boltz-api 0.30.4 → 0.35.3

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

@@ -229,7 +229,7 @@ export declare namespace LibraryScreenRetrieveResponse {
              * Chains selected from the uploaded structure, keyed by chain ID. Only chains
              * listed here are included in the engine run — any chains omitted from this
              * mapping are ignored. Each value defines which residues to keep, which are
-             * epitope residues, and which are flexible.
+             * epitope residues, which are non-binding residues, and which are flexible.
              */
             chain_selection: {
                 [key: string]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -251,7 +251,8 @@ export declare namespace LibraryScreenRetrieveResponse {
                 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>;
                 /**
@@ -259,6 +260,11 @@ export declare namespace LibraryScreenRetrieveResponse {
                  * regions). All indices must be present in crop_residues.
                  */
                 flexible_residues?: Array<number>;
+                /**
+                 * 0-indexed residue indices where binder contact should be discouraged. All
+                 * indices must be present in crop_residues and must not overlap epitope_residues.
+                 */
+                non_binding_residues?: Array<number>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -305,11 +311,19 @@ export declare namespace LibraryScreenRetrieveResponse {
             /**
              * Polymer chain residues where binder contact is desired (the epitope). Each key
              * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-             * indices.
+             * indices. Residues must not overlap non_binding_residues on the same chain.
              */
             epitope_residues?: {
                 [key: string]: Array<number>;
             };
+            /**
+             * Polymer chain residues where binder contact should be discouraged. Each key is a
+             * chain ID of a polymer entity, each value is an array of 0-indexed residue
+             * indices. Residues must not overlap epitope_residues on the same chain.
+             */
+            non_binding_residues?: {
+                [key: string]: Array<number>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -330,10 +344,10 @@ export declare namespace LibraryScreenRetrieveResponse {
                  * 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
                      */
@@ -345,17 +359,6 @@ export declare namespace LibraryScreenRetrieveResponse {
                      */
                     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 {
                 /**
@@ -374,10 +377,10 @@ export declare namespace LibraryScreenRetrieveResponse {
                 /**
                  * 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
                      */
@@ -389,17 +392,6 @@ export declare namespace LibraryScreenRetrieveResponse {
                      */
                     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 {
                 /**
@@ -418,10 +410,10 @@ export declare namespace LibraryScreenRetrieveResponse {
                 /**
                  * 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
                      */
@@ -433,17 +425,6 @@ export declare namespace LibraryScreenRetrieveResponse {
                      */
                     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 {
                 /**
@@ -870,10 +851,10 @@ export declare namespace LibraryScreenListResultsResponse {
          * 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
              */
@@ -885,17 +866,6 @@ export declare namespace LibraryScreenListResultsResponse {
              */
             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 {
         /**
@@ -914,10 +884,10 @@ export declare namespace LibraryScreenListResultsResponse {
         /**
          * 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
              */
@@ -929,17 +899,6 @@ export declare namespace LibraryScreenListResultsResponse {
              */
             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 {
         /**
@@ -958,10 +917,10 @@ export declare namespace LibraryScreenListResultsResponse {
         /**
          * 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
              */
@@ -973,17 +932,6 @@ export declare namespace LibraryScreenListResultsResponse {
              */
             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 {
         /**
@@ -1146,7 +1094,7 @@ export declare namespace LibraryScreenStartResponse {
              * Chains selected from the uploaded structure, keyed by chain ID. Only chains
              * listed here are included in the engine run — any chains omitted from this
              * mapping are ignored. Each value defines which residues to keep, which are
-             * epitope residues, and which are flexible.
+             * epitope residues, which are non-binding residues, and which are flexible.
              */
             chain_selection: {
                 [key: string]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -1168,7 +1116,8 @@ export declare namespace LibraryScreenStartResponse {
                 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>;
                 /**
@@ -1176,6 +1125,11 @@ export declare namespace LibraryScreenStartResponse {
                  * regions). All indices must be present in crop_residues.
                  */
                 flexible_residues?: Array<number>;
+                /**
+                 * 0-indexed residue indices where binder contact should be discouraged. All
+                 * indices must be present in crop_residues and must not overlap epitope_residues.
+                 */
+                non_binding_residues?: Array<number>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -1222,11 +1176,19 @@ export declare namespace LibraryScreenStartResponse {
             /**
              * Polymer chain residues where binder contact is desired (the epitope). Each key
              * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-             * indices.
+             * indices. Residues must not overlap non_binding_residues on the same chain.
              */
             epitope_residues?: {
                 [key: string]: Array<number>;
             };
+            /**
+             * Polymer chain residues where binder contact should be discouraged. Each key is a
+             * chain ID of a polymer entity, each value is an array of 0-indexed residue
+             * indices. Residues must not overlap epitope_residues on the same chain.
+             */
+            non_binding_residues?: {
+                [key: string]: Array<number>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -1247,10 +1209,10 @@ export declare namespace LibraryScreenStartResponse {
                  * 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
                      */
@@ -1262,17 +1224,6 @@ export declare namespace LibraryScreenStartResponse {
                      */
                     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 {
                 /**
@@ -1291,10 +1242,10 @@ export declare namespace LibraryScreenStartResponse {
                 /**
                  * 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
                      */
@@ -1306,17 +1257,6 @@ export declare namespace LibraryScreenStartResponse {
                      */
                     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 {
                 /**
@@ -1335,10 +1275,10 @@ export declare namespace LibraryScreenStartResponse {
                 /**
                  * 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
                      */
@@ -1350,17 +1290,6 @@ export declare namespace LibraryScreenStartResponse {
                      */
                     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 {
                 /**
@@ -1683,7 +1612,7 @@ export declare namespace LibraryScreenStopResponse {
              * Chains selected from the uploaded structure, keyed by chain ID. Only chains
              * listed here are included in the engine run — any chains omitted from this
              * mapping are ignored. Each value defines which residues to keep, which are
-             * epitope residues, and which are flexible.
+             * epitope residues, which are non-binding residues, and which are flexible.
              */
             chain_selection: {
                 [key: string]: StructureTemplateTargetResponse.StructureTemplateTargetPolymerChainSpec | StructureTemplateTargetResponse.StructureTemplateTargetLigandChainSpec;
@@ -1705,7 +1634,8 @@ export declare namespace LibraryScreenStopResponse {
                 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>;
                 /**
@@ -1713,6 +1643,11 @@ export declare namespace LibraryScreenStopResponse {
                  * regions). All indices must be present in crop_residues.
                  */
                 flexible_residues?: Array<number>;
+                /**
+                 * 0-indexed residue indices where binder contact should be discouraged. All
+                 * indices must be present in crop_residues and must not overlap epitope_residues.
+                 */
+                non_binding_residues?: Array<number>;
             }
             /**
              * Per-chain specification for a ligand chain in a structure template target. The
@@ -1759,11 +1694,19 @@ export declare namespace LibraryScreenStopResponse {
             /**
              * Polymer chain residues where binder contact is desired (the epitope). Each key
              * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-             * indices.
+             * indices. Residues must not overlap non_binding_residues on the same chain.
              */
             epitope_residues?: {
                 [key: string]: Array<number>;
             };
+            /**
+             * Polymer chain residues where binder contact should be discouraged. Each key is a
+             * chain ID of a polymer entity, each value is an array of 0-indexed residue
+             * indices. Residues must not overlap epitope_residues on the same chain.
+             */
+            non_binding_residues?: {
+                [key: string]: Array<number>;
+            };
         }
         namespace NoTemplateTargetResponse {
             interface ProteinEntityResponse {
@@ -1784,10 +1727,10 @@ export declare namespace LibraryScreenStopResponse {
                  * 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
                      */
@@ -1799,17 +1742,6 @@ export declare namespace LibraryScreenStopResponse {
                      */
                     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 {
                 /**
@@ -1828,10 +1760,10 @@ export declare namespace LibraryScreenStopResponse {
                 /**
                  * 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
                      */
@@ -1843,17 +1775,6 @@ export declare namespace LibraryScreenStopResponse {
                      */
                     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 {
                 /**
@@ -1872,10 +1793,10 @@ export declare namespace LibraryScreenStopResponse {
                 /**
                  * 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
                      */
@@ -1887,17 +1808,6 @@ export declare namespace LibraryScreenStopResponse {
                      */
                     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 {
                 /**
@@ -2196,10 +2106,10 @@ export declare namespace LibraryScreenEstimateCostParams {
              * 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
                  */
@@ -2211,17 +2121,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2240,10 +2139,10 @@ export declare namespace LibraryScreenEstimateCostParams {
             /**
              * 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
                  */
@@ -2255,17 +2154,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2284,10 +2172,10 @@ export declare namespace LibraryScreenEstimateCostParams {
             /**
              * 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
                  */
@@ -2299,17 +2187,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2343,7 +2220,7 @@ export declare namespace LibraryScreenEstimateCostParams {
          * Chains selected from the uploaded structure, keyed by chain ID. Only chains
          * listed here are included in the engine run — any chains omitted from this
          * mapping are ignored. Each value defines which residues to keep, which are
-         * epitope residues, and which are flexible.
+         * epitope residues, which are non-binding residues, and which are flexible.
          */
         chain_selection: {
             [key: string]: StructureTemplateTarget.StructureTemplateTargetPolymerChainSpec | StructureTemplateTarget.StructureTemplateTargetLigandChainSpec;
@@ -2369,7 +2246,8 @@ export declare namespace LibraryScreenEstimateCostParams {
             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>;
             /**
@@ -2377,6 +2255,11 @@ export declare namespace LibraryScreenEstimateCostParams {
              * regions). All indices must be present in crop_residues.
              */
             flexible_residues?: Array<number>;
+            /**
+             * 0-indexed residue indices where binder contact should be discouraged. All
+             * indices must be present in crop_residues and must not overlap epitope_residues.
+             */
+            non_binding_residues?: Array<number>;
         }
         /**
          * Per-chain specification for a ligand chain in a structure template target. The
@@ -2428,11 +2311,19 @@ export declare namespace LibraryScreenEstimateCostParams {
         /**
          * Polymer chain residues where binder contact is desired (the epitope). Each key
          * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-         * indices.
+         * indices. Residues must not overlap non_binding_residues on the same chain.
          */
         epitope_residues?: {
             [key: string]: Array<number>;
         };
+        /**
+         * Polymer chain residues where binder contact should be discouraged. Each key is a
+         * chain ID of a polymer entity, each value is an array of 0-indexed residue
+         * indices. Residues must not overlap epitope_residues on the same chain.
+         */
+        non_binding_residues?: {
+            [key: string]: Array<number>;
+        };
     }
     namespace NoTemplateTarget {
         interface ProteinEntity {
@@ -2453,10 +2344,10 @@ export declare namespace LibraryScreenEstimateCostParams {
              * 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
                  */
@@ -2468,17 +2359,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2497,10 +2377,10 @@ export declare namespace LibraryScreenEstimateCostParams {
             /**
              * 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
                  */
@@ -2512,17 +2392,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2541,10 +2410,10 @@ export declare namespace LibraryScreenEstimateCostParams {
             /**
              * 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
                  */
@@ -2556,17 +2425,6 @@ export declare namespace LibraryScreenEstimateCostParams {
                  */
                 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 {
             /**
@@ -2838,10 +2696,10 @@ export declare namespace LibraryScreenStartParams {
              * 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
                  */
@@ -2853,17 +2711,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**
@@ -2882,10 +2729,10 @@ export declare namespace LibraryScreenStartParams {
             /**
              * 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
                  */
@@ -2897,17 +2744,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**
@@ -2926,10 +2762,10 @@ export declare namespace LibraryScreenStartParams {
             /**
              * 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
                  */
@@ -2941,17 +2777,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**
@@ -2985,7 +2810,7 @@ export declare namespace LibraryScreenStartParams {
          * Chains selected from the uploaded structure, keyed by chain ID. Only chains
          * listed here are included in the engine run — any chains omitted from this
          * mapping are ignored. Each value defines which residues to keep, which are
-         * epitope residues, and which are flexible.
+         * epitope residues, which are non-binding residues, and which are flexible.
          */
         chain_selection: {
             [key: string]: StructureTemplateTarget.StructureTemplateTargetPolymerChainSpec | StructureTemplateTarget.StructureTemplateTargetLigandChainSpec;
@@ -3011,7 +2836,8 @@ export declare namespace LibraryScreenStartParams {
             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>;
             /**
@@ -3019,6 +2845,11 @@ export declare namespace LibraryScreenStartParams {
              * regions). All indices must be present in crop_residues.
              */
             flexible_residues?: Array<number>;
+            /**
+             * 0-indexed residue indices where binder contact should be discouraged. All
+             * indices must be present in crop_residues and must not overlap epitope_residues.
+             */
+            non_binding_residues?: Array<number>;
         }
         /**
          * Per-chain specification for a ligand chain in a structure template target. The
@@ -3070,11 +2901,19 @@ export declare namespace LibraryScreenStartParams {
         /**
          * Polymer chain residues where binder contact is desired (the epitope). Each key
          * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
-         * indices.
+         * indices. Residues must not overlap non_binding_residues on the same chain.
          */
         epitope_residues?: {
             [key: string]: Array<number>;
         };
+        /**
+         * Polymer chain residues where binder contact should be discouraged. Each key is a
+         * chain ID of a polymer entity, each value is an array of 0-indexed residue
+         * indices. Residues must not overlap epitope_residues on the same chain.
+         */
+        non_binding_residues?: {
+            [key: string]: Array<number>;
+        };
     }
     namespace NoTemplateTarget {
         interface ProteinEntity {
@@ -3095,10 +2934,10 @@ export declare namespace LibraryScreenStartParams {
              * 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
                  */
@@ -3110,17 +2949,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**
@@ -3139,10 +2967,10 @@ export declare namespace LibraryScreenStartParams {
             /**
              * 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
                  */
@@ -3154,17 +2982,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**
@@ -3183,10 +3000,10 @@ export declare namespace LibraryScreenStartParams {
             /**
              * 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
                  */
@@ -3198,17 +3015,6 @@ export declare namespace LibraryScreenStartParams {
                  */
                 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 {
             /**