boltz-api 0.35.2 → 0.36.0

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

@@ -249,7 +249,7 @@ export namespace DesignRetrieveResponse {
     num_molecules: number;
 
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     target: Input.Target;
 
@@ -279,7 +279,7 @@ export namespace DesignRetrieveResponse {
 
   export namespace Input {
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     export interface Target {
       /**
@@ -300,6 +300,12 @@ export namespace DesignRetrieveResponse {
        */
       constraints?: Array<Target.PocketConstraintResponse | Target.ContactConstraintResponse>;
 
+      /**
+       * When true, pocket_residues are also sent as a forced Boltz2 pocket constraint
+       * while scoring candidate molecules. Defaults to false.
+       */
+      enable_pocket_conditioning?: boolean;
+
       /**
        * 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
@@ -316,6 +322,12 @@ export namespace DesignRetrieveResponse {
        * detection.
        */
       reference_ligands?: Array<string>;
+
+      /**
+       * Target is defined directly by protein sequences rather than a structure
+       * template.
+       */
+      type?: 'no_template';
     }
 
     export namespace Target {
@@ -341,11 +353,11 @@ export namespace DesignRetrieveResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<Entity.CcdModificationResponse | Entity.SmilesModificationResponse>;
+        modifications?: Array<Entity.Modification>;
       }
 
       export namespace Entity {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -359,20 +371,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -1339,7 +1337,7 @@ export namespace DesignStartResponse {
     num_molecules: number;
 
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     target: Input.Target;
 
@@ -1369,7 +1367,7 @@ export namespace DesignStartResponse {
 
   export namespace Input {
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     export interface Target {
       /**
@@ -1390,6 +1388,12 @@ export namespace DesignStartResponse {
        */
       constraints?: Array<Target.PocketConstraintResponse | Target.ContactConstraintResponse>;
 
+      /**
+       * When true, pocket_residues are also sent as a forced Boltz2 pocket constraint
+       * while scoring candidate molecules. Defaults to false.
+       */
+      enable_pocket_conditioning?: boolean;
+
       /**
        * 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
@@ -1406,6 +1410,12 @@ export namespace DesignStartResponse {
        * detection.
        */
       reference_ligands?: Array<string>;
+
+      /**
+       * Target is defined directly by protein sequences rather than a structure
+       * template.
+       */
+      type?: 'no_template';
     }
 
     export namespace Target {
@@ -1431,11 +1441,11 @@ export namespace DesignStartResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<Entity.CcdModificationResponse | Entity.SmilesModificationResponse>;
+        modifications?: Array<Entity.Modification>;
       }
 
       export namespace Entity {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -1449,20 +1459,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -2130,7 +2126,7 @@ export namespace DesignStopResponse {
     num_molecules: number;
 
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     target: Input.Target;
 
@@ -2160,7 +2156,7 @@ export namespace DesignStopResponse {
 
   export namespace Input {
     /**
-     * Target protein with binding pocket for small molecule design or screening
+     * Target protein sequences for small molecule design or screening.
      */
     export interface Target {
       /**
@@ -2181,6 +2177,12 @@ export namespace DesignStopResponse {
        */
       constraints?: Array<Target.PocketConstraintResponse | Target.ContactConstraintResponse>;
 
+      /**
+       * When true, pocket_residues are also sent as a forced Boltz2 pocket constraint
+       * while scoring candidate molecules. Defaults to false.
+       */
+      enable_pocket_conditioning?: boolean;
+
       /**
        * 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
@@ -2197,6 +2199,12 @@ export namespace DesignStopResponse {
        * detection.
        */
       reference_ligands?: Array<string>;
+
+      /**
+       * Target is defined directly by protein sequences rather than a structure
+       * template.
+       */
+      type?: 'no_template';
     }
 
     export namespace Target {
@@ -2222,11 +2230,11 @@ export namespace DesignStopResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<Entity.CcdModificationResponse | Entity.SmilesModificationResponse>;
+        modifications?: Array<Entity.Modification>;
       }
 
       export namespace Entity {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2240,20 +2248,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -2857,7 +2851,7 @@ export interface DesignEstimateCostParams {
   num_molecules: number;
 
   /**
-   * Target protein with binding pocket for small molecule design or screening
+   * Target protein sequences for small molecule design or screening.
    */
   target: DesignEstimateCostParams.Target;
 
@@ -2887,7 +2881,7 @@ export interface DesignEstimateCostParams {
 
 export namespace DesignEstimateCostParams {
   /**
-   * Target protein with binding pocket for small molecule design or screening
+   * Target protein sequences for small molecule design or screening.
    */
   export interface Target {
     /**
@@ -2908,6 +2902,12 @@ export namespace DesignEstimateCostParams {
      */
     constraints?: Array<Target.PocketConstraint | Target.ContactConstraint>;
 
+    /**
+     * When true, pocket_residues are also sent as a forced Boltz2 pocket constraint
+     * while scoring candidate molecules. Defaults to false.
+     */
+    enable_pocket_conditioning?: boolean;
+
     /**
      * 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
@@ -2924,6 +2924,12 @@ export namespace DesignEstimateCostParams {
      * detection.
      */
     reference_ligands?: Array<string>;
+
+    /**
+     * Target is defined directly by protein sequences rather than a structure
+     * template.
+     */
+    type?: 'no_template';
   }
 
   export namespace Target {
@@ -2949,11 +2955,11 @@ export namespace DesignEstimateCostParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<Entity.CcdModification | Entity.SmilesModification>;
+      modifications?: Array<Entity.Modification>;
     }
 
     export namespace Entity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -2967,20 +2973,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     /**
@@ -3553,7 +3545,7 @@ export interface DesignStartParams {
   num_molecules: number;
 
   /**
-   * Target protein with binding pocket for small molecule design or screening
+   * Target protein sequences for small molecule design or screening.
    */
   target: DesignStartParams.Target;
 
@@ -3583,7 +3575,7 @@ export interface DesignStartParams {
 
 export namespace DesignStartParams {
   /**
-   * Target protein with binding pocket for small molecule design or screening
+   * Target protein sequences for small molecule design or screening.
    */
   export interface Target {
     /**
@@ -3604,6 +3596,12 @@ export namespace DesignStartParams {
      */
     constraints?: Array<Target.PocketConstraint | Target.ContactConstraint>;
 
+    /**
+     * When true, pocket_residues are also sent as a forced Boltz2 pocket constraint
+     * while scoring candidate molecules. Defaults to false.
+     */
+    enable_pocket_conditioning?: boolean;
+
     /**
      * 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
@@ -3620,6 +3618,12 @@ export namespace DesignStartParams {
      * detection.
      */
     reference_ligands?: Array<string>;
+
+    /**
+     * Target is defined directly by protein sequences rather than a structure
+     * template.
+     */
+    type?: 'no_template';
   }
 
   export namespace Target {
@@ -3645,11 +3649,11 @@ export namespace DesignStartParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<Entity.CcdModification | Entity.SmilesModification>;
+      modifications?: Array<Entity.Modification>;
     }
 
     export namespace Entity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3663,20 +3667,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     /**