boltz-api 0.30.4 → 0.35.3

package/src/resources/protein/design.ts

@@ -543,14 +543,11 @@ export namespace DesignRetrieveResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | DesignedProteinEntityResponse.CcdModificationResponse
-          | DesignedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -564,20 +561,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -604,14 +587,11 @@ export namespace DesignRetrieveResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | FixedProteinEntityResponse.CcdModificationResponse
-          | FixedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -625,20 +605,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedRnaEntityResponse {
@@ -662,13 +628,11 @@ export namespace DesignRetrieveResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -682,20 +646,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedDnaEntityResponse {
@@ -719,13 +669,11 @@ export namespace DesignRetrieveResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -739,20 +687,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedLigandSmilesEntityResponse {
@@ -962,7 +896,7 @@ export namespace DesignRetrieveResponse {
        * 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]:
@@ -991,7 +925,8 @@ export namespace DesignRetrieveResponse {
 
         /**
          * 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>;
 
@@ -1000,6 +935,12 @@ export namespace DesignRetrieveResponse {
          * 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>;
       }
 
       /**
@@ -1063,9 +1004,16 @@ export namespace DesignRetrieveResponse {
       /**
        * 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 {
@@ -1091,13 +1039,11 @@ export namespace DesignRetrieveResponse {
          * 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
            */
@@ -1111,20 +1057,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -1148,13 +1080,11 @@ export namespace DesignRetrieveResponse {
         /**
          * 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
            */
@@ -1168,20 +1098,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -1205,13 +1121,11 @@ export namespace DesignRetrieveResponse {
         /**
          * 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
            */
@@ -1225,20 +1139,6 @@ export namespace DesignRetrieveResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -1760,11 +1660,11 @@ export namespace DesignListResultsResponse {
      * 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
        */
@@ -1778,20 +1678,6 @@ export namespace DesignListResultsResponse {
        */
       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 {
@@ -1815,11 +1701,11 @@ export namespace DesignListResultsResponse {
     /**
      * 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
        */
@@ -1833,20 +1719,6 @@ export namespace DesignListResultsResponse {
        */
       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 {
@@ -1870,11 +1742,11 @@ export namespace DesignListResultsResponse {
     /**
      * 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
        */
@@ -1888,20 +1760,6 @@ export namespace DesignListResultsResponse {
        */
       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 {
@@ -2350,14 +2208,11 @@ export namespace DesignStartResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | DesignedProteinEntityResponse.CcdModificationResponse
-          | DesignedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2371,20 +2226,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -2411,14 +2252,11 @@ export namespace DesignStartResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | FixedProteinEntityResponse.CcdModificationResponse
-          | FixedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2432,20 +2270,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedRnaEntityResponse {
@@ -2469,13 +2293,11 @@ export namespace DesignStartResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2489,20 +2311,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedDnaEntityResponse {
@@ -2526,13 +2334,11 @@ export namespace DesignStartResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -2546,20 +2352,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedLigandSmilesEntityResponse {
@@ -2769,7 +2561,7 @@ export namespace DesignStartResponse {
        * 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]:
@@ -2798,7 +2590,8 @@ export namespace DesignStartResponse {
 
         /**
          * 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>;
 
@@ -2807,6 +2600,12 @@ export namespace DesignStartResponse {
          * 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>;
       }
 
       /**
@@ -2870,9 +2669,16 @@ export namespace DesignStartResponse {
       /**
        * 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 {
@@ -2898,13 +2704,11 @@ export namespace DesignStartResponse {
          * 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
            */
@@ -2918,20 +2722,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -2955,13 +2745,11 @@ export namespace DesignStartResponse {
         /**
          * 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
            */
@@ -2975,20 +2763,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -3012,13 +2786,11 @@ export namespace DesignStartResponse {
         /**
          * 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
            */
@@ -3032,20 +2804,6 @@ export namespace DesignStartResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -3684,14 +3442,11 @@ export namespace DesignStopResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | DesignedProteinEntityResponse.CcdModificationResponse
-          | DesignedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<DesignedProteinEntityResponse.Modification>;
       }
 
       export namespace DesignedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -3705,20 +3460,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       /**
@@ -3745,14 +3486,11 @@ export namespace DesignStopResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          | FixedProteinEntityResponse.CcdModificationResponse
-          | FixedProteinEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedProteinEntityResponse.Modification>;
       }
 
       export namespace FixedProteinEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -3766,20 +3504,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedRnaEntityResponse {
@@ -3803,13 +3527,11 @@ export namespace DesignStopResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedRnaEntityResponse.Modification>;
       }
 
       export namespace FixedRnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -3823,20 +3545,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedDnaEntityResponse {
@@ -3860,13 +3568,11 @@ export namespace DesignStopResponse {
         /**
          * Optional polymer modifications. Defaults to [] when omitted.
          */
-        modifications?: Array<
-          FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse
-        >;
+        modifications?: Array<FixedDnaEntityResponse.Modification>;
       }
 
       export namespace FixedDnaEntityResponse {
-        export interface CcdModificationResponse {
+        export interface Modification {
           /**
            * 0-based index of the residue to modify
            */
@@ -3880,20 +3586,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface FixedLigandSmilesEntityResponse {
@@ -4103,7 +3795,7 @@ export namespace DesignStopResponse {
        * 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]:
@@ -4132,7 +3824,8 @@ export namespace DesignStopResponse {
 
         /**
          * 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>;
 
@@ -4141,6 +3834,12 @@ export namespace DesignStopResponse {
          * 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>;
       }
 
       /**
@@ -4204,9 +3903,16 @@ export namespace DesignStopResponse {
       /**
        * 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 {
@@ -4232,13 +3938,11 @@ export namespace DesignStopResponse {
          * 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
            */
@@ -4252,20 +3956,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface RnaEntityResponse {
@@ -4289,13 +3979,11 @@ export namespace DesignStopResponse {
         /**
          * 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
            */
@@ -4309,20 +3997,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface DnaEntityResponse {
@@ -4346,13 +4020,11 @@ export namespace DesignStopResponse {
         /**
          * 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
            */
@@ -4366,20 +4038,6 @@ export namespace DesignStopResponse {
            */
           value: string;
         }
-
-        export interface SmilesModificationResponse {
-          /**
-           * 0-based index of the residue to modify
-           */
-          residue_index: number;
-
-          type: 'smiles';
-
-          /**
-           * SMILES string for the modification
-           */
-          value: string;
-        }
       }
 
       export interface LigandCcdEntityResponse {
@@ -4965,11 +4623,11 @@ export namespace DesignEstimateCostParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<DesignedProteinEntity.CcdModification | DesignedProteinEntity.SmilesModification>;
+      modifications?: Array<DesignedProteinEntity.Modification>;
     }
 
     export namespace DesignedProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -4983,20 +4641,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     /**
@@ -5023,11 +4667,11 @@ export namespace DesignEstimateCostParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedProteinEntity.CcdModification | FixedProteinEntity.SmilesModification>;
+      modifications?: Array<FixedProteinEntity.Modification>;
     }
 
     export namespace FixedProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -5041,20 +4685,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedRnaEntity {
@@ -5078,11 +4708,11 @@ export namespace DesignEstimateCostParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedRnaEntity.CcdModification | FixedRnaEntity.SmilesModification>;
+      modifications?: Array<FixedRnaEntity.Modification>;
     }
 
     export namespace FixedRnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -5096,20 +4726,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedDnaEntity {
@@ -5133,11 +4749,11 @@ export namespace DesignEstimateCostParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedDnaEntity.CcdModification | FixedDnaEntity.SmilesModification>;
+      modifications?: Array<FixedDnaEntity.Modification>;
     }
 
     export namespace FixedDnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -5151,20 +4767,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedLigandSmilesEntity {
@@ -5374,7 +4976,7 @@ export namespace DesignEstimateCostParams {
      * 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]:
@@ -5407,7 +5009,8 @@ export namespace DesignEstimateCostParams {
 
       /**
        * 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>;
 
@@ -5416,6 +5019,12 @@ export namespace DesignEstimateCostParams {
        * 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>;
     }
 
     /**
@@ -5485,9 +5094,16 @@ export namespace DesignEstimateCostParams {
     /**
      * 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 {
@@ -5513,11 +5129,11 @@ export namespace DesignEstimateCostParams {
        * 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
          */
@@ -5531,20 +5147,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface RnaEntity {
@@ -5568,11 +5170,11 @@ export namespace DesignEstimateCostParams {
       /**
        * 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
          */
@@ -5586,20 +5188,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface DnaEntity {
@@ -5623,11 +5211,11 @@ export namespace DesignEstimateCostParams {
       /**
        * 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
          */
@@ -5641,20 +5229,6 @@ export namespace DesignEstimateCostParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface LigandCcdEntity {
@@ -6209,11 +5783,11 @@ export namespace DesignStartParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<DesignedProteinEntity.CcdModification | DesignedProteinEntity.SmilesModification>;
+      modifications?: Array<DesignedProteinEntity.Modification>;
     }
 
     export namespace DesignedProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -6227,20 +5801,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     /**
@@ -6267,11 +5827,11 @@ export namespace DesignStartParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedProteinEntity.CcdModification | FixedProteinEntity.SmilesModification>;
+      modifications?: Array<FixedProteinEntity.Modification>;
     }
 
     export namespace FixedProteinEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -6285,20 +5845,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedRnaEntity {
@@ -6322,11 +5868,11 @@ export namespace DesignStartParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedRnaEntity.CcdModification | FixedRnaEntity.SmilesModification>;
+      modifications?: Array<FixedRnaEntity.Modification>;
     }
 
     export namespace FixedRnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -6340,20 +5886,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedDnaEntity {
@@ -6377,11 +5909,11 @@ export namespace DesignStartParams {
       /**
        * Optional polymer modifications. Defaults to [] when omitted.
        */
-      modifications?: Array<FixedDnaEntity.CcdModification | FixedDnaEntity.SmilesModification>;
+      modifications?: Array<FixedDnaEntity.Modification>;
     }
 
     export namespace FixedDnaEntity {
-      export interface CcdModification {
+      export interface Modification {
         /**
          * 0-based index of the residue to modify
          */
@@ -6395,20 +5927,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface FixedLigandSmilesEntity {
@@ -6618,7 +6136,7 @@ export namespace DesignStartParams {
      * 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]:
@@ -6651,7 +6169,8 @@ export namespace DesignStartParams {
 
       /**
        * 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>;
 
@@ -6660,6 +6179,12 @@ export namespace DesignStartParams {
        * 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>;
     }
 
     /**
@@ -6729,9 +6254,16 @@ export namespace DesignStartParams {
     /**
      * 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 {
@@ -6757,11 +6289,11 @@ export namespace DesignStartParams {
        * 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
          */
@@ -6775,20 +6307,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface RnaEntity {
@@ -6812,11 +6330,11 @@ export namespace DesignStartParams {
       /**
        * 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
          */
@@ -6830,20 +6348,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface DnaEntity {
@@ -6867,11 +6371,11 @@ export namespace DesignStartParams {
       /**
        * 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
          */
@@ -6885,20 +6389,6 @@ export namespace DesignStartParams {
          */
         value: string;
       }
-
-      export interface SmilesModification {
-        /**
-         * 0-based index of the residue to modify
-         */
-        residue_index: number;
-
-        type: 'smiles';
-
-        /**
-         * SMILES string for the modification
-         */
-        value: string;
-      }
     }
 
     export interface LigandCcdEntity {