boltz-api 0.30.4 → 0.35.3

package/src/resources/protein/library-screen.ts

@@ -300,7 +300,7 @@ export namespace LibraryScreenRetrieveResponse {
        * Chains selected from the uploaded structure, keyed by chain ID. Only chains
        * listed here are included in the engine run — any chains omitted from this
        * mapping are ignored. Each value defines which residues to keep, which are
-       * epitope residues, and which are flexible.
+       * epitope residues, which are non-binding residues, and which are flexible.
        */
       chain_selection: {
         [key: string]:
@@ -329,7 +329,8 @@ export namespace LibraryScreenRetrieveResponse {
 
         /**
          * 0-indexed residue indices where binder contact is desired (the epitope). All
-         * indices must be present in crop_residues.
+         * indices must be present in crop_residues and must not overlap
+         * non_binding_residues.
          */
         epitope_residues?: Array<number>;
 
@@ -338,6 +339,12 @@ export namespace LibraryScreenRetrieveResponse {
          * regions). All indices must be present in crop_residues.
          */
         flexible_residues?: Array<number>;
+
+        /**
+         * 0-indexed residue indices where binder contact should be discouraged. All
+         * indices must be present in crop_residues and must not overlap epitope_residues.
+         */
+        non_binding_residues?: Array<number>;
       }
 
       /**
@@ -401,9 +408,16 @@ export namespace LibraryScreenRetrieveResponse {
       /**
        * Polymer chain residues where binder contact is desired (the epitope). Each key
        * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-       * indices.
+       * indices. Residues must not overlap non_binding_residues on the same chain.
        */
       epitope_residues?: { [key: string]: Array<number> };
+
+      /**
+       * Polymer chain residues where binder contact should be discouraged. Each key is a
+       * chain ID of a polymer entity, each value is an array of 0-indexed residue
+       * indices. Residues must not overlap epitope_residues on the same chain.
+       */
+      non_binding_residues?: { [key: string]: Array<number> };
     }
 
     export namespace NoTemplateTargetResponse {
@@ -429,13 +443,11 @@ export namespace LibraryScreenRetrieveResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<
-          ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -449,20 +461,6 @@ export namespace LibraryScreenRetrieveResponse {
            */
           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;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -486,13 +484,11 @@ export namespace LibraryScreenRetrieveResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -506,20 +502,6 @@ export namespace LibraryScreenRetrieveResponse {
            */
           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;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -543,13 +525,11 @@ export namespace LibraryScreenRetrieveResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -563,20 +543,6 @@ export namespace LibraryScreenRetrieveResponse {
            */
           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;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -1113,11 +1079,11 @@ export namespace LibraryScreenListResultsResponse {
      * Post-translational modifications. Optional; defaults to an empty list when
      * omitted.
      */
-    modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+    modifications?: Array<ProteinEntity.Modification>;
   }
 
   export namespace ProteinEntity {
-    export interface CcdModification {
+    export interface Modification {
       /**
        * 0-based index of the residue to modify
        */
@@ -1131,20 +1097,6 @@ export namespace LibraryScreenListResultsResponse {
        */
       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;
-    }
   }
 
   export interface RnaEntity {
@@ -1168,11 +1120,11 @@ export namespace LibraryScreenListResultsResponse {
     /**
      * Chemical modifications. Optional; defaults to an empty list when omitted.
      */
-    modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+    modifications?: Array<RnaEntity.Modification>;
   }
 
   export namespace RnaEntity {
-    export interface CcdModification {
+    export interface Modification {
       /**
        * 0-based index of the residue to modify
        */
@@ -1186,20 +1138,6 @@ export namespace LibraryScreenListResultsResponse {
        */
       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;
-    }
   }
 
   export interface DnaEntity {
@@ -1223,11 +1161,11 @@ export namespace LibraryScreenListResultsResponse {
     /**
      * Chemical modifications. Optional; defaults to an empty list when omitted.
      */
-    modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+    modifications?: Array<DnaEntity.Modification>;
   }
 
   export namespace DnaEntity {
-    export interface CcdModification {
+    export interface Modification {
       /**
        * 0-based index of the residue to modify
        */
@@ -1241,20 +1179,6 @@ export namespace LibraryScreenListResultsResponse {
        */
       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;
-    }
   }
 
   export interface LigandCcdEntity {
@@ -1455,7 +1379,7 @@ export namespace LibraryScreenStartResponse {
        * Chains selected from the uploaded structure, keyed by chain ID. Only chains
        * listed here are included in the engine run — any chains omitted from this
        * mapping are ignored. Each value defines which residues to keep, which are
-       * epitope residues, and which are flexible.
+       * epitope residues, which are non-binding residues, and which are flexible.
        */
       chain_selection: {
         [key: string]:
@@ -1484,7 +1408,8 @@ export namespace LibraryScreenStartResponse {
 
         /**
          * 0-indexed residue indices where binder contact is desired (the epitope). All
-         * indices must be present in crop_residues.
+         * indices must be present in crop_residues and must not overlap
+         * non_binding_residues.
          */
         epitope_residues?: Array<number>;
 
@@ -1493,6 +1418,12 @@ export namespace LibraryScreenStartResponse {
          * regions). All indices must be present in crop_residues.
          */
         flexible_residues?: Array<number>;
+
+        /**
+         * 0-indexed residue indices where binder contact should be discouraged. All
+         * indices must be present in crop_residues and must not overlap epitope_residues.
+         */
+        non_binding_residues?: Array<number>;
       }
 
       /**
@@ -1556,9 +1487,16 @@ export namespace LibraryScreenStartResponse {
       /**
        * Polymer chain residues where binder contact is desired (the epitope). Each key
        * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-       * indices.
+       * indices. Residues must not overlap non_binding_residues on the same chain.
        */
       epitope_residues?: { [key: string]: Array<number> };
+
+      /**
+       * Polymer chain residues where binder contact should be discouraged. Each key is a
+       * chain ID of a polymer entity, each value is an array of 0-indexed residue
+       * indices. Residues must not overlap epitope_residues on the same chain.
+       */
+      non_binding_residues?: { [key: string]: Array<number> };
     }
 
     export namespace NoTemplateTargetResponse {
@@ -1584,13 +1522,11 @@ export namespace LibraryScreenStartResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<
-          ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -1604,20 +1540,6 @@ export namespace LibraryScreenStartResponse {
            */
           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;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -1641,13 +1563,11 @@ export namespace LibraryScreenStartResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -1661,20 +1581,6 @@ export namespace LibraryScreenStartResponse {
            */
           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;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -1698,13 +1604,11 @@ export namespace LibraryScreenStartResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -1718,20 +1622,6 @@ export namespace LibraryScreenStartResponse {
            */
           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;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -2127,7 +2017,7 @@ export namespace LibraryScreenStopResponse {
        * Chains selected from the uploaded structure, keyed by chain ID. Only chains
        * listed here are included in the engine run — any chains omitted from this
        * mapping are ignored. Each value defines which residues to keep, which are
-       * epitope residues, and which are flexible.
+       * epitope residues, which are non-binding residues, and which are flexible.
        */
       chain_selection: {
         [key: string]:
@@ -2156,7 +2046,8 @@ export namespace LibraryScreenStopResponse {
 
         /**
          * 0-indexed residue indices where binder contact is desired (the epitope). All
-         * indices must be present in crop_residues.
+         * indices must be present in crop_residues and must not overlap
+         * non_binding_residues.
          */
         epitope_residues?: Array<number>;
 
@@ -2165,6 +2056,12 @@ export namespace LibraryScreenStopResponse {
          * regions). All indices must be present in crop_residues.
          */
         flexible_residues?: Array<number>;
+
+        /**
+         * 0-indexed residue indices where binder contact should be discouraged. All
+         * indices must be present in crop_residues and must not overlap epitope_residues.
+         */
+        non_binding_residues?: Array<number>;
       }
 
       /**
@@ -2228,9 +2125,16 @@ export namespace LibraryScreenStopResponse {
       /**
        * Polymer chain residues where binder contact is desired (the epitope). Each key
        * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-       * indices.
+       * indices. Residues must not overlap non_binding_residues on the same chain.
        */
       epitope_residues?: { [key: string]: Array<number> };
+
+      /**
+       * Polymer chain residues where binder contact should be discouraged. Each key is a
+       * chain ID of a polymer entity, each value is an array of 0-indexed residue
+       * indices. Residues must not overlap epitope_residues on the same chain.
+       */
+      non_binding_residues?: { [key: string]: Array<number> };
     }
 
     export namespace NoTemplateTargetResponse {
@@ -2256,13 +2160,11 @@ export namespace LibraryScreenStopResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<
-          ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<ProteinEntityResponse.Modification>;
       }
 
       export namespace ProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2276,20 +2178,6 @@ export namespace LibraryScreenStopResponse {
            */
           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;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -2313,13 +2201,11 @@ export namespace LibraryScreenStopResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<RnaEntityResponse.Modification>;
       }
 
       export namespace RnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2333,20 +2219,6 @@ export namespace LibraryScreenStopResponse {
            */
           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;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -2370,13 +2242,11 @@ export namespace LibraryScreenStopResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<
-          DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DnaEntityResponse.Modification>;
       }
 
       export namespace DnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2390,20 +2260,6 @@ export namespace LibraryScreenStopResponse {
            */
           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;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -2773,11 +2629,11 @@ export namespace LibraryScreenEstimateCostParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+      modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -2791,20 +2647,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface RnaEntity {
@@ -2828,11 +2670,11 @@ export namespace LibraryScreenEstimateCostParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+      modifications?: Array<RnaEntity.Modification>;
     }
 
     export namespace RnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -2846,20 +2688,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface DnaEntity {
@@ -2883,11 +2711,11 @@ export namespace LibraryScreenEstimateCostParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+      modifications?: Array<DnaEntity.Modification>;
     }
 
     export namespace DnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -2901,20 +2729,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface LigandCcdEntity {
@@ -2955,7 +2769,7 @@ export namespace LibraryScreenEstimateCostParams {
      * Chains selected from the uploaded structure, keyed by chain ID. Only chains
      * listed here are included in the engine run — any chains omitted from this
      * mapping are ignored. Each value defines which residues to keep, which are
-     * epitope residues, and which are flexible.
+     * epitope residues, which are non-binding residues, and which are flexible.
      */
     chain_selection: {
       [key: string]:
@@ -2988,7 +2802,8 @@ export namespace LibraryScreenEstimateCostParams {
 
       /**
        * 0-indexed residue indices where binder contact is desired (the epitope). All
-       * indices must be present in crop_residues.
+       * indices must be present in crop_residues and must not overlap
+       * non_binding_residues.
        */
       epitope_residues?: Array<number>;
 
@@ -2997,6 +2812,12 @@ export namespace LibraryScreenEstimateCostParams {
        * regions). All indices must be present in crop_residues.
        */
       flexible_residues?: Array<number>;
+
+      /**
+       * 0-indexed residue indices where binder contact should be discouraged. All
+       * indices must be present in crop_residues and must not overlap epitope_residues.
+       */
+      non_binding_residues?: Array<number>;
     }
 
     /**
@@ -3066,9 +2887,16 @@ export namespace LibraryScreenEstimateCostParams {
     /**
      * Polymer chain residues where binder contact is desired (the epitope). Each key
      * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-     * indices.
+     * indices. Residues must not overlap non_binding_residues on the same chain.
      */
     epitope_residues?: { [key: string]: Array<number> };
+
+    /**
+     * Polymer chain residues where binder contact should be discouraged. Each key is a
+     * chain ID of a polymer entity, each value is an array of 0-indexed residue
+     * indices. Residues must not overlap epitope_residues on the same chain.
+     */
+    non_binding_residues?: { [key: string]: Array<number> };
   }
 
   export namespace NoTemplateTarget {
@@ -3094,11 +2922,11 @@ export namespace LibraryScreenEstimateCostParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+      modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3112,20 +2940,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface RnaEntity {
@@ -3149,11 +2963,11 @@ export namespace LibraryScreenEstimateCostParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+      modifications?: Array<RnaEntity.Modification>;
     }
 
     export namespace RnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3167,20 +2981,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface DnaEntity {
@@ -3204,11 +3004,11 @@ export namespace LibraryScreenEstimateCostParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+      modifications?: Array<DnaEntity.Modification>;
     }
 
     export namespace DnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3222,20 +3022,6 @@ export namespace LibraryScreenEstimateCostParams {
          */
         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;
-      }
     }
 
     export interface LigandCcdEntity {
@@ -3567,11 +3353,11 @@ export namespace LibraryScreenStartParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+      modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3585,20 +3371,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface RnaEntity {
@@ -3622,11 +3394,11 @@ export namespace LibraryScreenStartParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+      modifications?: Array<RnaEntity.Modification>;
     }
 
     export namespace RnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3640,20 +3412,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface DnaEntity {
@@ -3677,11 +3435,11 @@ export namespace LibraryScreenStartParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+      modifications?: Array<DnaEntity.Modification>;
     }
 
     export namespace DnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3695,20 +3453,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface LigandCcdEntity {
@@ -3749,7 +3493,7 @@ export namespace LibraryScreenStartParams {
      * Chains selected from the uploaded structure, keyed by chain ID. Only chains
      * listed here are included in the engine run — any chains omitted from this
      * mapping are ignored. Each value defines which residues to keep, which are
-     * epitope residues, and which are flexible.
+     * epitope residues, which are non-binding residues, and which are flexible.
      */
     chain_selection: {
       [key: string]:
@@ -3782,7 +3526,8 @@ export namespace LibraryScreenStartParams {
 
       /**
        * 0-indexed residue indices where binder contact is desired (the epitope). All
-       * indices must be present in crop_residues.
+       * indices must be present in crop_residues and must not overlap
+       * non_binding_residues.
        */
       epitope_residues?: Array<number>;
 
@@ -3791,6 +3536,12 @@ export namespace LibraryScreenStartParams {
        * regions). All indices must be present in crop_residues.
        */
       flexible_residues?: Array<number>;
+
+      /**
+       * 0-indexed residue indices where binder contact should be discouraged. All
+       * indices must be present in crop_residues and must not overlap epitope_residues.
+       */
+      non_binding_residues?: Array<number>;
     }
 
     /**
@@ -3860,9 +3611,16 @@ export namespace LibraryScreenStartParams {
     /**
      * Polymer chain residues where binder contact is desired (the epitope). Each key
      * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-     * indices.
+     * indices. Residues must not overlap non_binding_residues on the same chain.
      */
     epitope_residues?: { [key: string]: Array<number> };
+
+    /**
+     * Polymer chain residues where binder contact should be discouraged. Each key is a
+     * chain ID of a polymer entity, each value is an array of 0-indexed residue
+     * indices. Residues must not overlap epitope_residues on the same chain.
+     */
+    non_binding_residues?: { [key: string]: Array<number> };
   }
 
   export namespace NoTemplateTarget {
@@ -3888,11 +3646,11 @@ export namespace LibraryScreenStartParams {
        * Post-translational modifications. Optional; defaults to an empty list when
        * omitted.
        */
-      modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+      modifications?: Array<ProteinEntity.Modification>;
     }
 
     export namespace ProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3906,20 +3664,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface RnaEntity {
@@ -3943,11 +3687,11 @@ export namespace LibraryScreenStartParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+      modifications?: Array<RnaEntity.Modification>;
     }
 
     export namespace RnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -3961,20 +3705,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface DnaEntity {
@@ -3998,11 +3728,11 @@ export namespace LibraryScreenStartParams {
       /**
        * Chemical modifications. Optional; defaults to an empty list when omitted.
        */
-      modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+      modifications?: Array<DnaEntity.Modification>;
     }
 
     export namespace DnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -4016,20 +3746,6 @@ export namespace LibraryScreenStartParams {
          */
         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;
-      }
     }
 
     export interface LigandCcdEntity {