@cosmol-studio/cosmolkit-core-bio 0.6.0-rc.2 → 0.6.0-rc.4

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;
@@ -4657,6 +4660,7 @@ export class LigandRef {
     static Atom(atom: IndexInput): LigandRef;
     constructor(atom?: IndexInput | null);
     static readonly ImplicitHydrogen: LigandRef;
+    static readonly LonePair: LigandRef;
     readonly atomId: number | undefined;
 }
 
@@ -5694,6 +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;
@@ -5732,10 +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;
@@ -5753,7 +5762,7 @@ export class Molecule {
     setOnly3dConformer_(coordinates: Coordinates3D, params?: Coordinate3DInputParams | Coordinate3DInputParamsOptions | null): number;
     symmetrizedSssrWithParams(params: RingSearchParams | RingSearchParamsOptions): RingSearchResult;
     symmetrizedSssr(params?: RingSearchParams | RingSearchParamsOptions | null): RingSearchResult;
-    tetrahedralStereo(): ReadonlyArray<TetrahedralStereo>;
+    tetrahedralStereo(include_unassigned?: BoolInput | null): ReadonlyArray<TetrahedralStereo>;
     toBuilder(): MoleculeBuilder;
     toCxSmilesWithParams(params: CxSmilesWriteParams | CxSmilesWriteParamsOptions): string;
     toCxSmiles(params?: CxSmilesWriteParams | CxSmilesWriteParamsOptions | null): string;
@@ -8494,10 +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;
@@ -9453,9 +9462,9 @@ export enum TemplateAttachmentOrderErrorKind {
 export class TetrahedralStereo {
     free(): void;
     [Symbol.dispose](): void;
-    constructor(center: IndexInput, ligands: readonly [LigandRef, LigandRef, LigandRef, LigandRef]);
+    constructor(center: IndexInput, ligands?: readonly [LigandRef, LigandRef, LigandRef, LigandRef] | null);
     readonly center: number;
-    readonly ligands: readonly [LigandRef, LigandRef, LigandRef, LigandRef];
+    readonly ligands: readonly [LigandRef, LigandRef, LigandRef, LigandRef] | undefined;
 }
 
 export class TopologyBlock {
@@ -11879,6 +11888,7 @@ export interface InitOutput {
     readonly legacystereoerrordetails_valence: (a: number) => number;
     readonly ligandref_Atom: (a: number, b: number) => void;
     readonly ligandref_ImplicitHydrogen: () => number;
+    readonly ligandref_LonePair: () => number;
     readonly ligandref_atomId: (a: number) => number;
     readonly ligandref_new: (a: number, b: number) => void;
     readonly mappingvalidationerror_details: (a: number) => number;
@@ -12170,6 +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;
@@ -12238,7 +12249,7 @@ export interface InitOutput {
     readonly molecule_setOnly3dConformer_: (a: number, b: number, c: number, d: number) => void;
     readonly molecule_symmetrizedSssr: (a: number, b: number, c: number) => void;
     readonly molecule_symmetrizedSssrWithParams: (a: number, b: number, c: number) => void;
-    readonly molecule_tetrahedralStereo: (a: number, b: number) => void;
+    readonly molecule_tetrahedralStereo: (a: number, b: number, c: number) => void;
     readonly molecule_toBuilder: (a: number) => number;
     readonly molecule_toCxSmiles: (a: number, b: number, c: number) => void;
     readonly molecule_toCxSmilesWithParams: (a: number, b: number, c: number) => void;
@@ -13758,37 +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_3317: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3320: (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_3324: (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_3329: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3342: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3347: (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_3326: (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_3352: (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_3362: (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_3354: (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_3368: (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_3366: (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_3401: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_700_3408: (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_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_3411: (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_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_3416: (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;
@@ -13798,7 +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_2425: (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;
@@ -13817,18 +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_3367: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3384: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3409: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3412: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_753_3419: (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_3366: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3385: (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_3396: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_757_3404: (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;
@@ -13847,9 +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_3383: (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_3400: (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;