boltz-api 0.39.2 → 0.40.0

package/src/resources/protein/design.ts

@@ -541,18 +541,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -585,18 +593,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -626,18 +642,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -667,18 +691,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -1036,19 +1068,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Post-translational modifications. Optional; defaults to an empty list when
-         * omitted.
+         * CCD post-translational modifications. Optional; defaults to an empty list when
+         * omitted. SMILES modifications are not supported.
          */
         modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -1078,18 +1117,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -1119,18 +1166,26 @@ export namespace DesignRetrieveResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -1414,6 +1469,18 @@ export namespace DesignRetrieveResponse {
      * ID of the most recently generated result
      */
     latest_result_id?: string;
+
+    /**
+     * Cumulative number of designs produced by the model before filtering and
+     * deduplication. Useful for monitoring generation efficiency.
+     */
+    total_proteins_generated_pre_filter?: number;
+
+    /**
+     * Cumulative number of designs that survived filtering and deduplication and
+     * became scoreable samples.
+     */
+    total_proteins_inserted?: number;
   }
 }
 
@@ -1505,6 +1572,18 @@ export namespace DesignListResponse {
      * ID of the most recently generated result
      */
     latest_result_id?: string;
+
+    /**
+     * Cumulative number of designs produced by the model before filtering and
+     * deduplication. Useful for monitoring generation efficiency.
+     */
+    total_proteins_generated_pre_filter?: number;
+
+    /**
+     * Cumulative number of designs that survived filtering and deduplication and
+     * became scoreable samples.
+     */
+    total_proteins_inserted?: number;
   }
 }
 
@@ -1658,19 +1737,26 @@ export namespace DesignListResultsResponse {
     cyclic?: boolean;
 
     /**
-     * Post-translational modifications. Optional; defaults to an empty list when
-     * omitted.
+     * CCD post-translational modifications. Optional; defaults to an empty list when
+     * omitted. SMILES modifications are not supported.
      */
     modifications?: Array<ProteinEntity.Modification>;
   }
 
   export namespace ProteinEntity {
+    /**
+     * 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';
 
       /**
@@ -1700,18 +1786,26 @@ export namespace DesignListResultsResponse {
     cyclic?: boolean;
 
     /**
-     * Chemical modifications. Optional; defaults to an empty list when omitted.
+     * 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';
 
       /**
@@ -1741,18 +1835,26 @@ export namespace DesignListResultsResponse {
     cyclic?: boolean;
 
     /**
-     * Chemical modifications. Optional; defaults to an empty list when omitted.
+     * 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';
 
       /**
@@ -2207,18 +2309,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2251,18 +2361,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2292,18 +2410,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2333,18 +2459,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2702,19 +2836,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Post-translational modifications. Optional; defaults to an empty list when
-         * omitted.
+         * CCD post-translational modifications. Optional; defaults to an empty list when
+         * omitted. SMILES modifications are not supported.
          */
         modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2744,18 +2885,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -2785,18 +2934,26 @@ export namespace DesignStartResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3080,6 +3237,18 @@ export namespace DesignStartResponse {
      * ID of the most recently generated result
      */
     latest_result_id?: string;
+
+    /**
+     * Cumulative number of designs produced by the model before filtering and
+     * deduplication. Useful for monitoring generation efficiency.
+     */
+    total_proteins_generated_pre_filter?: number;
+
+    /**
+     * Cumulative number of designs that survived filtering and deduplication and
+     * became scoreable samples.
+     */
+    total_proteins_inserted?: number;
   }
 }
 
@@ -3441,18 +3610,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3485,18 +3662,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3526,18 +3711,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3567,18 +3760,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Optional polymer modifications. Defaults to [] when omitted.
+         * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+         * modifications are not supported.
          */
         modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3936,19 +4137,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Post-translational modifications. Optional; defaults to an empty list when
-         * omitted.
+         * CCD post-translational modifications. Optional; defaults to an empty list when
+         * omitted. SMILES modifications are not supported.
          */
         modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -3978,18 +4186,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -4019,18 +4235,26 @@ export namespace DesignStopResponse {
         cyclic?: boolean;
 
         /**
-         * Chemical modifications. Optional; defaults to an empty list when omitted.
+         * CCD chemical modifications. Optional; defaults to an empty list when omitted.
+         * SMILES modifications are not supported.
          */
         modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
+        /**
+         * 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';
 
           /**
@@ -4314,6 +4538,18 @@ export namespace DesignStopResponse {
      * ID of the most recently generated result
      */
     latest_result_id?: string;
+
+    /**
+     * Cumulative number of designs produced by the model before filtering and
+     * deduplication. Useful for monitoring generation efficiency.
+     */
+    total_proteins_generated_pre_filter?: number;
+
+    /**
+     * Cumulative number of designs that survived filtering and deduplication and
+     * became scoreable samples.
+     */
+    total_proteins_inserted?: number;
   }
 }
 
@@ -4622,18 +4858,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<DesignedProteinEntity.Modification>;
     }
 
     export namespace DesignedProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -4666,18 +4910,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedProteinEntity.Modification>;
     }
 
     export namespace FixedProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -4707,18 +4959,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedRnaEntity.Modification>;
     }
 
     export namespace FixedRnaEntity {
+      /**
+       * 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';
 
         /**
@@ -4748,18 +5008,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedDnaEntity.Modification>;
     }
 
     export namespace FixedDnaEntity {
+      /**
+       * 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';
 
         /**
@@ -5127,19 +5395,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Post-translational modifications. Optional; defaults to an empty list when
-       * omitted.
+       * CCD post-translational modifications. Optional; defaults to an empty list when
+       * omitted. SMILES modifications are not supported.
        */
       modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -5169,18 +5444,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Chemical modifications. Optional; defaults to an empty list when omitted.
+       * 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';
 
         /**
@@ -5210,18 +5493,26 @@ export namespace DesignEstimateCostParams {
       cyclic?: boolean;
 
       /**
-       * Chemical modifications. Optional; defaults to an empty list when omitted.
+       * 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';
 
         /**
@@ -5782,18 +6073,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<DesignedProteinEntity.Modification>;
     }
 
     export namespace DesignedProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -5826,18 +6125,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedProteinEntity.Modification>;
     }
 
     export namespace FixedProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -5867,18 +6174,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedRnaEntity.Modification>;
     }
 
     export namespace FixedRnaEntity {
+      /**
+       * 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';
 
         /**
@@ -5908,18 +6223,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Optional polymer modifications. Defaults to [] when omitted.
+       * Optional CCD polymer modifications. Defaults to [] when omitted. SMILES
+       * modifications are not supported.
        */
       modifications?: Array<FixedDnaEntity.Modification>;
     }
 
     export namespace FixedDnaEntity {
+      /**
+       * 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';
 
         /**
@@ -6287,19 +6610,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Post-translational modifications. Optional; defaults to an empty list when
-       * omitted.
+       * CCD post-translational modifications. Optional; defaults to an empty list when
+       * omitted. SMILES modifications are not supported.
        */
       modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
+      /**
+       * 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';
 
         /**
@@ -6329,18 +6659,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Chemical modifications. Optional; defaults to an empty list when omitted.
+       * 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';
 
         /**
@@ -6370,18 +6708,26 @@ export namespace DesignStartParams {
       cyclic?: boolean;
 
       /**
-       * Chemical modifications. Optional; defaults to an empty list when omitted.
+       * 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';
 
         /**