boltz-api 0.38.0 → 0.39.1

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

@@ -7,7 +7,7 @@ import { RequestOptions } from '../../internal/request-options';
 import { path } from '../../internal/utils/path';
 
 /**
- * Predict 3D structure coordinates, per-residue confidence scores, and binding metrics for a molecular complex.
+ * Predict 3D structure coordinates, per-residue confidence scores, and binding metrics for a molecular complex. Supports optional template-guided folding and per-protein MSA control.
  */
 export class StructureAndBinding extends APIResource {
   /**
@@ -103,7 +103,10 @@ export class StructureAndBinding extends APIResource {
 
   /**
    * Submit a prediction job that produces 3D structure coordinates and confidence
-   * scores for the input molecular complex, with optional binding metrics.
+   * scores for the input molecular complex, with optional binding metrics. Protein
+   * entities can use automatic MSA generation, custom A3M/CSV MSAs, or empty MSA
+   * mode. Boltz-2.1 predictions can also include up to 4 CIF or PDB templates to
+   * guide protein-chain geometry.
    *
    * @example
    * ```ts
@@ -228,7 +231,7 @@ export namespace StructureAndBindingRetrieveResponse {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntityResponse
+      | Input.Boltz2ProteinEntityResponse
       | Input.RnaEntityResponse
       | Input.DnaEntityResponse
       | Input.LigandCcdEntityResponse
@@ -258,13 +261,15 @@ export namespace StructureAndBindingRetrieveResponse {
 
     /**
      * Template structure files to guide protein-chain prediction. Supports up to 4 CIF
-     * or PDB templates from HTTPS URLs or base64 uploads.
+     * or PDB templates from HTTPS URLs or base64 uploads. Use chain_id and template_id
+     * to map request chains to template chains when the IDs differ or when providing
+     * multi-chain templates.
      */
     templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntityResponse {
+    export interface Boltz2ProteinEntityResponse {
       /**
        * Chain IDs for this entity
        */
@@ -286,10 +291,20 @@ export namespace StructureAndBindingRetrieveResponse {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntityResponse.Modification>;
+      modifications?: Array<Boltz2ProteinEntityResponse.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?:
+        | Boltz2ProteinEntityResponse.Boltz2CustomMsaResponse
+        | Boltz2ProteinEntityResponse.Boltz2EmptyMsaResponse;
     }
 
-    export namespace ProteinEntityResponse {
+    export namespace Boltz2ProteinEntityResponse {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -304,6 +319,46 @@ export namespace StructureAndBindingRetrieveResponse {
          */
         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 Boltz2CustomMsaResponse {
+        /**
+         * Custom MSA file format. Base64 uploads must use media_type text/x-a3m for A3M or
+         * text/csv for CSV.
+         */
+        format: 'a3m' | 'csv';
+
+        source: Boltz2CustomMsaResponse.Source;
+
+        type: 'custom';
+      }
+
+      export namespace Boltz2CustomMsaResponse {
+        export interface Source {
+          /**
+           * URL to download the file
+           */
+          url: string;
+
+          /**
+           * When the presigned URL expires
+           */
+          url_expires_at: string;
+        }
+      }
+
+      /**
+       * 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 Boltz2EmptyMsaResponse {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntityResponse {
@@ -681,16 +736,23 @@ export namespace StructureAndBindingRetrieveResponse {
       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 {
       /**
-       * Template structure format. Base64 sources must use a matching media_type.
+       * Template structure format. Base64 uploads must use media_type chemical/x-cif for
+       * CIF or chemical/x-pdb for PDB.
        */
       format: 'cif' | 'pdb';
 
       source: Template.Source;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       chain_id?: string | Array<string>;
 
@@ -700,7 +762,9 @@ export namespace StructureAndBindingRetrieveResponse {
       force?: boolean;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       template_id?: string | Array<string>;
 
@@ -1150,7 +1214,7 @@ export namespace StructureAndBindingStartResponse {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntityResponse
+      | Input.Boltz2ProteinEntityResponse
       | Input.RnaEntityResponse
       | Input.DnaEntityResponse
       | Input.LigandCcdEntityResponse
@@ -1180,13 +1244,15 @@ export namespace StructureAndBindingStartResponse {
 
     /**
      * Template structure files to guide protein-chain prediction. Supports up to 4 CIF
-     * or PDB templates from HTTPS URLs or base64 uploads.
+     * or PDB templates from HTTPS URLs or base64 uploads. Use chain_id and template_id
+     * to map request chains to template chains when the IDs differ or when providing
+     * multi-chain templates.
      */
     templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntityResponse {
+    export interface Boltz2ProteinEntityResponse {
       /**
        * Chain IDs for this entity
        */
@@ -1208,10 +1274,20 @@ export namespace StructureAndBindingStartResponse {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntityResponse.Modification>;
+      modifications?: Array<Boltz2ProteinEntityResponse.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?:
+        | Boltz2ProteinEntityResponse.Boltz2CustomMsaResponse
+        | Boltz2ProteinEntityResponse.Boltz2EmptyMsaResponse;
     }
 
-    export namespace ProteinEntityResponse {
+    export namespace Boltz2ProteinEntityResponse {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -1226,6 +1302,46 @@ export namespace StructureAndBindingStartResponse {
          */
         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 Boltz2CustomMsaResponse {
+        /**
+         * Custom MSA file format. Base64 uploads must use media_type text/x-a3m for A3M or
+         * text/csv for CSV.
+         */
+        format: 'a3m' | 'csv';
+
+        source: Boltz2CustomMsaResponse.Source;
+
+        type: 'custom';
+      }
+
+      export namespace Boltz2CustomMsaResponse {
+        export interface Source {
+          /**
+           * URL to download the file
+           */
+          url: string;
+
+          /**
+           * When the presigned URL expires
+           */
+          url_expires_at: string;
+        }
+      }
+
+      /**
+       * 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 Boltz2EmptyMsaResponse {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntityResponse {
@@ -1603,16 +1719,23 @@ export namespace StructureAndBindingStartResponse {
       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 {
       /**
-       * Template structure format. Base64 sources must use a matching media_type.
+       * Template structure format. Base64 uploads must use media_type chemical/x-cif for
+       * CIF or chemical/x-pdb for PDB.
        */
       format: 'cif' | 'pdb';
 
       source: Template.Source;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       chain_id?: string | Array<string>;
 
@@ -1622,7 +1745,9 @@ export namespace StructureAndBindingStartResponse {
       force?: boolean;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       template_id?: string | Array<string>;
 
@@ -1879,7 +2004,7 @@ export namespace StructureAndBindingEstimateCostParams {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntity
+      | Input.Boltz2ProteinEntity
       | Input.RnaEntity
       | Input.DnaEntity
       | Input.LigandCcdEntity
@@ -1909,13 +2034,15 @@ export namespace StructureAndBindingEstimateCostParams {
 
     /**
      * Template structure files to guide protein-chain prediction. Supports up to 4 CIF
-     * or PDB templates from HTTPS URLs or base64 uploads.
+     * or PDB templates from HTTPS URLs or base64 uploads. Use chain_id and template_id
+     * to map request chains to template chains when the IDs differ or when providing
+     * multi-chain templates.
      */
     templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntity {
+    export interface Boltz2ProteinEntity {
       /**
        * Chain IDs for this entity
        */
@@ -1937,10 +2064,18 @@ export namespace StructureAndBindingEstimateCostParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.Modification>;
+      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 ProteinEntity {
+    export namespace Boltz2ProteinEntity {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -1955,6 +2090,57 @@ export namespace StructureAndBindingEstimateCostParams {
          */
         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 {
@@ -2328,9 +2514,14 @@ export namespace StructureAndBindingEstimateCostParams {
       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 {
       /**
-       * Template structure format. Base64 sources must use a matching media_type.
+       * Template structure format. Base64 uploads must use media_type chemical/x-cif for
+       * CIF or chemical/x-pdb for PDB.
        */
       format: 'cif' | 'pdb';
 
@@ -2340,7 +2531,9 @@ export namespace StructureAndBindingEstimateCostParams {
       source: Template.URLSource | Template.Base64Source;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       chain_id?: string | Array<string>;
 
@@ -2350,7 +2543,9 @@ export namespace StructureAndBindingEstimateCostParams {
       force?: boolean;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       template_id?: string | Array<string>;
 
@@ -2410,7 +2605,7 @@ export namespace StructureAndBindingStartParams {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntity
+      | Input.Boltz2ProteinEntity
       | Input.RnaEntity
       | Input.DnaEntity
       | Input.LigandCcdEntity
@@ -2440,13 +2635,15 @@ export namespace StructureAndBindingStartParams {
 
     /**
      * Template structure files to guide protein-chain prediction. Supports up to 4 CIF
-     * or PDB templates from HTTPS URLs or base64 uploads.
+     * or PDB templates from HTTPS URLs or base64 uploads. Use chain_id and template_id
+     * to map request chains to template chains when the IDs differ or when providing
+     * multi-chain templates.
      */
     templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntity {
+    export interface Boltz2ProteinEntity {
       /**
        * Chain IDs for this entity
        */
@@ -2468,10 +2665,18 @@ export namespace StructureAndBindingStartParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.Modification>;
+      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 ProteinEntity {
+    export namespace Boltz2ProteinEntity {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -2486,6 +2691,57 @@ export namespace StructureAndBindingStartParams {
          */
         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 {
@@ -2859,9 +3115,14 @@ export namespace StructureAndBindingStartParams {
       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 {
       /**
-       * Template structure format. Base64 sources must use a matching media_type.
+       * Template structure format. Base64 uploads must use media_type chemical/x-cif for
+       * CIF or chemical/x-pdb for PDB.
        */
       format: 'cif' | 'pdb';
 
@@ -2871,7 +3132,9 @@ export namespace StructureAndBindingStartParams {
       source: Template.URLSource | Template.Base64Source;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       chain_id?: string | Array<string>;
 
@@ -2881,7 +3144,9 @@ export namespace StructureAndBindingStartParams {
       force?: boolean;
 
       /**
-       * One query/template chain ID, or an ordered list of chain IDs.
+       * One chain ID, or an ordered list of chain IDs for multi-chain templates. For
+       * chain_id, values refer to input chains; for template_id, values refer to chains
+       * in the template file.
        */
       template_id?: string | Array<string>;
 

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = '0.38.0'; // x-release-please-version
+export const VERSION = '0.39.1'; // x-release-please-version

package/version.d.mts

@@ -1,2 +1,2 @@
-export declare const VERSION = "0.38.0";
+export declare const VERSION = "0.39.1";
 //# sourceMappingURL=version.d.mts.map

package/version.d.ts

@@ -1,2 +1,2 @@
-export declare const VERSION = "0.38.0";
+export declare const VERSION = "0.39.1";
 //# sourceMappingURL=version.d.ts.map

package/version.js

@@ -1,5 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = '0.38.0'; // x-release-please-version
+exports.VERSION = '0.39.1'; // x-release-please-version
 //# sourceMappingURL=version.js.map

package/version.mjs

@@ -1,2 +1,2 @@
-export const VERSION = '0.38.0'; // x-release-please-version
+export const VERSION = '0.39.1'; // x-release-please-version
 //# sourceMappingURL=version.mjs.map