@cosmol-studio/cosmolkit 0.5.0-rc.18 → 0.5.0-rc.21

package/wasm_wasm.d.ts

@@ -6,6 +6,13 @@ export interface ProteinResidueIter extends IterableIterator<ProteinResidueRef>
 export interface ProteinAtomIter extends IterableIterator<ProteinAtomRef> {}
 
 
+export interface AvalonFingerprintOptions {
+    nBits?: number;
+    isQuery?: boolean;
+    bitFlags?: number;
+}
+
+
 export interface LayeredFingerprintOptions {
     layers?: number;
     minPath?: number;
@@ -18,6 +25,40 @@ 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> {}
 
@@ -282,6 +323,44 @@ export class AtomSourceIds {
     serial(): number | null;
 }
 
+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;
@@ -2096,6 +2175,99 @@ 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 MmffAtomProperties {
     private constructor();
     free(): void;
@@ -2340,6 +2512,10 @@ 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.
      */
@@ -2415,6 +2591,8 @@ 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;
@@ -2459,6 +2637,10 @@ export class Molecule {
     fingerprintTopologicalWithParams(params: TopologicalFingerprintParams): Fingerprint;
     fingerprintTopological(): Fingerprint;
     fractionCsp3(): number;
+    /**
+     * Sanitized components in source order, including conformers; self is unchanged.
+     */
+    fragments(): Molecule[];
     static fromInchiWithParams(text: string, params: InchiReadParams): Molecule;
     static fromInchi(text: string, params?: InchiReadParams | { sanitize?: boolean; removeHs?: boolean }): Molecule;
     static fromMol2WithParams(text: string, params: Mol2ReadParams): Molecule;
@@ -2484,6 +2666,10 @@ 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;
     mmffEnergyGradientWithParams(params: MmffEvaluationParams): MmffEnergyGradient | null;
@@ -2498,10 +2684,22 @@ 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.
      */
@@ -2576,6 +2774,10 @@ 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;
@@ -2656,6 +2858,10 @@ 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;
@@ -3151,6 +3357,24 @@ export class ProteinSelectionSummary {
     readonly residues: number;
 }
 
+/**
+ * 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;
@@ -3354,9 +3578,10 @@ export class ReactionRunError {
 export class ReactionRunParams {
     free(): void;
     [Symbol.dispose](): void;
-    constructor(max_products?: number, coordinate_selections?: ReactionCoordinateSelection[]);
-    readonly coordinateSelections: ReactionCoordinateSelection[];
-    readonly maxProducts: number;
+    constructor(max_products?: number, coordinate_selections?: ReactionCoordinateSelection[], copy_atom_properties?: boolean);
+    coordinateSelections: ReactionCoordinateSelection[];
+    copyAtomProperties: boolean;
+    maxProducts: number;
 }
 
 export class ReactionSingleRunParams {
@@ -4851,6 +5076,10 @@ export function fingerprintTopologicalQueryWithParams(query: QueryGraph, params:
 
 export function inchiToKey(text: string): string;
 
+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;
@@ -4900,6 +5129,10 @@ export interface InitOutput {
     readonly __wbg_atompairreaderror_free: (a: number, b: number) => void;
     readonly __wbg_atompairsparameters_free: (a: number, b: number) => void;
     readonly __wbg_atomsourceids_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;
@@ -5031,6 +5264,11 @@ 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_mmffatomproperties_free: (a: number, b: number) => void;
     readonly __wbg_mmffconformeroptimizationparams_free: (a: number, b: number) => void;
     readonly __wbg_mmffenergygradient_free: (a: number, b: number) => void;
@@ -5081,6 +5319,7 @@ export interface InitOutput {
     readonly __wbg_proteinresidueiter_free: (a: number, b: number) => void;
     readonly __wbg_proteinresidueref_free: (a: number, b: number) => void;
     readonly __wbg_proteinselectionsummary_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_reaction_free: (a: number, b: number) => void;
@@ -5295,6 +5534,24 @@ export interface InitOutput {
     readonly atompairsparameters_numTypeBits: () => number;
     readonly atompairsparameters_version: () => [number, number];
     readonly atomsourceids_serial: (a: number) => any;
+    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;
@@ -6266,6 +6523,64 @@ 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 mmffatomproperties_atomType: (a: number) => number;
     readonly mmffatomproperties_formalCharge: (a: number) => number;
     readonly mmffatomproperties_partialCharge: (a: number) => number;
@@ -6377,6 +6692,7 @@ 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_bestAlignmentTo: (a: number, b: number) => [number, number, number];
@@ -6444,6 +6760,8 @@ 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];
@@ -6488,6 +6806,7 @@ 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_fromInchi: (a: number, b: number, c: any) => [number, number, number];
     readonly molecule_fromInchiWithParams: (a: number, b: number, c: number) => [number, number, number];
     readonly molecule_fromMol: (a: number, b: number) => [number, number, number];
@@ -6513,6 +6832,7 @@ 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_mmffEnergyGradient: (a: number) => [number, number, number];
@@ -6527,7 +6847,10 @@ 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_num3dConformers: (a: number) => number;
     readonly molecule_numAliphaticCarbocycles: (a: number) => [number, number, number];
@@ -6577,6 +6900,7 @@ 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];
@@ -6657,6 +6981,7 @@ 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];
@@ -6966,6 +7291,15 @@ export interface InitOutput {
     readonly proteinselectionsummary_atoms: (a: number) => number;
     readonly proteinselectionsummary_chains: (a: number) => number;
     readonly proteinselectionsummary_residues: (a: 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];
@@ -7086,8 +7420,12 @@ export interface InitOutput {
     readonly reactionrunerror_set: (a: number) => [number, number, number];
     readonly reactionrunerror_template: (a: number) => [number, number, number];
     readonly reactionrunparams_coordinateSelections: (a: number) => any;
+    readonly reactionrunparams_copyAtomProperties: (a: number) => number;
     readonly reactionrunparams_maxProducts: (a: number) => number;
-    readonly reactionrunparams_new: (a: any, b: any) => [number, number, number];
+    readonly reactionrunparams_new: (a: any, b: any, c: any) => [number, number, number];
+    readonly reactionrunparams_set_coordinateSelections: (a: number, b: any) => [number, number];
+    readonly reactionrunparams_set_copyAtomProperties: (a: number, b: any) => [number, number];
+    readonly reactionrunparams_set_maxProducts: (a: number, b: any) => [number, number];
     readonly reactionsinglerunparams_coordinateSelection: (a: number) => number;
     readonly reactionsinglerunparams_new: (a: any) => [number, number, number];
     readonly reactiontemplateremoval_reaction: (a: number) => number;
@@ -7646,52 +7984,56 @@ 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__h0064a98766fb0224: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0064a98766fb0224_1687: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0064a98766fb0224_1959: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0064a98766fb0224_2446: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0d1dcec420f59771: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0d1dcec420f59771_1119: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0d1dcec420f59771_1688: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0d1dcec420f59771_2361: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0e6bd8b84df1fce1: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0e6bd8b84df1fce1_2298: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0e6bd8b84df1fce1_2369: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0e6bd8b84df1fce1_2467: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h0e6bd8b84df1fce1_490: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h127729248a6c8009: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h1a472963d24d20a6: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2218d91e4996a10d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fa2bd6861932b9d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h367854f3909c6b72: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h4e6875dc92366367: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h590f60ef0b121ea7: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5ab2fa88a0d77621: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5ab2fa88a0d77621_886: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_1827: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_2074: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_2128: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_2252: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_2275: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h5bc8a5d04dbc67f5_2370: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h70ac3ddb712ddf2e: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h730d32035049500d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h85b777a3b19d8bca: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h896f474846a4b769: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h99b7ff61ce79e10b: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h9afea99fa1a7df0d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hada9f3926956c01d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hae82e598cad2b40f: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hb5f0c2af90259ff8: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hbb9bb400d0faf17a: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd60bb4dcb664a8e5: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd7206a4f1e3cc39d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd76cc1aaf71726d3: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__he3247ab5a8c3ce7d: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__he454338561b431c1: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__he454338561b431c1_1826: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hf1f0a4beb5806796: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h01b1e606e450b2ac: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc_2353: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc_2384: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc_2470: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc_2568: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h020f698551eb66cc_490: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h07bf0e008bdc76b0: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h08d497340505e30a: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a06d3ba8cca1299: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15445680e15d01b7: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15445680e15d01b7_1119: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15445680e15d01b7_1694: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h15445680e15d01b7_2462: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h16fdeae93d3368ad: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h27810e84141e08c7: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2999e6d37eb6d327: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34ed44600ce80f7c: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34ed44600ce80f7c_2195: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34ed44600ce80f7c_2197: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h470e7b9ab969d4aa: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h470e7b9ab969d4aa_1695: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h470e7b9ab969d4aa_1966: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h470e7b9ab969d4aa_2547: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h4a7bb9932676e4b9: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h51446d6480d774fd: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h51446d6480d774fd_886: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h5c52935f5062dd76: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h603896e89802abef: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h6570fdcd861f2f1d: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h6b3d527f431eaa7a: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7aeedf70ce4571e2: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_1834: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_2081: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_2135: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_2320: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_2343: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h7cde413cc7e0fe8a_2471: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h8c6f2c7593f176e2: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h97d112a15c00bcbf: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h9e6d12766b45a609: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hb326c2acdf46da8a: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hc68671597d64b287: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hcb848668c5a09202: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hcb848668c5a09202_1833: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__he4a7ba0d7e23aa39: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__he50bd5777becc806: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__heba3efe5d84c454f: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hf78da8f4f7fd1802: (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;