boltz-api 0.37.1 → 0.39.0

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

@@ -228,7 +228,7 @@ export namespace StructureAndBindingRetrieveResponse {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntityResponse
+      | Input.Boltz2ProteinEntityResponse
       | Input.RnaEntityResponse
       | Input.DnaEntityResponse
       | Input.LigandCcdEntityResponse
@@ -255,10 +255,16 @@ export namespace StructureAndBindingRetrieveResponse {
      * 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.
+     */
+    templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntityResponse {
+    export interface Boltz2ProteinEntityResponse {
       /**
        * Chain IDs for this entity
        */
@@ -280,10 +286,18 @@ 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 to use automatic MSA generation; use custom
+       * for user-provided A3M/CSV; use empty for single-sequence mode.
+       */
+      msa?:
+        | Boltz2ProteinEntityResponse.Boltz2CustomMsaResponse
+        | Boltz2ProteinEntityResponse.Boltz2EmptyMsaResponse;
     }
 
-    export namespace ProteinEntityResponse {
+    export namespace Boltz2ProteinEntityResponse {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -298,6 +312,41 @@ export namespace StructureAndBindingRetrieveResponse {
          */
         value: string;
       }
+
+      /**
+       * Custom MSA file to use for this protein entity.
+       */
+      export interface Boltz2CustomMsaResponse {
+        /**
+         * Custom MSA file format. Boltz supports A3M and CSV MSA files.
+         */
+        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.
+       */
+      export interface Boltz2EmptyMsaResponse {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntityResponse {
@@ -674,6 +723,49 @@ export namespace StructureAndBindingRetrieveResponse {
        */
       step_scale?: number;
     }
+
+    export interface Template {
+      /**
+       * Template structure format. Base64 sources must use a matching media_type.
+       */
+      format: 'cif' | 'pdb';
+
+      source: Template.Source;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      chain_id?: string | Array<string>;
+
+      /**
+       * Force the template alignment within threshold.
+       */
+      force?: boolean;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      template_id?: string | Array<string>;
+
+      /**
+       * Distance threshold in angstroms used when force is true.
+       */
+      threshold?: number;
+    }
+
+    export namespace Template {
+      export interface Source {
+        /**
+         * URL to download the file
+         */
+        url: string;
+
+        /**
+         * When the presigned URL expires
+         */
+        url_expires_at: string;
+      }
+    }
   }
 
   /**
@@ -1101,7 +1193,7 @@ export namespace StructureAndBindingStartResponse {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntityResponse
+      | Input.Boltz2ProteinEntityResponse
       | Input.RnaEntityResponse
       | Input.DnaEntityResponse
       | Input.LigandCcdEntityResponse
@@ -1128,10 +1220,16 @@ export namespace StructureAndBindingStartResponse {
      * 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.
+     */
+    templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntityResponse {
+    export interface Boltz2ProteinEntityResponse {
       /**
        * Chain IDs for this entity
        */
@@ -1153,10 +1251,18 @@ 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 to use automatic MSA generation; use custom
+       * for user-provided A3M/CSV; use empty for single-sequence mode.
+       */
+      msa?:
+        | Boltz2ProteinEntityResponse.Boltz2CustomMsaResponse
+        | Boltz2ProteinEntityResponse.Boltz2EmptyMsaResponse;
     }
 
-    export namespace ProteinEntityResponse {
+    export namespace Boltz2ProteinEntityResponse {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -1171,6 +1277,41 @@ export namespace StructureAndBindingStartResponse {
          */
         value: string;
       }
+
+      /**
+       * Custom MSA file to use for this protein entity.
+       */
+      export interface Boltz2CustomMsaResponse {
+        /**
+         * Custom MSA file format. Boltz supports A3M and CSV MSA files.
+         */
+        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.
+       */
+      export interface Boltz2EmptyMsaResponse {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntityResponse {
@@ -1547,6 +1688,49 @@ export namespace StructureAndBindingStartResponse {
        */
       step_scale?: number;
     }
+
+    export interface Template {
+      /**
+       * Template structure format. Base64 sources must use a matching media_type.
+       */
+      format: 'cif' | 'pdb';
+
+      source: Template.Source;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      chain_id?: string | Array<string>;
+
+      /**
+       * Force the template alignment within threshold.
+       */
+      force?: boolean;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      template_id?: string | Array<string>;
+
+      /**
+       * Distance threshold in angstroms used when force is true.
+       */
+      threshold?: number;
+    }
+
+    export namespace Template {
+      export interface Source {
+        /**
+         * URL to download the file
+         */
+        url: string;
+
+        /**
+         * When the presigned URL expires
+         */
+        url_expires_at: string;
+      }
+    }
   }
 
   /**
@@ -1781,7 +1965,7 @@ export namespace StructureAndBindingEstimateCostParams {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntity
+      | Input.Boltz2ProteinEntity
       | Input.RnaEntity
       | Input.DnaEntity
       | Input.LigandCcdEntity
@@ -1808,10 +1992,16 @@ export namespace StructureAndBindingEstimateCostParams {
      * 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.
+     */
+    templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntity {
+    export interface Boltz2ProteinEntity {
       /**
        * Chain IDs for this entity
        */
@@ -1833,10 +2023,16 @@ 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 to use automatic MSA generation; use custom
+       * for user-provided A3M/CSV; use empty for single-sequence mode.
+       */
+      msa?: Boltz2ProteinEntity.Boltz2CustomMsa | Boltz2ProteinEntity.Boltz2EmptyMsa;
     }
 
-    export namespace ProteinEntity {
+    export namespace Boltz2ProteinEntity {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -1851,6 +2047,52 @@ export namespace StructureAndBindingEstimateCostParams {
          */
         value: string;
       }
+
+      /**
+       * Custom MSA file to use for this protein entity.
+       */
+      export interface Boltz2CustomMsa {
+        /**
+         * Custom MSA file format. Boltz supports A3M and CSV MSA files.
+         */
+        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.
+       */
+      export interface Boltz2EmptyMsa {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntity {
@@ -2223,6 +2465,60 @@ export namespace StructureAndBindingEstimateCostParams {
        */
       step_scale?: number;
     }
+
+    export interface Template {
+      /**
+       * Template structure format. Base64 sources must use a matching media_type.
+       */
+      format: 'cif' | 'pdb';
+
+      /**
+       * How to provide a file to the API
+       */
+      source: Template.URLSource | Template.Base64Source;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      chain_id?: string | Array<string>;
+
+      /**
+       * Force the template alignment within threshold.
+       */
+      force?: boolean;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      template_id?: string | Array<string>;
+
+      /**
+       * Distance threshold in angstroms used when force is true.
+       */
+      threshold?: number;
+    }
+
+    export namespace Template {
+      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';
+      }
+    }
   }
 }
 
@@ -2252,7 +2548,7 @@ export namespace StructureAndBindingStartParams {
      * determines chain assignment.
      */
     entities: Array<
-      | Input.ProteinEntity
+      | Input.Boltz2ProteinEntity
       | Input.RnaEntity
       | Input.DnaEntity
       | Input.LigandCcdEntity
@@ -2279,10 +2575,16 @@ export namespace StructureAndBindingStartParams {
      * 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.
+     */
+    templates?: Array<Input.Template>;
   }
 
   export namespace Input {
-    export interface ProteinEntity {
+    export interface Boltz2ProteinEntity {
       /**
        * Chain IDs for this entity
        */
@@ -2304,10 +2606,16 @@ 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 to use automatic MSA generation; use custom
+       * for user-provided A3M/CSV; use empty for single-sequence mode.
+       */
+      msa?: Boltz2ProteinEntity.Boltz2CustomMsa | Boltz2ProteinEntity.Boltz2EmptyMsa;
     }
 
-    export namespace ProteinEntity {
+    export namespace Boltz2ProteinEntity {
       export interface Modification {
         /**
          * 0-based index of the residue to modify
@@ -2322,6 +2630,52 @@ export namespace StructureAndBindingStartParams {
          */
         value: string;
       }
+
+      /**
+       * Custom MSA file to use for this protein entity.
+       */
+      export interface Boltz2CustomMsa {
+        /**
+         * Custom MSA file format. Boltz supports A3M and CSV MSA files.
+         */
+        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.
+       */
+      export interface Boltz2EmptyMsa {
+        type: 'empty';
+      }
     }
 
     export interface RnaEntity {
@@ -2694,6 +3048,60 @@ export namespace StructureAndBindingStartParams {
        */
       step_scale?: number;
     }
+
+    export interface Template {
+      /**
+       * Template structure format. Base64 sources must use a matching media_type.
+       */
+      format: 'cif' | 'pdb';
+
+      /**
+       * How to provide a file to the API
+       */
+      source: Template.URLSource | Template.Base64Source;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      chain_id?: string | Array<string>;
+
+      /**
+       * Force the template alignment within threshold.
+       */
+      force?: boolean;
+
+      /**
+       * One query/template chain ID, or an ordered list of chain IDs.
+       */
+      template_id?: string | Array<string>;
+
+      /**
+       * Distance threshold in angstroms used when force is true.
+       */
+      threshold?: number;
+    }
+
+    export namespace Template {
+      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';
+      }
+    }
   }
 }
 

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = '0.37.1'; // x-release-please-version
+export const VERSION = '0.39.0'; // x-release-please-version

package/version.d.mts

@@ -1,2 +1,2 @@
-export declare const VERSION = "0.37.1";
+export declare const VERSION = "0.39.0";
 //# sourceMappingURL=version.d.mts.map

package/version.d.ts

@@ -1,2 +1,2 @@
-export declare const VERSION = "0.37.1";
+export declare const VERSION = "0.39.0";
 //# 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 = '0.37.1'; // x-release-please-version
+exports.VERSION = '0.39.0'; // x-release-please-version
 //# sourceMappingURL=version.js.map

package/version.mjs

@@ -1,2 +1,2 @@
-export const VERSION = '0.37.1'; // x-release-please-version
+export const VERSION = '0.39.0'; // x-release-please-version
 //# sourceMappingURL=version.mjs.map