@cosmol-studio/cosmolkit-core-bio 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"];
 }
@@ -1547,7 +1548,8 @@ 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;
@@ -1565,7 +1567,8 @@ 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);
@@ -3911,8 +3914,8 @@ 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;
@@ -5695,6 +5698,11 @@ 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;
@@ -5733,10 +5741,10 @@ 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;
@@ -8495,10 +8503,10 @@ 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;
@@ -12172,6 +12180,7 @@ 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;
@@ -13760,37 +13769,37 @@ 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_700: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3318: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3321: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3319: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3322: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3323: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3325: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3324: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3326: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3330: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3343: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3348: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3327: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3331: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3344: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3349: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3350: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3351: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3353: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3352: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3354: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3363: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3355: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3364: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3365: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3366: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3369: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3367: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3370: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3371: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3372: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3402: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3409: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3411: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3373: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3403: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3410: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3412: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3414: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3416: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3413: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3415: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3417: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3418: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_3419: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_700_3420: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_37: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_39: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_700_40: (a: number, b: number, c: number) => void;
@@ -13800,7 +13809,7 @@ export interface InitOutput {
     readonly __wasm_bindgen_func_elem_709: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_711: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_713: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_713_2426: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_713_2427: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_715: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_717: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_719: (a: number, b: number, c: number) => void;
@@ -13819,18 +13828,18 @@ export interface InitOutput {
     readonly __wasm_bindgen_func_elem_747: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_751: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_753: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3368: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3385: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3410: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3413: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3420: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_753_3369: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_753_3386: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_753_3411: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_753_3414: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_753_3421: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_754: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_757: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3367: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3386: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3388: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3397: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3405: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_757_3368: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_757_3387: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_757_3389: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_757_3398: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_757_3406: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_763: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_765: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_767: (a: number, b: number, c: number) => void;
@@ -13849,9 +13858,9 @@ export interface InitOutput {
     readonly __wasm_bindgen_func_elem_799: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_801: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_803: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_803_3384: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_803_3385: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_804: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_804_3401: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_804_3402: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_805: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_807: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_809: (a: number, b: number, c: number) => void;