boltz-api 0.30.4 → 0.35.3

package/resources/protein/design.d.mts

@@ -423,10 +423,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<DesignedProteinEntityResponse.CcdModificationResponse | DesignedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DesignedProteinEntityResponse.Modification>;
             }
             namespace DesignedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -438,17 +438,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             /**
              * A fixed protein entity whose sequence is not redesigned.
@@ -470,10 +459,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedProteinEntityResponse.CcdModificationResponse | FixedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedProteinEntityResponse.Modification>;
             }
             namespace FixedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -485,17 +474,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedRnaEntityResponse {
                 /**
@@ -514,10 +492,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedRnaEntityResponse.Modification>;
             }
             namespace FixedRnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -529,17 +507,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedDnaEntityResponse {
                 /**
@@ -558,10 +525,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedDnaEntityResponse.Modification>;
             }
             namespace FixedDnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -573,17 +540,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedLigandSmilesEntityResponse {
                 /**
@@ -761,7 +717,7 @@ export declare 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]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -783,7 +739,8 @@ export declare namespace DesignRetrieveResponse {
                 crop_residues: Array<number> | 'all';
                 /**
                  * 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>;
                 /**
@@ -791,6 +748,11 @@ export declare 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>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -837,11 +799,19 @@ export declare 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>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -862,10 +832,10 @@ export declare namespace DesignRetrieveResponse {
                  * Post-translational modifications. Optional; defaults to an empty list when
                  * omitted.
                  */
-                modifications?: Array<ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<ProteinEntityResponse.Modification>;
             }
             namespace ProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -877,17 +847,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface RnaEntityResponse {
                 /**
@@ -906,10 +865,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<RnaEntityResponse.Modification>;
             }
             namespace RnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -921,17 +880,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface DnaEntityResponse {
                 /**
@@ -950,10 +898,10 @@ export declare namespace DesignRetrieveResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DnaEntityResponse.Modification>;
             }
             namespace DnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -965,17 +913,6 @@ export declare namespace DesignRetrieveResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface LigandCcdEntityResponse {
                 /**
@@ -1390,10 +1327,10 @@ export declare namespace DesignListResultsResponse {
          * Post-translational modifications. Optional; defaults to an empty list when
          * omitted.
          */
-        modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+        modifications?: Array<ProteinEntity.Modification>;
     }
     namespace ProteinEntity {
-        interface CcdModification {
+        interface Modification {
             /**
              * 0-based index of the residue to modify
              */
@@ -1405,17 +1342,6 @@ export declare namespace DesignListResultsResponse {
              */
             value: string;
         }
-        interface SmilesModification {
-            /**
-             * 0-based index of the residue to modify
-             */
-            residue_index: number;
-            type: 'smiles';
-            /**
-             * SMILES string for the modification
-             */
-            value: string;
-        }
     }
     interface RnaEntity {
         /**
@@ -1434,10 +1360,10 @@ export declare namespace DesignListResultsResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+        modifications?: Array<RnaEntity.Modification>;
     }
     namespace RnaEntity {
-        interface CcdModification {
+        interface Modification {
             /**
              * 0-based index of the residue to modify
              */
@@ -1449,17 +1375,6 @@ export declare namespace DesignListResultsResponse {
              */
             value: string;
         }
-        interface SmilesModification {
-            /**
-             * 0-based index of the residue to modify
-             */
-            residue_index: number;
-            type: 'smiles';
-            /**
-             * SMILES string for the modification
-             */
-            value: string;
-        }
     }
     interface DnaEntity {
         /**
@@ -1478,10 +1393,10 @@ export declare namespace DesignListResultsResponse {
         /**
          * Chemical modifications. Optional; defaults to an empty list when omitted.
          */
-        modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+        modifications?: Array<DnaEntity.Modification>;
     }
     namespace DnaEntity {
-        interface CcdModification {
+        interface Modification {
             /**
              * 0-based index of the residue to modify
              */
@@ -1493,17 +1408,6 @@ export declare namespace DesignListResultsResponse {
              */
             value: string;
         }
-        interface SmilesModification {
-            /**
-             * 0-based index of the residue to modify
-             */
-            residue_index: number;
-            type: 'smiles';
-            /**
-             * SMILES string for the modification
-             */
-            value: string;
-        }
     }
     interface LigandCcdEntity {
         /**
@@ -1864,10 +1768,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<DesignedProteinEntityResponse.CcdModificationResponse | DesignedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DesignedProteinEntityResponse.Modification>;
             }
             namespace DesignedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -1879,17 +1783,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             /**
              * A fixed protein entity whose sequence is not redesigned.
@@ -1911,10 +1804,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedProteinEntityResponse.CcdModificationResponse | FixedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedProteinEntityResponse.Modification>;
             }
             namespace FixedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -1926,17 +1819,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedRnaEntityResponse {
                 /**
@@ -1955,10 +1837,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedRnaEntityResponse.Modification>;
             }
             namespace FixedRnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -1970,17 +1852,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedDnaEntityResponse {
                 /**
@@ -1999,10 +1870,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedDnaEntityResponse.Modification>;
             }
             namespace FixedDnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2014,17 +1885,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedLigandSmilesEntityResponse {
                 /**
@@ -2202,7 +2062,7 @@ export declare 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]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -2224,7 +2084,8 @@ export declare namespace DesignStartResponse {
                 crop_residues: Array<number> | 'all';
                 /**
                  * 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>;
                 /**
@@ -2232,6 +2093,11 @@ export declare 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>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -2278,11 +2144,19 @@ export declare 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>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -2303,10 +2177,10 @@ export declare namespace DesignStartResponse {
                  * Post-translational modifications. Optional; defaults to an empty list when
                  * omitted.
                  */
-                modifications?: Array<ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<ProteinEntityResponse.Modification>;
             }
             namespace ProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2318,17 +2192,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface RnaEntityResponse {
                 /**
@@ -2347,10 +2210,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<RnaEntityResponse.Modification>;
             }
             namespace RnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2362,17 +2225,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface DnaEntityResponse {
                 /**
@@ -2391,10 +2243,10 @@ export declare namespace DesignStartResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DnaEntityResponse.Modification>;
             }
             namespace DnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2406,17 +2258,6 @@ export declare namespace DesignStartResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface LigandCcdEntityResponse {
                 /**
@@ -2933,10 +2774,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<DesignedProteinEntityResponse.CcdModificationResponse | DesignedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DesignedProteinEntityResponse.Modification>;
             }
             namespace DesignedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2948,17 +2789,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             /**
              * A fixed protein entity whose sequence is not redesigned.
@@ -2980,10 +2810,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedProteinEntityResponse.CcdModificationResponse | FixedProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedProteinEntityResponse.Modification>;
             }
             namespace FixedProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -2995,17 +2825,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedRnaEntityResponse {
                 /**
@@ -3024,10 +2843,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedRnaEntityResponse.CcdModificationResponse | FixedRnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedRnaEntityResponse.Modification>;
             }
             namespace FixedRnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -3039,17 +2858,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedDnaEntityResponse {
                 /**
@@ -3068,10 +2876,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Optional polymer modifications. Defaults to [] when omitted.
                  */
-                modifications?: Array<FixedDnaEntityResponse.CcdModificationResponse | FixedDnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<FixedDnaEntityResponse.Modification>;
             }
             namespace FixedDnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -3083,17 +2891,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface FixedLigandSmilesEntityResponse {
                 /**
@@ -3271,7 +3068,7 @@ export declare 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]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -3293,7 +3090,8 @@ export declare namespace DesignStopResponse {
                 crop_residues: Array<number> | 'all';
                 /**
                  * 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>;
                 /**
@@ -3301,6 +3099,11 @@ export declare 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>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -3347,11 +3150,19 @@ export declare 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>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -3372,10 +3183,10 @@ export declare namespace DesignStopResponse {
                  * Post-translational modifications. Optional; defaults to an empty list when
                  * omitted.
                  */
-                modifications?: Array<ProteinEntityResponse.CcdModificationResponse | ProteinEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<ProteinEntityResponse.Modification>;
             }
             namespace ProteinEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -3387,17 +3198,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface RnaEntityResponse {
                 /**
@@ -3416,10 +3216,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<RnaEntityResponse.CcdModificationResponse | RnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<RnaEntityResponse.Modification>;
             }
             namespace RnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -3431,17 +3231,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface DnaEntityResponse {
                 /**
@@ -3460,10 +3249,10 @@ export declare namespace DesignStopResponse {
                 /**
                  * Chemical modifications. Optional; defaults to an empty list when omitted.
                  */
-                modifications?: Array<DnaEntityResponse.CcdModificationResponse | DnaEntityResponse.SmilesModificationResponse>;
+                modifications?: Array<DnaEntityResponse.Modification>;
             }
             namespace DnaEntityResponse {
-                interface CcdModificationResponse {
+                interface Modification {
                     /**
                      * 0-based index of the residue to modify
                      */
@@ -3475,17 +3264,6 @@ export declare namespace DesignStopResponse {
                      */
                     value: string;
                 }
-                interface SmilesModificationResponse {
-                    /**
-                     * 0-based index of the residue to modify
-                     */
-                    residue_index: number;
-                    type: 'smiles';
-                    /**
-                     * SMILES string for the modification
-                     */
-                    value: string;
-                }
             }
             interface LigandCcdEntityResponse {
                 /**
@@ -3963,10 +3741,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<DesignedProteinEntity.CcdModification | DesignedProteinEntity.SmilesModification>;
+            modifications?: Array<DesignedProteinEntity.Modification>;
         }
         namespace DesignedProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -3978,17 +3756,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         /**
          * A fixed protein entity whose sequence is not redesigned.
@@ -4010,10 +3777,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedProteinEntity.CcdModification | FixedProteinEntity.SmilesModification>;
+            modifications?: Array<FixedProteinEntity.Modification>;
         }
         namespace FixedProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4025,17 +3792,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedRnaEntity {
             /**
@@ -4054,10 +3810,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedRnaEntity.CcdModification | FixedRnaEntity.SmilesModification>;
+            modifications?: Array<FixedRnaEntity.Modification>;
         }
         namespace FixedRnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4069,17 +3825,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedDnaEntity {
             /**
@@ -4098,10 +3843,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedDnaEntity.CcdModification | FixedDnaEntity.SmilesModification>;
+            modifications?: Array<FixedDnaEntity.Modification>;
         }
         namespace FixedDnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4113,17 +3858,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedLigandSmilesEntity {
             /**
@@ -4301,7 +4035,7 @@ export declare 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]: StructureTemplateTarget.StructureTemplateTargetPolymerChainSpec | StructureTemplateTarget.StructureTemplateTargetLigandChainSpec;
@@ -4327,7 +4061,8 @@ export declare namespace DesignEstimateCostParams {
             crop_residues: Array<number> | 'all';
             /**
              * 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>;
             /**
@@ -4335,6 +4070,11 @@ export declare 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>;
         }
         /**
          * Per-chain specification for a ligand chain in a structure template target. The
@@ -4386,11 +4126,19 @@ export declare 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>;
+        };
     }
     namespace NoTemplateTarget {
         interface ProteinEntity {
@@ -4411,10 +4159,10 @@ export declare namespace DesignEstimateCostParams {
              * Post-translational modifications. Optional; defaults to an empty list when
              * omitted.
              */
-            modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+            modifications?: Array<ProteinEntity.Modification>;
         }
         namespace ProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4426,17 +4174,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface RnaEntity {
             /**
@@ -4455,10 +4192,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Chemical modifications. Optional; defaults to an empty list when omitted.
              */
-            modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+            modifications?: Array<RnaEntity.Modification>;
         }
         namespace RnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4470,17 +4207,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface DnaEntity {
             /**
@@ -4499,10 +4225,10 @@ export declare namespace DesignEstimateCostParams {
             /**
              * Chemical modifications. Optional; defaults to an empty list when omitted.
              */
-            modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+            modifications?: Array<DnaEntity.Modification>;
         }
         namespace DnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4514,17 +4240,6 @@ export declare namespace DesignEstimateCostParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface LigandCcdEntity {
             /**
@@ -4979,10 +4694,10 @@ export declare namespace DesignStartParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<DesignedProteinEntity.CcdModification | DesignedProteinEntity.SmilesModification>;
+            modifications?: Array<DesignedProteinEntity.Modification>;
         }
         namespace DesignedProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -4994,17 +4709,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         /**
          * A fixed protein entity whose sequence is not redesigned.
@@ -5026,10 +4730,10 @@ export declare namespace DesignStartParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedProteinEntity.CcdModification | FixedProteinEntity.SmilesModification>;
+            modifications?: Array<FixedProteinEntity.Modification>;
         }
         namespace FixedProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5041,17 +4745,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedRnaEntity {
             /**
@@ -5070,10 +4763,10 @@ export declare namespace DesignStartParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedRnaEntity.CcdModification | FixedRnaEntity.SmilesModification>;
+            modifications?: Array<FixedRnaEntity.Modification>;
         }
         namespace FixedRnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5085,17 +4778,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedDnaEntity {
             /**
@@ -5114,10 +4796,10 @@ export declare namespace DesignStartParams {
             /**
              * Optional polymer modifications. Defaults to [] when omitted.
              */
-            modifications?: Array<FixedDnaEntity.CcdModification | FixedDnaEntity.SmilesModification>;
+            modifications?: Array<FixedDnaEntity.Modification>;
         }
         namespace FixedDnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5129,17 +4811,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface FixedLigandSmilesEntity {
             /**
@@ -5317,7 +4988,7 @@ export declare 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]: StructureTemplateTarget.StructureTemplateTargetPolymerChainSpec | StructureTemplateTarget.StructureTemplateTargetLigandChainSpec;
@@ -5343,7 +5014,8 @@ export declare namespace DesignStartParams {
             crop_residues: Array<number> | 'all';
             /**
              * 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>;
             /**
@@ -5351,6 +5023,11 @@ export declare 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>;
         }
         /**
          * Per-chain specification for a ligand chain in a structure template target. The
@@ -5402,11 +5079,19 @@ export declare 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>;
+        };
     }
     namespace NoTemplateTarget {
         interface ProteinEntity {
@@ -5427,10 +5112,10 @@ export declare namespace DesignStartParams {
              * Post-translational modifications. Optional; defaults to an empty list when
              * omitted.
              */
-            modifications?: Array<ProteinEntity.CcdModification | ProteinEntity.SmilesModification>;
+            modifications?: Array<ProteinEntity.Modification>;
         }
         namespace ProteinEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5442,17 +5127,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface RnaEntity {
             /**
@@ -5471,10 +5145,10 @@ export declare namespace DesignStartParams {
             /**
              * Chemical modifications. Optional; defaults to an empty list when omitted.
              */
-            modifications?: Array<RnaEntity.CcdModification | RnaEntity.SmilesModification>;
+            modifications?: Array<RnaEntity.Modification>;
         }
         namespace RnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5486,17 +5160,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface DnaEntity {
             /**
@@ -5515,10 +5178,10 @@ export declare namespace DesignStartParams {
             /**
              * Chemical modifications. Optional; defaults to an empty list when omitted.
              */
-            modifications?: Array<DnaEntity.CcdModification | DnaEntity.SmilesModification>;
+            modifications?: Array<DnaEntity.Modification>;
         }
         namespace DnaEntity {
-            interface CcdModification {
+            interface Modification {
                 /**
                  * 0-based index of the residue to modify
                  */
@@ -5530,17 +5193,6 @@ export declare namespace DesignStartParams {
                  */
                 value: string;
             }
-            interface SmilesModification {
-                /**
-                 * 0-based index of the residue to modify
-                 */
-                residue_index: number;
-                type: 'smiles';
-                /**
-                 * SMILES string for the modification
-                 */
-                value: string;
-            }
         }
         interface LigandCcdEntity {
             /**