boltz-api 0.39.2 → 0.40.0

package/resources/protein/design.d.ts

@@ -421,16 +421,24 @@ export declare 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>;
             }
             namespace DesignedProteinEntityResponse {
+                /**
+                 * 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
@@ -457,16 +465,24 @@ export declare 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>;
             }
             namespace FixedProteinEntityResponse {
+                /**
+                 * 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
@@ -490,16 +506,24 @@ export declare 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>;
             }
             namespace FixedRnaEntityResponse {
+                /**
+                 * 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
@@ -523,16 +547,24 @@ export declare 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>;
             }
             namespace FixedDnaEntityResponse {
+                /**
+                 * 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
@@ -829,17 +861,24 @@ export declare 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>;
             }
             namespace ProteinEntityResponse {
+                /**
+                 * 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
@@ -863,16 +902,24 @@ export declare 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>;
             }
             namespace RnaEntityResponse {
+                /**
+                 * 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
@@ -896,16 +943,24 @@ export declare 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>;
             }
             namespace DnaEntityResponse {
+                /**
+                 * 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
@@ -1139,6 +1194,16 @@ export declare 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;
     }
 }
 /**
@@ -1210,6 +1275,16 @@ export declare 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;
     }
 }
 export interface DesignDeleteDataResponse {
@@ -1324,17 +1399,24 @@ export declare 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>;
     }
     namespace ProteinEntity {
+        /**
+         * 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
@@ -1358,16 +1440,24 @@ export declare 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>;
     }
     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
@@ -1391,16 +1481,24 @@ export declare 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>;
     }
     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
@@ -1766,16 +1864,24 @@ export declare 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>;
             }
             namespace DesignedProteinEntityResponse {
+                /**
+                 * 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
@@ -1802,16 +1908,24 @@ export declare 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>;
             }
             namespace FixedProteinEntityResponse {
+                /**
+                 * 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
@@ -1835,16 +1949,24 @@ export declare 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>;
             }
             namespace FixedRnaEntityResponse {
+                /**
+                 * 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
@@ -1868,16 +1990,24 @@ export declare 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>;
             }
             namespace FixedDnaEntityResponse {
+                /**
+                 * 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
@@ -2174,17 +2304,24 @@ export declare 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>;
             }
             namespace ProteinEntityResponse {
+                /**
+                 * 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
@@ -2208,16 +2345,24 @@ export declare 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>;
             }
             namespace RnaEntityResponse {
+                /**
+                 * 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
@@ -2241,16 +2386,24 @@ export declare 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>;
             }
             namespace DnaEntityResponse {
+                /**
+                 * 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
@@ -2484,6 +2637,16 @@ export declare 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;
     }
 }
 /**
@@ -2772,16 +2935,24 @@ export declare 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>;
             }
             namespace DesignedProteinEntityResponse {
+                /**
+                 * 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
@@ -2808,16 +2979,24 @@ export declare 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>;
             }
             namespace FixedProteinEntityResponse {
+                /**
+                 * 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
@@ -2841,16 +3020,24 @@ export declare 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>;
             }
             namespace FixedRnaEntityResponse {
+                /**
+                 * 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
@@ -2874,16 +3061,24 @@ export declare 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>;
             }
             namespace FixedDnaEntityResponse {
+                /**
+                 * 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
@@ -3180,17 +3375,24 @@ export declare 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>;
             }
             namespace ProteinEntityResponse {
+                /**
+                 * 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
@@ -3214,16 +3416,24 @@ export declare 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>;
             }
             namespace RnaEntityResponse {
+                /**
+                 * 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
@@ -3247,16 +3457,24 @@ export declare 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>;
             }
             namespace DnaEntityResponse {
+                /**
+                 * 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
@@ -3490,6 +3708,16 @@ export declare 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;
     }
 }
 export interface DesignRetrieveParams {
@@ -3739,16 +3967,24 @@ export declare 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>;
         }
         namespace DesignedProteinEntity {
+            /**
+             * 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
@@ -3775,16 +4011,24 @@ export declare 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>;
         }
         namespace FixedProteinEntity {
+            /**
+             * 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
@@ -3808,16 +4052,24 @@ export declare 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>;
         }
         namespace FixedRnaEntity {
+            /**
+             * 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
@@ -3841,16 +4093,24 @@ export declare 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>;
         }
         namespace FixedDnaEntity {
+            /**
+             * 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
@@ -4156,17 +4416,24 @@ export declare 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>;
         }
         namespace ProteinEntity {
+            /**
+             * 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
@@ -4190,16 +4457,24 @@ export declare 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>;
         }
         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
@@ -4223,16 +4498,24 @@ export declare 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>;
         }
         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
@@ -4692,16 +4975,24 @@ export declare 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>;
         }
         namespace DesignedProteinEntity {
+            /**
+             * 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
@@ -4728,16 +5019,24 @@ export declare 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>;
         }
         namespace FixedProteinEntity {
+            /**
+             * 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
@@ -4761,16 +5060,24 @@ export declare 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>;
         }
         namespace FixedRnaEntity {
+            /**
+             * 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
@@ -4794,16 +5101,24 @@ export declare 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>;
         }
         namespace FixedDnaEntity {
+            /**
+             * 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
@@ -5109,17 +5424,24 @@ export declare 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>;
         }
         namespace ProteinEntity {
+            /**
+             * 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
@@ -5143,16 +5465,24 @@ export declare 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>;
         }
         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
@@ -5176,16 +5506,24 @@ export declare 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>;
         }
         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