@cosmol-studio/cosmolkit-core-analysis 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

@@ -187,7 +187,8 @@ 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"];
 }
@@ -2451,7 +2452,8 @@ 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;
@@ -2469,7 +2471,8 @@ 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);
@@ -3398,8 +3401,8 @@ 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;
@@ -5366,6 +5369,11 @@ 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;
     chi0NWithParams(force: BoolInput): number;
@@ -5531,10 +5539,10 @@ export class Molecule {
     qed(): number;
     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;
@@ -7662,10 +7670,10 @@ 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;
@@ -11992,6 +12000,7 @@ 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;
@@ -14083,55 +14092,55 @@ 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_708: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3469: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3472: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3470: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3473: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3474: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3475: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3476: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3477: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3482: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3478: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3483: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3484: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3485: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3486: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3487: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3488: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3490: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3493: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3489: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3491: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3494: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3499: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3495: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3500: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3501: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3502: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3505: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3503: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3506: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3507: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3508: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3509: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3510: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3511: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3515: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3517: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3512: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3516: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3518: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3520: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3531: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3519: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3521: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3532: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3533: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3534: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3535: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3536: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3538: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3537: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3539: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3541: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3540: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3542: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3544: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3543: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3545: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_708_3547: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3546: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3548: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3549: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3550: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_3551: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_708_3552: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_40: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_42: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_708_43: (a: number, b: number, c: number) => void;
@@ -14140,20 +14149,20 @@ export interface InitOutput {
     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;
-    readonly __wasm_bindgen_func_elem_719_2579: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_719_2580: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_725: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_729: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_731: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3504: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3516: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3540: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3543: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3546: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_731_3552: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3505: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3517: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3541: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3544: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3547: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_731_3553: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_733: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_736: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_736_3503: (a: number, b: number, c: number) => void;
-    readonly __wasm_bindgen_func_elem_736_3524: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_736_3504: (a: number, b: number, c: number) => void;
+    readonly __wasm_bindgen_func_elem_736_3525: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_740: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_744: (a: number, b: number, c: number) => void;
     readonly __wasm_bindgen_func_elem_746: (a: number, b: number, c: number) => void;