@cosmol-studio/cosmolkit-core-analysis 0.5.0-rc.19 → 0.5.0-rc.22

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cosmol-studio/cosmolkit-core-analysis",
-  "version": "0.5.0-rc.19",
+  "version": "0.5.0-rc.22",
   "cosmolkitPreset": "core-analysis",
-  "cosmolkitVersion": "0.5.0-rc.19",
+  "cosmolkitVersion": "0.5.0-rc.22",
   "publishConfig": {
     "access": "public",
     "tag": "rc"

package/snippets/wasm-wasm-c2a0268e5e2ee274/inline15.js

@@ -0,0 +1 @@
+export function visitMcsBondCompareParameters(v,f){try{f(v);}catch(cause){throw new TypeError('invalid McsBondCompareParameters',{cause});}}

package/snippets/wasm-wasm-c2a0268e5e2ee274/inline16.js

@@ -0,0 +1 @@
+export function visitMcsMolecule(v,f){try{f(v);}catch(cause){throw new TypeError('invalid Molecule',{cause});}}

package/snippets/wasm-wasm-c2a0268e5e2ee274/inline17.js

@@ -0,0 +1 @@
+export function visitMcsAtomCompareParameters(v,f){try{f(v);}catch(cause){throw new TypeError('invalid McsAtomCompareParameters',{cause});}}

package/snippets/wasm-wasm-c2a0268e5e2ee274/inline18.js

@@ -0,0 +1 @@
+export function visitMcsParameters(v,f){try{f(v);}catch(cause){throw new TypeError('invalid McsParameters',{cause});}}

package/snippets/wasm-wasm-c2a0268e5e2ee274/inline20.js

@@ -0,0 +1 @@
+export function visitAvalonParams(value,visit){visit(value);}

package/wasm_wasm.d.ts

@@ -1,5 +1,12 @@
 /* tslint:disable */
 /* eslint-disable */
+export interface AvalonFingerprintOptions {
+    nBits?: number;
+    isQuery?: boolean;
+    bitFlags?: number;
+}
+
+
 export interface LayeredFingerprintOptions {
     layers?: number;
     minPath?: number;
@@ -12,6 +19,40 @@ export interface LayeredFingerprintOptions {
 }
 
 
+export interface McsAtomCompareParametersOptions {
+    matchValences?: boolean;
+    matchChiralTag?: boolean;
+    matchFormalCharge?: boolean;
+    ringMatchesRingOnly?: boolean;
+    completeRingsOnly?: boolean;
+    matchIsotope?: boolean;
+    maxDistance?: number;
+}
+
+
+export interface McsBondCompareParametersOptions {
+    ringMatchesRingOnly?: boolean;
+    completeRingsOnly?: boolean;
+    matchFusedRings?: boolean;
+    matchFusedRingsStrict?: boolean;
+    matchStereo?: boolean;
+}
+
+
+export interface McsParametersOptions {
+    storeAll?: boolean;
+    maximizeBonds?: boolean;
+    threshold?: number;
+    timeout?: number;
+    verbose?: boolean;
+    atomCompareParameters?: McsAtomCompareParameters | McsAtomCompareParametersOptions;
+    bondCompareParameters?: McsBondCompareParameters | McsBondCompareParametersOptions;
+    atomComparator?: McsAtomComparator;
+    bondComparator?: McsBondComparator;
+    initialSeed?: string;
+}
+
+
 export interface SdfBatchIterator extends IterableIterator<MoleculeBatch> {}
 export interface SdfReaderBatchIterator extends IterableIterator<MoleculeBatch> {}
 
@@ -171,6 +212,44 @@ export class AtomPairsParameters {
     static version(): string;
 }
 
+export class AvalonEngineError {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    readonly domain: string;
+    readonly kind: string;
+    readonly reason: string;
+}
+
+export class AvalonFingerprintError {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    readonly cause: Error | null;
+    readonly domain: string;
+    readonly kind: string;
+    readonly message: string;
+}
+
+export class AvalonFingerprintFlags {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    bits(): number;
+    static fromBitsRetain(bits: number): AvalonFingerprintFlags;
+    toString(): string;
+}
+
+export class AvalonFingerprintParams {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor(n_bits?: number, is_query?: boolean, bit_flags?: number);
+    toString(): string;
+    bitFlags: number;
+    isQuery: boolean;
+    nBits: number;
+}
+
 export class BatchError {
     private constructor();
     free(): void;
@@ -679,6 +758,99 @@ export class MatrixError {
     readonly secondPosition: number | null;
 }
 
+export enum McsAtomComparator {
+    Any = 0,
+    Elements = 1,
+    Isotopes = 2,
+    AnyHeavyAtom = 3,
+}
+
+export class McsAtomCompareParameters {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor(match_valences?: boolean, match_chiral_tag?: boolean, match_formal_charge?: boolean, ring_matches_ring_only?: boolean, complete_rings_only?: boolean, match_isotope?: boolean, max_distance?: number);
+    get completeRingsOnly(): boolean;
+    set completeRingsOnly(value: any);
+    get matchChiralTag(): boolean;
+    set matchChiralTag(value: any);
+    get matchFormalCharge(): boolean;
+    set matchFormalCharge(value: any);
+    get matchIsotope(): boolean;
+    set matchIsotope(value: any);
+    get matchValences(): boolean;
+    set matchValences(value: any);
+    get maxDistance(): number;
+    set maxDistance(value: any);
+    get ringMatchesRingOnly(): boolean;
+    set ringMatchesRingOnly(value: any);
+}
+
+export enum McsBondComparator {
+    Any = 0,
+    Order = 1,
+    OrderExact = 2,
+}
+
+export class McsBondCompareParameters {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor(ring_matches_ring_only?: boolean, complete_rings_only?: boolean, match_fused_rings?: boolean, match_fused_rings_strict?: boolean, match_stereo?: boolean);
+    get completeRingsOnly(): boolean;
+    set completeRingsOnly(value: any);
+    get matchFusedRingsStrict(): boolean;
+    set matchFusedRingsStrict(value: any);
+    get matchFusedRings(): boolean;
+    set matchFusedRings(value: any);
+    get matchStereo(): boolean;
+    set matchStereo(value: any);
+    get ringMatchesRingOnly(): boolean;
+    set ringMatchesRingOnly(value: any);
+}
+
+export class McsError {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    readonly domain: string;
+    readonly kind: string;
+    readonly message: string;
+}
+
+export class McsParameters {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor(store_all?: boolean, maximize_bonds?: boolean, threshold?: number, timeout?: number, verbose?: boolean, atom_compare_parameters?: McsAtomCompareParameters | McsAtomCompareParametersOptions, bond_compare_parameters?: McsBondCompareParameters | McsBondCompareParametersOptions, atom_comparator?: McsAtomComparator, bond_comparator?: McsBondComparator, initial_seed?: string);
+    atomComparator: McsAtomComparator;
+    get atomCompareParameters(): McsAtomCompareParameters;
+    set atomCompareParameters(value: McsAtomCompareParameters | McsAtomCompareParametersOptions);
+    bondComparator: McsBondComparator;
+    get bondCompareParameters(): McsBondCompareParameters;
+    set bondCompareParameters(value: McsBondCompareParameters | McsBondCompareParametersOptions);
+    initialSeed: string;
+    get maximizeBonds(): boolean;
+    set maximizeBonds(value: any);
+    get storeAll(): boolean;
+    set storeAll(value: any);
+    get threshold(): number;
+    set threshold(value: any);
+    get timeout(): number;
+    set timeout(value: any);
+    get verbose(): boolean;
+    set verbose(value: any);
+}
+
+export class McsResult {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    readonly atomCount: number;
+    readonly bondCount: number;
+    readonly completed: boolean;
+    readonly degenerate: Map<string, QueryGraph>;
+    readonly query: QueryGraph | null;
+    readonly smarts: string;
+}
+
 export class Mol2PostError {
     private constructor();
     free(): void;
@@ -794,6 +966,10 @@ export class Molecule {
     assignValenceWithParams(params: ValenceParams): void;
     assignValence(): void;
     atomPropertyString(id: number, key: string): string | null;
+    /**
+     * Read typed user metadata; a missing key returns null.
+     */
+    atomProperty(atom: number, key: string): boolean | number | string | number[] | string[] | null;
     /**
      * Returns atomic numbers in molecule atom order.
      */
@@ -852,6 +1028,8 @@ export class Molecule {
     fingerprintAtomPairSparse(): SparseBitFingerprint;
     fingerprintAtomPairWithParams(params: AtomPairFingerprintParams, additional_output: FingerprintAdditionalOutput | null): Fingerprint;
     fingerprintAtomPair(): Fingerprint;
+    fingerprintAvalonWithParams(params: AvalonFingerprintParams): Fingerprint;
+    fingerprintAvalon(params?: AvalonFingerprintParams | AvalonFingerprintOptions): Fingerprint;
     fingerprintLayeredWithOutputWithParams(params: LayeredFingerprintParams): LayeredFingerprintResult;
     fingerprintLayeredWithOutput(params?: LayeredFingerprintParams | LayeredFingerprintOptions): LayeredFingerprintResult;
     fingerprintLayeredWithParams(params: LayeredFingerprintParams): Fingerprint;
@@ -896,6 +1074,10 @@ export class Molecule {
     fingerprintTopologicalWithParams(params: TopologicalFingerprintParams): Fingerprint;
     fingerprintTopological(): Fingerprint;
     fractionCsp3(): number;
+    /**
+     * Sanitized components in source order, including conformers; self is unchanged.
+     */
+    fragments(): Molecule[];
     static fromMol2WithParams(text: string, params: Mol2ReadParams): Molecule;
     static fromMol2(text: string): Molecule;
     static fromMolWithParams(text: string, params: SdfReadParams): Molecule;
@@ -919,6 +1101,10 @@ export class Molecule {
     labuteAsaContributions(): LabuteAsaContributions;
     labuteAsaWithParams(include_hydrogens: boolean, force: boolean): number;
     labuteAsa(): number;
+    /**
+     * Most atoms, last on ties. Empty input throws OperationError.
+     */
+    largestFragment(): Molecule;
     lipinskiHba(): number;
     lipinskiHbd(): number;
     molecularFormulaWithParams(separate_isotopes: boolean, abbreviate_h_isotopes: boolean): string;
@@ -928,10 +1114,22 @@ export class Molecule {
     molecularWeightWithParams(only_heavy: boolean): number;
     molecularWeight(): number;
     mqns(force?: boolean): Uint32Array;
+    /**
+     * ChemTransforms MurckoDecompose; retains ring-exocyclic double bonds.
+     */
+    murckoDecompose(): Molecule;
+    /**
+     * MolHash MurckoScaffold; returns a new molecule.
+     */
+    murckoScaffold(): Molecule;
     /**
      * Returns the molecule name, or an empty string when no name is stored.
      */
     nameOrEmpty(): string;
+    /**
+     * MolHash ExtendedMurcko; neighboring substituents become dummy atoms.
+     */
+    netScaffold(): Molecule;
     /**
      * Creates an empty molecule.
      */
@@ -1002,6 +1200,10 @@ export class Molecule {
      * Returns the first SDF data-field value with `name`, or an empty string.
      */
     sdfDataFieldOrEmpty(name: string): string;
+    /**
+     * Set metadata in place; COW keeps other molecule copies unchanged.
+     */
+    setAtomProperty(atom: number, key: string, value: boolean | number | string | number[] | string[]): void;
     slogpVsa10(): number;
     slogpVsa11(): number;
     slogpVsa12(): number;
@@ -1059,6 +1261,10 @@ export class Molecule {
     withAssignedValenceWithParams(params: ValenceParams): Molecule;
     withAssignedValence(): Molecule;
     withAtomPairAtomCode(atom_id: number, branch_subtract?: number, include_chirality?: boolean, use_legacy_stereo_perception?: boolean): AtomPairAtomCodeResult;
+    /**
+     * Return a new molecule; the receiver and its shared copies are unchanged.
+     */
+    withAtomProperty(atom: number, key: string, value: boolean | number | string | number[] | string[]): Molecule;
     withHydrogensWithParams(params: AddHsParams): Molecule;
     withHydrogens(): Molecule;
     withKekulizedBondsWithParams(params: KekulizeParams): Molecule;
@@ -1361,6 +1567,24 @@ export enum PropertyValueKind {
     StringVector = 6,
 }
 
+/**
+ * Read-only query carrier, including wildcard atomic identities.
+ */
+export class QueryAtom {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    atomMap(): number | null;
+    atomicNumber(): number;
+    explicitHydrogens(): number;
+    formalCharge(): number;
+    id(): number;
+    isAromatic(): boolean;
+    isotope(): number | null;
+    noImplicit(): boolean;
+    radicalElectrons(): number;
+}
+
 export class QueryCompileError {
     private constructor();
     free(): void;
@@ -2152,6 +2376,10 @@ export function fingerprintTopologicalQueryWithOutputWithParams(query: QueryGrap
 
 export function fingerprintTopologicalQueryWithParams(query: QueryGraph, params: TopologicalFingerprintParams): Fingerprint;
 
+export function maximumCommonSubstructure(molecules: Molecule[], params?: McsParameters | McsParametersOptions): McsResult;
+
+export function maximumCommonSubstructureWithParams(molecules: Molecule[], params: McsParameters): McsResult;
+
 export function parseSmarts(text: string): QueryGraph;
 
 export function parseSmartsWithParams(text: string, params: SmartsParseParams): QueryGraph;
@@ -2180,6 +2408,10 @@ export interface InitOutput {
     readonly __wbg_atompairparams_free: (a: number, b: number) => void;
     readonly __wbg_atompairreaderror_free: (a: number, b: number) => void;
     readonly __wbg_atompairsparameters_free: (a: number, b: number) => void;
+    readonly __wbg_avalonengineerror_free: (a: number, b: number) => void;
+    readonly __wbg_avalonfingerprinterror_free: (a: number, b: number) => void;
+    readonly __wbg_avalonfingerprintflags_free: (a: number, b: number) => void;
+    readonly __wbg_avalonfingerprintparams_free: (a: number, b: number) => void;
     readonly __wbg_batcherror_free: (a: number, b: number) => void;
     readonly __wbg_batchexportparams_free: (a: number, b: number) => void;
     readonly __wbg_batchexportreport_free: (a: number, b: number) => void;
@@ -2222,6 +2454,11 @@ export interface InitOutput {
     readonly __wbg_matcherror_free: (a: number, b: number) => void;
     readonly __wbg_matchresult_free: (a: number, b: number) => void;
     readonly __wbg_matrixerror_free: (a: number, b: number) => void;
+    readonly __wbg_mcsatomcompareparameters_free: (a: number, b: number) => void;
+    readonly __wbg_mcsbondcompareparameters_free: (a: number, b: number) => void;
+    readonly __wbg_mcserror_free: (a: number, b: number) => void;
+    readonly __wbg_mcsparameters_free: (a: number, b: number) => void;
+    readonly __wbg_mcsresult_free: (a: number, b: number) => void;
     readonly __wbg_mol2posterror_free: (a: number, b: number) => void;
     readonly __wbg_mol2readerror_free: (a: number, b: number) => void;
     readonly __wbg_mol2readparams_free: (a: number, b: number) => void;
@@ -2247,6 +2484,7 @@ export interface InitOutput {
     readonly __wbg_propertystringerror_free: (a: number, b: number) => void;
     readonly __wbg_propertyvalue_free: (a: number, b: number) => void;
     readonly __wbg_propertyvalueerror_free: (a: number, b: number) => void;
+    readonly __wbg_queryatom_free: (a: number, b: number) => void;
     readonly __wbg_querycompileerror_free: (a: number, b: number) => void;
     readonly __wbg_querygraph_free: (a: number, b: number) => void;
     readonly __wbg_removehsparams_free: (a: number, b: number) => void;
@@ -2367,6 +2605,24 @@ export interface InitOutput {
     readonly atompairsparameters_numPiBits: () => number;
     readonly atompairsparameters_numTypeBits: () => number;
     readonly atompairsparameters_version: () => [number, number];
+    readonly avalonengineerror_domain: (a: number) => [number, number];
+    readonly avalonengineerror_kind: (a: number) => [number, number];
+    readonly avalonengineerror_reason: (a: number) => [number, number];
+    readonly avalonfingerprinterror_cause: (a: number) => any;
+    readonly avalonfingerprinterror_domain: (a: number) => [number, number];
+    readonly avalonfingerprinterror_kind: (a: number) => [number, number];
+    readonly avalonfingerprinterror_message: (a: number) => [number, number];
+    readonly avalonfingerprintflags_bits: (a: number) => number;
+    readonly avalonfingerprintflags_fromBitsRetain: (a: any) => [number, number, number];
+    readonly avalonfingerprintflags_toString: (a: number) => [number, number];
+    readonly avalonfingerprintparams_bitFlags: (a: number) => number;
+    readonly avalonfingerprintparams_isQuery: (a: number) => number;
+    readonly avalonfingerprintparams_nBits: (a: number) => number;
+    readonly avalonfingerprintparams_new: (a: any, b: any, c: any) => [number, number, number];
+    readonly avalonfingerprintparams_set_bitFlags: (a: number, b: any) => [number, number];
+    readonly avalonfingerprintparams_set_isQuery: (a: number, b: any) => [number, number];
+    readonly avalonfingerprintparams_set_nBits: (a: number, b: any) => [number, number];
+    readonly avalonfingerprintparams_toString: (a: number) => [number, number];
     readonly batcherror_asDict: (a: number) => [number, number, number];
     readonly batcherror_cause: (a: number) => [number, number, number];
     readonly batcherror_index: (a: number) => number;
@@ -2607,6 +2863,64 @@ export interface InitOutput {
     readonly matrixerror_order: (a: number) => [number, number, number];
     readonly matrixerror_position: (a: number) => [number, number, number];
     readonly matrixerror_secondPosition: (a: number) => [number, number, number];
+    readonly maximumCommonSubstructure: (a: any, b: any) => [number, number, number];
+    readonly maximumCommonSubstructureWithParams: (a: any, b: number) => [number, number, number];
+    readonly mcsatomcompareparameters_completeRingsOnly: (a: number) => number;
+    readonly mcsatomcompareparameters_matchChiralTag: (a: number) => number;
+    readonly mcsatomcompareparameters_matchFormalCharge: (a: number) => number;
+    readonly mcsatomcompareparameters_matchIsotope: (a: number) => number;
+    readonly mcsatomcompareparameters_matchValences: (a: number) => number;
+    readonly mcsatomcompareparameters_maxDistance: (a: number) => number;
+    readonly mcsatomcompareparameters_new: (a: any, b: any, c: any, d: any, e: any, f: any, g: any) => [number, number, number];
+    readonly mcsatomcompareparameters_ringMatchesRingOnly: (a: number) => number;
+    readonly mcsatomcompareparameters_set_completeRingsOnly: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_matchChiralTag: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_matchFormalCharge: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_matchIsotope: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_matchValences: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_maxDistance: (a: number, b: any) => [number, number];
+    readonly mcsatomcompareparameters_set_ringMatchesRingOnly: (a: number, b: any) => [number, number];
+    readonly mcsbondcompareparameters_completeRingsOnly: (a: number) => number;
+    readonly mcsbondcompareparameters_matchFusedRings: (a: number) => number;
+    readonly mcsbondcompareparameters_matchFusedRingsStrict: (a: number) => number;
+    readonly mcsbondcompareparameters_matchStereo: (a: number) => number;
+    readonly mcsbondcompareparameters_new: (a: any, b: any, c: any, d: any, e: any) => [number, number, number];
+    readonly mcsbondcompareparameters_ringMatchesRingOnly: (a: number) => number;
+    readonly mcsbondcompareparameters_set_completeRingsOnly: (a: number, b: any) => [number, number];
+    readonly mcsbondcompareparameters_set_matchFusedRings: (a: number, b: any) => [number, number];
+    readonly mcsbondcompareparameters_set_matchFusedRingsStrict: (a: number, b: any) => [number, number];
+    readonly mcsbondcompareparameters_set_matchStereo: (a: number, b: any) => [number, number];
+    readonly mcsbondcompareparameters_set_ringMatchesRingOnly: (a: number, b: any) => [number, number];
+    readonly mcserror_domain: (a: number) => [number, number];
+    readonly mcserror_kind: (a: number) => [number, number];
+    readonly mcserror_message: (a: number) => [number, number];
+    readonly mcsparameters_atomComparator: (a: number) => number;
+    readonly mcsparameters_atomCompareParameters: (a: number) => number;
+    readonly mcsparameters_bondComparator: (a: number) => number;
+    readonly mcsparameters_bondCompareParameters: (a: number) => number;
+    readonly mcsparameters_initialSeed: (a: number) => [number, number];
+    readonly mcsparameters_maximizeBonds: (a: number) => number;
+    readonly mcsparameters_new: (a: any, b: any, c: any, d: any, e: any, f: any, g: any, h: any, i: any, j: any) => [number, number, number];
+    readonly mcsparameters_set_atomComparator: (a: number, b: number) => [number, number];
+    readonly mcsparameters_set_atomCompareParameters: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_bondComparator: (a: number, b: number) => [number, number];
+    readonly mcsparameters_set_bondCompareParameters: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_initialSeed: (a: number, b: number, c: number) => [number, number];
+    readonly mcsparameters_set_maximizeBonds: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_storeAll: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_threshold: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_timeout: (a: number, b: any) => [number, number];
+    readonly mcsparameters_set_verbose: (a: number, b: any) => [number, number];
+    readonly mcsparameters_storeAll: (a: number) => number;
+    readonly mcsparameters_threshold: (a: number) => number;
+    readonly mcsparameters_timeout: (a: number) => number;
+    readonly mcsparameters_verbose: (a: number) => number;
+    readonly mcsresult_atomCount: (a: number) => number;
+    readonly mcsresult_bondCount: (a: number) => number;
+    readonly mcsresult_completed: (a: number) => number;
+    readonly mcsresult_degenerate: (a: number) => [number, number, number];
+    readonly mcsresult_query: (a: number) => any;
+    readonly mcsresult_smarts: (a: number) => [number, number, number, number];
     readonly mol2posterror_cause: (a: number) => any;
     readonly mol2posterror_domain: (a: number) => [number, number];
     readonly mol2posterror_kind: (a: number) => [number, number];
@@ -2662,6 +2976,7 @@ export interface InitOutput {
     readonly molecule_assignRings: (a: number) => [number, number];
     readonly molecule_assignValence: (a: number) => [number, number];
     readonly molecule_assignValenceWithParams: (a: number, b: number) => [number, number];
+    readonly molecule_atomProperty: (a: number, b: any, c: number, d: number) => [number, number, number];
     readonly molecule_atomPropertyString: (a: number, b: any, c: number, d: number) => [number, number, number];
     readonly molecule_atomicNumbers: (a: number) => [number, number];
     readonly molecule_bondPropertyString: (a: number, b: any, c: number, d: number) => [number, number, number];
@@ -2712,6 +3027,8 @@ export interface InitOutput {
     readonly molecule_fingerprintAtomPairSparseCountWithParams: (a: number, b: number, c: any) => [number, number, number];
     readonly molecule_fingerprintAtomPairSparseWithParams: (a: number, b: number, c: any) => [number, number, number];
     readonly molecule_fingerprintAtomPairWithParams: (a: number, b: number, c: any) => [number, number, number];
+    readonly molecule_fingerprintAvalon: (a: number, b: any) => [number, number, number];
+    readonly molecule_fingerprintAvalonWithParams: (a: number, b: number) => [number, number, number];
     readonly molecule_fingerprintLayered: (a: number, b: any) => [number, number, number];
     readonly molecule_fingerprintLayeredWithOutput: (a: number, b: any) => [number, number, number];
     readonly molecule_fingerprintLayeredWithOutputWithParams: (a: number, b: number) => [number, number, number];
@@ -2756,6 +3073,7 @@ export interface InitOutput {
     readonly molecule_fingerprintTopologicalWithOutputWithParams: (a: number, b: number, c: number) => [number, number, number];
     readonly molecule_fingerprintTopologicalWithParams: (a: number, b: number) => [number, number, number];
     readonly molecule_fractionCsp3: (a: number) => [number, number, number];
+    readonly molecule_fragments: (a: number) => [number, number, number, number];
     readonly molecule_fromMol: (a: number, b: number) => [number, number, number];
     readonly molecule_fromMol2: (a: number, b: number) => [number, number, number];
     readonly molecule_fromMol2WithParams: (a: number, b: number, c: any) => [number, number, number];
@@ -2779,6 +3097,7 @@ export interface InitOutput {
     readonly molecule_labuteAsaContributions: (a: number) => [number, number, number];
     readonly molecule_labuteAsaContributionsWithParams: (a: number, b: any, c: any) => [number, number, number];
     readonly molecule_labuteAsaWithParams: (a: number, b: any, c: any) => [number, number, number];
+    readonly molecule_largestFragment: (a: number) => [number, number, number];
     readonly molecule_lipinskiHba: (a: number) => [number, number, number];
     readonly molecule_lipinskiHbd: (a: number) => [number, number, number];
     readonly molecule_molecularFormula: (a: number) => [number, number, number, number];
@@ -2788,7 +3107,10 @@ export interface InitOutput {
     readonly molecule_molecularWeight: (a: number) => [number, number, number];
     readonly molecule_molecularWeightWithParams: (a: number, b: any) => [number, number, number];
     readonly molecule_mqns: (a: number, b: any) => [number, number, number, number];
+    readonly molecule_murckoDecompose: (a: number) => [number, number, number];
+    readonly molecule_murckoScaffold: (a: number) => [number, number, number];
     readonly molecule_nameOrEmpty: (a: number) => [number, number, number, number];
+    readonly molecule_netScaffold: (a: number) => [number, number, number];
     readonly molecule_new: () => number;
     readonly molecule_numAliphaticCarbocycles: (a: number) => [number, number, number];
     readonly molecule_numAliphaticHeterocycles: (a: number) => [number, number, number];
@@ -2834,6 +3156,7 @@ export interface InitOutput {
     readonly molecule_sanitize_: (a: number) => [number, number];
     readonly molecule_sdfDataFieldNames: (a: number) => [number, number, number, number];
     readonly molecule_sdfDataFieldOrEmpty: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly molecule_setAtomProperty: (a: number, b: any, c: number, d: number, e: any) => [number, number];
     readonly molecule_slogpVsa: (a: number) => [number, number, number, number];
     readonly molecule_slogpVsa1: (a: number) => [number, number, number];
     readonly molecule_slogpVsa10: (a: number) => [number, number, number];
@@ -2891,6 +3214,7 @@ export interface InitOutput {
     readonly molecule_withAssignedValence: (a: number) => [number, number, number];
     readonly molecule_withAssignedValenceWithParams: (a: number, b: number) => [number, number, number];
     readonly molecule_withAtomPairAtomCode: (a: number, b: any, c: any, d: any, e: any) => [number, number, number];
+    readonly molecule_withAtomProperty: (a: number, b: any, c: number, d: number, e: any) => [number, number, number];
     readonly molecule_withHydrogens: (a: number) => [number, number, number];
     readonly molecule_withHydrogensWithParams: (a: number, b: any) => [number, number, number];
     readonly molecule_withKekulizedBonds: (a: number) => [number, number, number];
@@ -3096,6 +3420,15 @@ export interface InitOutput {
     readonly propertyvalueerror_expected: (a: number) => number;
     readonly propertyvalueerror_kind: (a: number) => [number, number];
     readonly propertyvalueerror_message: (a: number) => [number, number];
+    readonly queryatom_atomMap: (a: number) => any;
+    readonly queryatom_atomicNumber: (a: number) => number;
+    readonly queryatom_explicitHydrogens: (a: number) => number;
+    readonly queryatom_formalCharge: (a: number) => number;
+    readonly queryatom_id: (a: number) => number;
+    readonly queryatom_isAromatic: (a: number) => number;
+    readonly queryatom_isotope: (a: number) => any;
+    readonly queryatom_noImplicit: (a: number) => number;
+    readonly queryatom_radicalElectrons: (a: number) => number;
     readonly querycompileerror_cause: (a: number) => [number, number, number];
     readonly querycompileerror_domain: (a: number) => [number, number];
     readonly querycompileerror_kind: (a: number) => [number, number];
@@ -3516,44 +3849,48 @@ export interface InitOutput {
     readonly xyzwriteparams_conformerId: (a: number) => any;
     readonly xyzwriteparams_new: (a: any, b: any) => [number, number, number];
     readonly xyzwriteparams_precision: (a: number) => number;
-    readonly wasm_bindgen__convert__closures________invoke__h04b85bf8c7a5d53a: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0a1711ba6a40e5dc: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0a1711ba6a40e5dc_816: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0ef956d33909cd50: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0fadd38bb2ebf9d9: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0fadd38bb2ebf9d9_1187: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0fadd38bb2ebf9d9_882: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h13013e8961c184dc: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h19931d001c12874d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h378cb266eeca5897: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h378cb266eeca5897_1099: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h378cb266eeca5897_1171: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h378cb266eeca5897_1208: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h4bd07848b94d9a57: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h51a0f71a92698ef7: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h572251164f825cc5: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h66a7794182ed85dd: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h66a7794182ed85dd_1163: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6745ac9aa5b4dfcf: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4_1025: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4_1077: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4_1172: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4_817: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6f1a651a3736ffd4_971: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h70d3bfb24a5813b1: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h75ae9a35ef4be912: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h77c8ccb8f3076e53: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h7e20d7ee6bb38e9d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h871ec560dc538198: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h9008de65da98b8fd: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hbd7a69223813583b: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hc1372534dcb0e864: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd9901587baba3819: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hda7e2004ca410b17: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hdd5dce4031ecbd30: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hee5110d3121a453e: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hffd7a704e417cbe7: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h09b3c46f59d2bd38: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h09b3c46f59d2bd38_1151: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h09b3c46f59d2bd38_1182: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h09b3c46f59d2bd38_1269: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h09b3c46f59d2bd38_1305: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15_1028: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15_1141: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15_1268: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15_820: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15bf4bfe2214fa15_974: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h16c42a2810c64992: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bf994e0f9212ce8: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h220141274c6f8a74: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2d4043a71d7773cb: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2f92515d3a154720: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2fb58ee3467537ff: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h36ec9c48397d6779: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h37e499b341a66fd9: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h3c395666b0650bdf: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h3c395666b0650bdf_1260: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4821b232b3abf892: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4821b232b3abf892_1284: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4821b232b3abf892_885: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4e2bdf03ca75e848: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4e2bdf03ca75e848_1089: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4e2bdf03ca75e848_1090: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h64c962ac2b098521: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7a52b9afd2fec67f: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h8538282d14c3f2c6: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h8538282d14c3f2c6_819: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h8e77c768297d1ca4: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__ha13d16aa928b00b1: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__haea3c69896f41f29: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hbf36c3235ac72906: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hcbd1922ecc991004: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hcd91937bb68771b4: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hea18f39168f34e99: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hec3271e02ee4bf16: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hec480d635374192e: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hecde5fc3be0591d0: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hf47469c0c724e97b: (a: number, b: number, c: number) => void;
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
     readonly __wbindgen_exn_store: (a: number) => void;