@cosmol-studio/cosmolkit-core-search 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"];
 }
@@ -1461,7 +1462,8 @@ 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;
@@ -1479,7 +1481,8 @@ 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);
@@ -2280,8 +2283,8 @@ 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;
@@ -3735,6 +3738,11 @@ 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;
@@ -3771,10 +3779,10 @@ export class Molecule {
     property(key: TextInput): PropertyValue | undefined;
     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;
@@ -5410,10 +5418,10 @@ 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;
@@ -8626,6 +8634,7 @@ 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;
@@ -10135,71 +10144,71 @@ export interface InitOutput {
     readonly xyzwriteparams_precision: (a: number, b: number) => void;
     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_537: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2485: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2488: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2489: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2490: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2491: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2492: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2493: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2498: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2499: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2500: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2501: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2503: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2508: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2509: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2510: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2511: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2514: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2515: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2516: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2517: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2518: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2527: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2528: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2529: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2531: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2533: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2534: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2536: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2537: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2538: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2539: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_2540: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_29: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_31: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_32: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_537_33: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_542: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2486: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2489: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2490: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2491: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2492: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2493: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2494: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2499: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2500: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2501: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2502: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2504: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2509: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2510: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2511: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2512: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2515: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2516: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2517: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2518: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2519: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2528: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2529: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2530: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2532: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2534: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2535: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2537: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2538: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2539: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2540: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_2541: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_29: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_31: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_32: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_539_33: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_544: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_546: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_548: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_548_1857: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_552: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_556: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_550: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_550_1858: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_554: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_558: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_558_2513: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_558_2532: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_558_2535: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_558_2541: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_560: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_563: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_563_2512: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_563_2523: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_567: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_571: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_560_2514: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_560_2533: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_560_2536: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_560_2542: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_562: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_565: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_565_2513: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_565_2524: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_569: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_573: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_575: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_577: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_581: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_579: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_583: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_585: (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_587: (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_593: (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_595: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_599: (a: number, b: number, c: number) => void;
     readonly __wbindgen_export: (a: number, b: number) => number;
     readonly __wbindgen_export2: (a: number, b: number, c: number, d: number) => number;
     readonly __wbindgen_export3: (a: number) => void;