@cosmol-studio/cosmolkit-core 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"];
 }
@@ -1233,7 +1234,8 @@ 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;
@@ -1251,7 +1253,8 @@ 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);
@@ -1999,8 +2002,8 @@ 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;
@@ -3149,6 +3152,11 @@ 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;
@@ -3183,10 +3191,10 @@ 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;
@@ -4751,10 +4759,10 @@ 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;
@@ -7326,6 +7334,7 @@ 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;
@@ -8641,64 +8650,64 @@ 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_468: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2162: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2165: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2166: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2167: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2172: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2173: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2174: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2175: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2177: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2182: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2183: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2184: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2185: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2188: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2189: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2190: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2191: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_22: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2201: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2203: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2204: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2206: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2207: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2208: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2209: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2210: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_24: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_25: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_26: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_473: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_475: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_477: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_479: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_479_1581: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_483: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_487: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2187: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2202: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2205: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2211: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_491: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_494: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_494_2186: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_494_2196: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_496: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_500: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_502: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_504: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_506: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_510: (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_514: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_516: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_518: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_520: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_524: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2163: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2166: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2167: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2168: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2173: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2174: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2175: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2176: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2178: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2183: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2184: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2185: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2186: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2189: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2190: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2191: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2192: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_22: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2202: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2204: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2205: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2207: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2208: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2209: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2210: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_2211: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_24: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_25: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_469_26: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_474: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_476: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_478: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_480: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_480_1582: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_484: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_488: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_490: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_490_2188: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_490_2203: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_490_2206: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_490_2212: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_492: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_495: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_495_2187: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_495_2197: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_497: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_501: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_503: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_505: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_507: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_511: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_513: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_515: (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_525: (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;