@cosmol-studio/cosmolkit-core-reaction 0.6.0-rc.3 → 0.6.0

package/README.md

@@ -1,4 +1,4 @@
-# COSMolKit for JavaScript and TypeScript
+# COSMolKit 0.6 for JavaScript and TypeScript
 
 WebAssembly bindings to the public Rust API, with generated TypeScript declarations.
 

package/cosmolkit_wasm.d.ts

@@ -62,7 +62,8 @@ export interface BatchQueryParamsOptions {
      */
     progressBar?: BatchQueryParams["progressBar"];
     /**
-     * One notification after every completed input row, including invalid rows.
+     * One notification after every completed query row. Retained input errors
+     * reject the query before any notification.
      */
     progressCallback?: BatchQueryParams["progressCallback"];
 }
@@ -1564,7 +1565,8 @@ export class BatchParams {
 }
 
 /**
- * Runtime overrides for ordered read results; newly failed queries always raise.
+ * Runtime overrides for ordered read results; retained failures reject a query
+ * before computation. New query failures also raise.
  */
 export class BatchQueryParams {
     free(): void;
@@ -1582,7 +1584,8 @@ export class BatchQueryParams {
     get progressBar(): boolean | undefined;
     set progressBar(value: BoolInput | null | undefined);
     /**
-     * One notification after every completed input row, including invalid rows.
+     * One notification after every completed query row. Retained input errors
+     * reject the query before any notification.
      */
     get progressCallback(): (() => void) | undefined;
     set progressCallback(value: (() => void) | null | undefined);
@@ -2401,8 +2404,8 @@ export class CxSmilesFields {
     [Symbol.dispose](): void;
     contains(other: CxSmilesFields): boolean;
     union(other: CxSmilesFields): CxSmilesFields;
-    static readonly ALL: CxSmilesFields;
     static readonly ALL_BUT_COORDS: CxSmilesFields;
+    static readonly ALL: CxSmilesFields;
     static readonly ATOM_LABELS: CxSmilesFields;
     static readonly ATOM_PROPS: CxSmilesFields;
     static readonly BOND_ATROPISOMER: CxSmilesFields;
@@ -3835,10 +3838,10 @@ export class Molecule {
     add3dConformer_(coordinates: Coordinates3D, params?: Coordinate3DInputParams | Coordinate3DInputParamsOptions | null): number;
     addHydrogensWithParams_(params: AddHsParams | AddHsParamsOptions): void;
     addHydrogens_(params?: AddHsParams | AddHsParamsOptions | null): void;
-    applyReactionWithParams(reaction: Reaction, params: ReactionApplyParams | ReactionApplyParamsOptions): ReactionApplyResult;
     applyReactionWithParams_(reaction: Reaction, params: ReactionApplyParams | ReactionApplyParamsOptions): boolean;
-    applyReaction(reaction: Reaction, params?: ReactionApplyParams | ReactionApplyParamsOptions | null): ReactionApplyResult;
+    applyReactionWithParams(reaction: Reaction, params: ReactionApplyParams | ReactionApplyParamsOptions): ReactionApplyResult;
     applyReaction_(reaction: Reaction, params?: ReactionApplyParams | ReactionApplyParamsOptions | null): boolean;
+    applyReaction(reaction: Reaction, params?: ReactionApplyParams | ReactionApplyParamsOptions | null): ReactionApplyResult;
     assignAromaticityWithParams_(params: AromaticityParams | AromaticityParamsOptions): void;
     assignAromaticity_(params?: AromaticityParams | AromaticityParamsOptions | null): void;
     assignChiralTagsFromStructureWithParams_(params: StructureTagParams | StructureTagParamsOptions): void;
@@ -3860,6 +3863,11 @@ export class Molecule {
     atomPropertyString(atom: IndexInput, key: TextInput): string | undefined;
     atomPropertyUint(atom: IndexInput, key: TextInput): number | undefined;
     atom(index: IndexInput): MoleculeAtom | undefined;
+    /**
+     * Return an independent Uint8Array of atomic numbers in atom-index order.
+     * No atom handles are created; dummy atoms are zero. No free() is needed.
+     */
+    atomicNumbers(): Uint8Array;
     bondPropertyString(bond: IndexInput, key: TextInput): string | undefined;
     bond(index: IndexInput): Bond | undefined;
     clear3dConformers_(): void;
@@ -3899,10 +3907,10 @@ export class Molecule {
     reactionProducts(reaction: Reaction, reactant_template: IndexInput, params?: ReactionSingleRunParams | ReactionSingleRunParamsOptions | null): ReadonlyArray<ReadonlyArray<Molecule>>;
     removeHydrogensWithParams_(params: RemoveHsParams | RemoveHsParamsOptions): void;
     removeHydrogens_(params?: RemoveHsParams | RemoveHsParamsOptions | null): void;
-    sanitizeWithParams(params: SanitizeParams | SanitizeParamsOptions): Molecule;
     sanitizeWithParams_(params: SanitizeParams | SanitizeParamsOptions): void;
-    sanitize(params?: SanitizeParams | SanitizeParamsOptions | null): Molecule;
+    sanitizeWithParams(params: SanitizeParams | SanitizeParamsOptions): Molecule;
     sanitize_(params?: SanitizeParams | SanitizeParamsOptions | null): void;
+    sanitize(params?: SanitizeParams | SanitizeParamsOptions | null): Molecule;
     set2dCoordinatesWithParams_(coordinates: CoordinateRows, params: Coordinate2DInputParams | Coordinate2DInputParamsOptions): void;
     set2dCoordinates_(coordinates: CoordinateRows, params?: Coordinate2DInputParams | Coordinate2DInputParamsOptions | null): void;
     set3dCoordinatesWithParams_(coordinates: Coordinates3D, params: Replace3DCoordinatesParams | Replace3DCoordinatesParamsOptions): void;
@@ -6143,10 +6151,10 @@ export class SanitizeOperations {
     union(other: SanitizeOperations): SanitizeOperations;
     static readonly ADJUST_HS: SanitizeOperations;
     static readonly ALL: SanitizeOperations;
-    static readonly CLEANUP: SanitizeOperations;
     static readonly CLEANUP_ATROPISOMERS: SanitizeOperations;
     static readonly CLEANUP_CHIRALITY: SanitizeOperations;
     static readonly CLEANUP_ORGANOMETALLICS: SanitizeOperations;
+    static readonly CLEANUP: SanitizeOperations;
     static readonly FIND_RADICALS: SanitizeOperations;
     static readonly KEKULIZE: SanitizeOperations;
     static readonly NONE: SanitizeOperations;
@@ -9406,6 +9414,7 @@ export interface InitOutput {
     readonly molecule_atomPropertyString: (a: number, b: number, c: number, d: number) => void;
     readonly molecule_atomPropertyStringVector: (a: number, b: number, c: number, d: number) => void;
     readonly molecule_atomPropertyUint: (a: number, b: number, c: number, d: number) => void;
+    readonly molecule_atomicNumbers: (a: number, b: number) => void;
     readonly molecule_atoms: (a: number, b: number) => void;
     readonly molecule_bond: (a: number, b: number, c: number) => void;
     readonly molecule_bondPropertyString: (a: number, b: number, c: number, d: number) => void;
@@ -11158,46 +11167,46 @@ export interface InitOutput {
     readonly xyzwriteparams_set_conformerId: (a: number, b: number, c: number) => void;
     readonly xyzwriteparams_set_precision: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2737: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2740: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2738: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2741: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2742: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2743: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2744: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2745: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2750: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2746: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2751: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2752: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2753: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2755: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2759: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2761: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2754: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2756: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2760: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2762: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2763: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2765: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2764: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2766: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2767: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2769: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2768: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2770: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2771: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2772: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2775: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2773: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2776: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2777: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2778: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2779: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2788: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2780: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2789: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2790: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2792: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2794: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2791: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2793: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2795: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2796: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_580_2798: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2797: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2799: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2800: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2801: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_2802: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_580_2803: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_32: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_34: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_580_35: (a: number, b: number, c: number) => void;
@@ -11206,19 +11215,19 @@ export interface InitOutput {
     readonly __wasm_bindgen_func_elem_587: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_589: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_591: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_591_2027: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_591_2028: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_597: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_601: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_603: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_603_2774: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_603_2793: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_603_2797: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_603_2803: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_603_2775: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_603_2794: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_603_2798: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_603_2804: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_605: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_610: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_610_2764: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_610_2773: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_610_2784: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_610_2765: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_610_2774: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_610_2785: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_614: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_618: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_620: (a: number, b: number, c: number) => void;