrics: BestSample.Metrics;
             structure: BestSample.Structure;
+            ligand_structure?: BestSample.LigandStructure;
         }
         namespace BestSample {
             interface Metrics {
@@ -1575,6 +1634,16 @@ export declare namespace StructureAndBindingStartResponse {
                  */
                 url_expires_at: string;
             }
+            interface LigandStructure {
+                /**
+                 * URL to download the file
+                 */
+                url: string;
+                /**
+                 * When the presigned URL expires
+                 */
+                url_expires_at: string;
+            }
         }
         interface Archive {
             /**
@@ -1607,6 +1676,18 @@ export declare 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
@@ -2652,7 +2733,522 @@ export declare 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 declare namespace StructureAndBindingTokenCountParams {
+    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>;
+    }
+    namespace Input {
+        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;
+        }
+        namespace Boltz2ProteinEntity {
+            /**
+             * Polymer residue modification. Only CCD codes are supported; SMILES modifications
+             * are not accepted.
+             */
+            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.
+             */
+            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';
+            }
+            namespace Boltz2CustomMsa {
+                interface URLSource {
+                    type: 'url';
+                    url: string;
+                }
+                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.
+             */
+            interface Boltz2EmptyMsa {
+                type: 'empty';
+            }
+        }
+        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>;
+        }
+        namespace RnaEntity {
+            /**
+             * Polymer residue modification. Only CCD codes are supported; SMILES modifications
+             * are not accepted.
+             */
+            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;
+            }
+        }
+        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>;
+        }
+        namespace DnaEntity {
+            /**
+             * Polymer residue modification. Only CCD codes are supported; SMILES modifications
+             * are not accepted.
+             */
+            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;
+            }
+        }
+        interface LigandCcdEntity {
+            /**
+             * Chain IDs for this ligand
+             */
+            chain_ids: Array<string>;
+            type: 'ligand_ccd';
+            /**
+             * CCD code (e.g., ATP, ADP)
+             */
+            value: string;
+        }
+        interface LigandSmilesEntity {
+            /**
+             * Chain IDs for this ligand
+             */
+            chain_ids: Array<string>;
+            type: 'ligand_smiles';
+            /**
+             * SMILES string representing the ligand
+             */
+            value: string;
+        }
+        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';
+        }
+        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.
+         */
+        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;
+        }
+        namespace Bond {
+            /**
+             * Ligand atom reference. Atom-level ligand references currently support ligand_ccd
+             * entities only; ligand_smiles is unsupported.
+             */
+            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';
+            }
+            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.
+             */
+            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';
+            }
+            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.
+         */
+        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.
+         */
+        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;
+        }
+        namespace ContactConstraint {
+            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.
+             */
+            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';
+            }
+            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.
+             */
+            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';
+            }
+        }
+        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.
+         */
+        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;
+        }
+        namespace Template {
+            /**
+             * Mapping from one request chain to the corresponding chain in the template
+             * structure file.
+             */
+            interface TemplateChain {
+                /**
+                 * Chain ID in this prediction request
+                 */
+                input_chain_id: string;
+                /**
+                 * Corresponding chain ID in the template structure file
+                 */
+                template_chain_id: string;
+            }
+            interface URLSource {
+                type: 'url';
+                url: string;
+            }
+            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, type StructureAndBindingListResponse as StructureAndBindingListResponse, type StructureAndBindingDeleteDataResponse as StructureAndBindingDeleteDataResponse, type StructureAndBindingEstimateCostResponse as StructureAndBindingEstimateCostResponse, type StructureAndBindingStartResponse as StructureAndBindingStartResponse, type StructureAndBindingListResponsesCursorPage as StructureAndBindingListResponsesCursorPage, type StructureAndBindingRetrieveParams as StructureAndBindingRetrieveParams, type StructureAndBindingListParams as StructureAndBindingListParams, type StructureAndBindingEstimateCostParams as StructureAndBindingEstimateCostParams, type StructureAndBindingStartParams as StructureAndBindingStartParams, };
+    export { type StructureAndBindingRetrieveResponse as StructureAndBindingRetrieveResponse, type StructureAndBindingListResponse as StructureAndBindingListResponse, 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, };
 }
 //# sourceMappingURL=structure-and-binding.d.mts.map