@cosmol-studio/cosmolkit-core 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"];
 }
@@ -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;
@@ -2683,6 +2686,7 @@ export class LigandRef {
     static Atom(atom: IndexInput): LigandRef;
     constructor(atom?: IndexInput | null);
     static readonly ImplicitHydrogen: LigandRef;
+    static readonly LonePair: LigandRef;
     readonly atomId: number | undefined;
 }
 
@@ -3148,6 +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;
@@ -3182,10 +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;
@@ -3203,7 +3212,7 @@ 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;
@@ -4750,10 +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;
@@ -5709,9 +5718,9 @@ 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 {
@@ -7197,6 +7206,7 @@ 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;
@@ -7324,6 +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;
@@ -7388,7 +7399,7 @@ 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;
@@ -8640,32 +8651,32 @@ 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_468: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2161: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2164: (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_2163: (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_2171: (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_2167: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_468_2168: (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_2176: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_468_2181: (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_2178: (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_2187: (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_2185: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_468_2186: (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_2192: (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_2200: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_468_2202: (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_2205: (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_2211: (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;
@@ -8673,18 +8684,18 @@ export interface InitOutput {
     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_1580: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_479_1582: (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_2186: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2201: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2204: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_489_2210: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_489_2188: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_489_2203: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_489_2206: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_489_2212: (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_2185: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_494_2195: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_494_2187: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_494_2197: (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;