@cosmol-studio/cosmolkit-core-depict 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"];
 }
@@ -1292,7 +1293,8 @@ 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;
@@ -1310,7 +1312,8 @@ 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);
@@ -2283,8 +2286,8 @@ 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;
@@ -3570,6 +3573,11 @@ 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;
@@ -3604,10 +3612,10 @@ 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;
@@ -5239,10 +5247,10 @@ 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;
@@ -8200,6 +8208,7 @@ 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;
@@ -9619,51 +9628,51 @@ export interface InitOutput {
     readonly xyzwriteparams_set_precision: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_22: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2383: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2386: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2384: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2387: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2388: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2389: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2394: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2390: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2395: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2396: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2397: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2399: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2398: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_24: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2404: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2400: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2405: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2406: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2407: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2410: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2408: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2411: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2412: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2413: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2423: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2425: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2414: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2424: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2426: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_512_2428: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2427: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2429: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2430: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2431: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_2432: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_512_2433: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_25: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_512_26: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_517: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_519: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_521: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_523: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_523_1763: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_523_1764: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_527: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_531: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_533: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_533_2409: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_533_2424: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_533_2427: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_533_2433: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_533_2410: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_533_2425: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_533_2428: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_533_2434: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_535: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_538: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_538_2408: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_538_2418: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_538_2409: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_538_2419: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_540: (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;