JavaScript / TypeScript API¶

wasm_wasm.d.canonicalTautomerFromMolecules(molecules: Molecule[], params: TautomerParamsOptions | TautomerParams) → Molecule¶

wasm_wasm.d.canonicalTautomerFromMoleculesWithParams(molecules: Molecule[], params: TautomerParams) → Molecule¶

wasm_wasm.d.compileQuery(query: QueryGraph) → CompiledQuery¶

async wasm_wasm.d.default(module_or_path: InitInput | Promise<InitInput> | { module_or_path: InitInput | Promise<InitInput>; }) → Promise<InitOutput>¶

If module_or_path is {RequestInfo} or {URL}, makes a request and for everything else, calls WebAssembly.instantiate directly.

Arguments:

• module_or_path – Passing InitInput directly is deprecated.

wasm_wasm.d.defaultTautomerScoreTerms() → TautomerScoreTerm[]¶

wasm_wasm.d.elementInfo(element: Element) → ElementInfo¶

wasm_wasm.d.expandOneLetter(code: string, kind: ResidueInfoKind) → string | null¶

wasm_wasm.d.expandOneLetterSequence(seq: string, kind: ResidueInfoKind) → string[]¶

wasm_wasm.d.explainPathScore(score: bigint, size: number) → [string, number, number][]¶

wasm_wasm.d.featureSpec(name: string) → FeatureSpec | null¶

wasm_wasm.d.featureSpecs() → FeatureSpecIter¶

wasm_wasm.d.findResidueInfo(name: string) → ResidueInfo¶

wasm_wasm.d.findResidueInfoIndex(name: string) → number¶

wasm_wasm.d.fingerprintLayeredQueryWithOutputWithParams(query: QueryGraph, params: LayeredFingerprintParams) → LayeredFingerprintResult¶

wasm_wasm.d.fingerprintLayeredQueryWithParams(query: QueryGraph, params: LayeredFingerprintParams) → Fingerprint¶

wasm_wasm.d.fingerprintPatternQuery(query: QueryGraph, params: PatternFingerprintParamsOptions | PatternFingerprintParams) → Fingerprint¶

wasm_wasm.d.fingerprintPatternQueryWithParams(query: QueryGraph, params: PatternFingerprintParams) → Fingerprint¶

wasm_wasm.d.fingerprintTopologicalQueryWithOutputWithParams(query: QueryGraph, params: TopologicalFingerprintParams, request: TopologicalFingerprintOutputRequest) → TopologicalFingerprintResult¶

wasm_wasm.d.fingerprintTopologicalQueryWithParams(query: QueryGraph, params: TopologicalFingerprintParams) → Fingerprint¶

wasm_wasm.d.inchiToKey(text: string) → string¶

wasm_wasm.d.initSync(module: SyncInitInput | { module: SyncInitInput; }) → InitOutput¶

Instantiates the given module, which can either be bytes or a precompiled WebAssembly.Module.

Arguments:

• module – Passing SyncInitInput directly is deprecated.

wasm_wasm.d.maximumCommonSubstructure(molecules: Molecule[], params: McsParametersOptions | McsParameters) → McsResult¶

wasm_wasm.d.maximumCommonSubstructureWithParams(molecules: Molecule[], params: McsParameters) → McsResult¶

wasm_wasm.d.operationInvariant(method: string) → OperationInvariantEntry | null¶

wasm_wasm.d.operationInvariantMatrix() → OperationInvariantEntry[]¶

wasm_wasm.d.operationParity(method: string) → ParityMatrixEntry | null¶

wasm_wasm.d.operationSpec(method: string) → MoleculeOpSpec | null¶

wasm_wasm.d.operationSpecs() → MoleculeOpSpec[]¶

wasm_wasm.d.parityMatrix() → ParityMatrixEntry[]¶

wasm_wasm.d.parseSmarts(text: string, params: SmartsParseParamsOptions | SmartsParseParams) → QueryGraph¶

wasm_wasm.d.parseSmartsWithParams(text: string, params: SmartsParseParams) → QueryGraph¶

wasm_wasm.d.parseSmirks(text: string, params: ReactionParseParamsOptions | ReactionParseParams) → Reaction¶

wasm_wasm.d.parseSmirksWithParams(text: string, params: ReactionParseParams) → Reaction¶

wasm_wasm.d.propertyValueToText(value: PropertyValue) → string¶

wasm_wasm.d.residueCode(name: string) → ResidueCode¶

wasm_wasm.d.residueInfo(index: number) → ResidueInfo¶

wasm_wasm.d.residueInfoChecked(index: number) → ResidueInfo | null¶

wasm_wasm.d.supportMatrix() → SupportMatrixEntry[]¶

wasm_wasm.d.version() → string¶

Returns the COSMolKit version through the binding-facing crate.

wasm_wasm.d.writeCxSmarts(query: QueryGraph, params: SmartsWriteParams) → string¶

wasm_wasm.d.writeSmarts(query: QueryGraph, params: SmartsWriteParams) → string¶

class wasm_wasm.d.Molecule()¶

exported from wasm_wasm.d

Members (417)

Molecule.[Symbol․dispose]() → void¶

Molecule.add3dConformer(coordinates: number[][], params: Coordinate3DInputParamsOptions | Coordinate3DInputParams) → number¶

Molecule.add3dConformerWithParams(coordinates: number[][], params: Coordinate3DInputParams) → number¶

Molecule.addHydrogens(params: AddHsParamsOptions | AddHsParams) → void¶

Molecule.addHydrogensWithParams(params: AddHsParams) → void¶

Molecule.alignConformers(params: ConformerAlignmentParametersOptions | ConformerAlignmentParameters) → ConformerAlignmentReport¶

Molecule.alignConformersWithParams(params: ConformerAlignmentParameters) → ConformerAlignmentReport¶

Molecule.alignTo(reference: Molecule, params: AlignmentParametersOptions | AlignmentParameters) → AlignmentResult¶

Molecule.alignToWithParams(reference: Molecule, params: AlignmentParameters) → AlignmentResult¶

Molecule.alignmentTransformTo(reference: Molecule, params: AlignmentParametersOptions | AlignmentParameters) → AlignmentResult¶

Molecule.alignmentTransformToWithParams(reference: Molecule, params: AlignmentParameters) → AlignmentResult¶

Molecule.allConformerBestRmsds(params: AllConformerRmsdParametersOptions | AllConformerRmsdParameters) → ConformerRmsd[]¶

Molecule.allConformerBestRmsdsWithParams(params: AllConformerRmsdParameters) → ConformerRmsd[]¶

Molecule.applyReaction(reaction: Reaction, params: ReactionApplyParamsOptions | ReactionApplyParams) → ReactionApplyResult¶

Molecule.applyReactionWithParams(reaction: Reaction, params: ReactionApplyParams) → ReactionApplyResult¶

Molecule.applyReactionWithParams_(reaction: Reaction, params: ReactionApplyParams) → boolean¶

Molecule.applyReaction_(reaction: Reaction, params: ReactionApplyParamsOptions | ReactionApplyParams) → boolean¶

Molecule.assignAromaticity(params: AromaticityParamsOptions | AromaticityParams) → void¶

Molecule.assignAromaticityWithParams(params: AromaticityParams) → void¶

Molecule.assignChiralTagsFromStructure(params: StructureTagParamsOptions | StructureTagParams) → void¶

Molecule.assignChiralTagsFromStructureWithParams(params: StructureTagParams) → void¶

Molecule.assignCipLabels(options: CipLabelOptionsOptions | CipLabelOptions) → void¶

Molecule.assignCipLabelsWithOptions(options: CipLabelOptions) → void¶

Molecule.assignRadicals() → void¶

Molecule.assignRingFamilies(params: RingSearchParamsOptions | RingSearchParams) → void¶

Molecule.assignRingFamiliesWithParams(params: RingSearchParams) → void¶

Molecule.assignRings() → void¶

Molecule.assignValence(params: ValenceParamsOptions | ValenceParams) → void¶

Molecule.assignValenceWithParams(params: ValenceParams) → void¶

Molecule.atom(index: number) → Atom | null¶

Molecule.atomMetadata(recalculate: boolean) → AtomMetadata[]¶

Molecule.atomProperty(atom: number, key: string) → string | number | boolean | string[] | number[] | null¶

Read typed user metadata; a missing key returns null.

Molecule.atomPropertyString(id: number, key: string) → string | null¶

Molecule.atomicNumbers() → Uint8Array¶

Returns atomic numbers in molecule atom order.

Molecule.atoms() → Atom[]¶

Molecule.bestAlignmentTo(reference: Molecule, params: BestAlignmentParametersOptions | BestAlignmentParameters) → AlignmentResult¶

Molecule.bestAlignmentToWithParams(reference: Molecule, params: BestAlignmentParameters) → AlignmentResult¶

Molecule.bestRmsdTo(reference: Molecule, params: BestAlignmentParametersOptions | BestAlignmentParameters) → number¶

Molecule.bestRmsdToWithParams(reference: Molecule, params: BestAlignmentParameters) → number¶

Molecule.bond(index: number) → Bond | null¶

Molecule.bondPropertyString(id: number, key: string) → string | null¶

Molecule.bonds() → Bond[]¶

Molecule.canonicalTautomer(params: TautomerParamsOptions | TautomerParams) → Molecule¶

Molecule.canonicalTautomerWithParams(params: TautomerParams) → Molecule¶

Molecule.chi0() → number¶

Molecule.chi0N() → number¶

Molecule.chi0NWithParams(force: boolean) → number¶

Molecule.chi0V() → number¶

Molecule.chi0VWithParams(force: boolean) → number¶

Molecule.chi1() → number¶

Molecule.chi1N() → number¶

Molecule.chi1NWithParams(force: boolean) → number¶

Molecule.chi1V() → number¶

Molecule.chi1VWithParams(force: boolean) → number¶

Molecule.chi2N() → number¶

Molecule.chi2NWithParams(force: boolean) → number¶

Molecule.chi2V() → number¶

Molecule.chi2VWithParams(force: boolean) → number¶

Molecule.chi3N() → number¶

Molecule.chi3NWithParams(force: boolean) → number¶

Molecule.chi3V() → number¶

Molecule.chi3VWithParams(force: boolean) → number¶

Molecule.chi4N() → number¶

Molecule.chi4NWithParams(force: boolean) → number¶

Molecule.chi4V() → number¶

Molecule.chi4VWithParams(force: boolean) → number¶

Molecule.chiNN(order: number) → number¶

Molecule.chiNNWithParams(order: number, force: boolean) → number¶

Molecule.chiNV(order: number) → number¶

Molecule.chiNVWithParams(order: number, force: boolean) → number¶

Molecule.cipComputed() → boolean¶

Molecule.clear3dConformers() → void¶

Molecule.compute2dCoordinates(params: Coordinate2DParamsOptions | Coordinate2DParams) → void¶

Molecule.compute2dCoordinatesWithParams(params: Coordinate2DParams) → void¶

Molecule.conformers3d() → Conformer3D[]¶

Molecule.coordinateRmsdTo(reference: Molecule, params: CoordinateRmsdParametersOptions | CoordinateRmsdParameters) → number¶

Molecule.coordinateRmsdToWithParams(reference: Molecule, params: CoordinateRmsdParameters) → number¶

Molecule.coordinates2d() → Float64Array¶

Returns the first 2D conformer as a flattened [x0, y0, ...] array.

Molecule.coordinates3d(conformer_id: number) → Float64Array¶

Molecule.crippenDescriptors() → CrippenTotals¶

Molecule.crippenDescriptorsWithParams(include_hydrogens: boolean, force: boolean) → CrippenTotals¶

Molecule.detectChemistryProblems(params: SanitizeParamsOptions | SanitizeParams) → ChemistryProblemReport¶

Molecule.detectChemistryProblemsWithParams(params: SanitizeParams) → ChemistryProblemReport¶

Molecule.dgBoundsMatrix() → number[][]¶

Molecule.distanceMatrix(params: DistanceMatrixParamsOptions | DistanceMatrixParams) → DenseMatrix¶

Molecule.distanceMatrix3d(params: DistanceMatrix3dParamsOptions | DistanceMatrix3dParams) → DenseMatrix¶

Molecule.distanceMatrix3dWithParams(params: DistanceMatrix3dParams) → DenseMatrix¶

Molecule.distanceMatrixWithParams(params: DistanceMatrixParams) → DenseMatrix¶

Molecule.embed3dConformer(params: EmbedParamsOptions | EmbedParams) → void¶

Molecule.embed3dConformerResult(params: EmbedParamsOptions | EmbedParams) → EmbedMoleculeResult¶

Molecule.embed3dConformerResultWithParams(params: EmbedParams) → EmbedMoleculeResult¶

Molecule.embed3dConformerWithParams(params: EmbedParams) → void¶

Molecule.embed3dConformers(num_confs: number, params: EmbedParamsOptions | EmbedParams) → void¶

Molecule.embed3dConformersResult(num_confs: number, params: EmbedParamsOptions | EmbedParams) → EmbedMultipleConfsResult¶

Molecule.embed3dConformersResultWithParams(num_confs: number, params: EmbedParams) → EmbedMultipleConfsResult¶

Molecule.embed3dConformersWithParams(num_confs: number, params: EmbedParams) → void¶

Molecule.enumerateStereoisomers(options: StereoisomerOptionsConfiguration | StereoisomerOptions) → StereoisomerIterator¶

Molecule.enumerateStereoisomersWithOptions(options: StereoisomerOptions) → StereoisomerIterator¶

Molecule.enumerateStereoisomersWithRandomBits(options: StereoisomerOptions, callback: (bitCount: number) => bigint) → StereoisomerIterator¶

Molecule.enumerateTautomers(params: TautomerParamsOptions | TautomerParams) → TautomerEnumeration¶

Molecule.enumerateTautomersWithParams(params: TautomerParams) → TautomerEnumeration¶

Molecule.exactMolecularWeight() → number¶

Molecule.exactMolecularWeightWithParams(only_heavy: boolean) → number¶

Molecule.findChiralCenters(include_unassigned: boolean) → [number, string][]¶

Molecule.fingerprintAtomPair(params: AtomPairFingerprintParamsOptions | AtomPairFingerprintParams) → Fingerprint¶

Molecule.fingerprintAtomPairCount(params: AtomPairFingerprintParamsOptions | AtomPairFingerprintParams) → SparseCountFingerprint32¶

Molecule.fingerprintAtomPairCountWithParams(params: AtomPairFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint32¶

Molecule.fingerprintAtomPairSparse(params: AtomPairFingerprintParamsOptions | AtomPairFingerprintParams) → SparseBitFingerprint¶

Molecule.fingerprintAtomPairSparseCount(params: AtomPairFingerprintParamsOptions | AtomPairFingerprintParams) → SparseCountFingerprint¶

Molecule.fingerprintAtomPairSparseCountWithParams(params: AtomPairFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint¶

Molecule.fingerprintAtomPairSparseWithParams(params: AtomPairFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseBitFingerprint¶

Molecule.fingerprintAtomPairWithParams(params: AtomPairFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → Fingerprint¶

Molecule.fingerprintAvalon(params: AvalonFingerprintOptions | AvalonFingerprintParams) → Fingerprint¶

Molecule.fingerprintAvalonWithParams(params: AvalonFingerprintParams) → Fingerprint¶

Molecule.fingerprintLayered(params: LayeredFingerprintOptions | LayeredFingerprintParams) → Fingerprint¶

Molecule.fingerprintLayeredWithOutput(params: LayeredFingerprintOptions | LayeredFingerprintParams) → LayeredFingerprintResult¶

Molecule.fingerprintLayeredWithOutputWithParams(params: LayeredFingerprintParams) → LayeredFingerprintResult¶

Molecule.fingerprintLayeredWithParams(params: LayeredFingerprintParams) → Fingerprint¶

Molecule.fingerprintMaccs(params: MaccsFingerprintParamsOptions | MaccsFingerprintParams) → Fingerprint¶

Molecule.fingerprintMaccsRaw() → Fingerprint¶

Molecule.fingerprintMaccsWithParams(params: MaccsFingerprintParams) → Fingerprint¶

Molecule.fingerprintMorgan(params: MorganFingerprintParamsOptions | MorganFingerprintParams) → Fingerprint¶

Molecule.fingerprintMorganCount(params: MorganFingerprintParamsOptions | MorganFingerprintParams) → SparseCountFingerprint32¶

Molecule.fingerprintMorganCountWithGenerator(generator: MorganFingerprintGenerator, params: MorganCallParams | null, output: FingerprintAdditionalOutput | null) → SparseCountFingerprint32¶

Molecule.fingerprintMorganCountWithParams(params: MorganFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint32¶

Molecule.fingerprintMorganSparse(params: MorganFingerprintParamsOptions | MorganFingerprintParams) → SparseBitFingerprint¶

Molecule.fingerprintMorganSparseCount(params: MorganFingerprintParamsOptions | MorganFingerprintParams) → SparseCountFingerprint¶

Molecule.fingerprintMorganSparseCountWithGenerator(generator: MorganFingerprintGenerator, params: MorganCallParams | null, output: FingerprintAdditionalOutput | null) → SparseCountFingerprint¶

Molecule.fingerprintMorganSparseCountWithParams(params: MorganFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint¶

Molecule.fingerprintMorganSparseWithGenerator(generator: MorganFingerprintGenerator, params: MorganCallParams | null, output: FingerprintAdditionalOutput | null) → SparseBitFingerprint¶

Molecule.fingerprintMorganSparseWithParams(params: MorganFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseBitFingerprint¶

Molecule.fingerprintMorganWithGenerator(generator: MorganFingerprintGenerator, params: MorganCallParams | null, output: FingerprintAdditionalOutput | null) → Fingerprint¶

Molecule.fingerprintMorganWithParams(params: MorganFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → Fingerprint¶

Molecule.fingerprintPattern(params: PatternFingerprintParamsOptions | PatternFingerprintParams) → Fingerprint¶

Molecule.fingerprintPatternWithParams(params: PatternFingerprintParams) → Fingerprint¶

Molecule.fingerprintTopological(params: TopologicalFingerprintParamsOptions | TopologicalFingerprintParams) → Fingerprint¶

Molecule.fingerprintTopologicalTorsion(params: TopologicalTorsionFingerprintParamsOptions | TopologicalTorsionFingerprintParams) → Fingerprint¶

Molecule.fingerprintTopologicalTorsionCount(params: TopologicalTorsionFingerprintParamsOptions | TopologicalTorsionFingerprintParams) → SparseCountFingerprint32¶

Molecule.fingerprintTopologicalTorsionCountLegacy(params: LegacyTopologicalTorsionParamsOptions | LegacyTopologicalTorsionParams) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionCountLegacyWithParams(params: LegacyTopologicalTorsionParams) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionCountWithGenerator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | null, output: FingerprintAdditionalOutput | null) → SparseCountFingerprint32¶

Molecule.fingerprintTopologicalTorsionCountWithParams(params: TopologicalTorsionFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint32¶

Molecule.fingerprintTopologicalTorsionLegacy(params: LegacyTopologicalTorsionParamsOptions | LegacyTopologicalTorsionParams) → Fingerprint¶

Molecule.fingerprintTopologicalTorsionLegacyWithParams(params: LegacyTopologicalTorsionParams) → Fingerprint¶

Molecule.fingerprintTopologicalTorsionSparse(params: TopologicalTorsionFingerprintParamsOptions | TopologicalTorsionFingerprintParams) → SparseBitFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseCount(params: TopologicalTorsionFingerprintParamsOptions | TopologicalTorsionFingerprintParams) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseCountLegacy(params: LegacyTopologicalTorsionParamsOptions | LegacyTopologicalTorsionParams) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseCountLegacyWithParams(params: LegacyTopologicalTorsionParams) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseCountWithGenerator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | null, output: FingerprintAdditionalOutput | null) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseCountWithParams(params: TopologicalTorsionFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseCountFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseWithGenerator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | null, output: FingerprintAdditionalOutput | null) → SparseBitFingerprint¶

Molecule.fingerprintTopologicalTorsionSparseWithParams(params: TopologicalTorsionFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → SparseBitFingerprint¶

Molecule.fingerprintTopologicalTorsionWithGenerator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | null, output: FingerprintAdditionalOutput | null) → Fingerprint¶

Molecule.fingerprintTopologicalTorsionWithParams(params: TopologicalTorsionFingerprintParams, additional_output: FingerprintAdditionalOutput | null) → Fingerprint¶

Molecule.fingerprintTopologicalWithOutput(params: TopologicalFingerprintParamsOptions | TopologicalFingerprintParams, request: TopologicalFingerprintOutputRequestOptions | TopologicalFingerprintOutputRequest) → TopologicalFingerprintResult¶

Molecule.fingerprintTopologicalWithOutputWithParams(params: TopologicalFingerprintParams, request: TopologicalFingerprintOutputRequest) → TopologicalFingerprintResult¶

Molecule.fingerprintTopologicalWithParams(params: TopologicalFingerprintParams) → Fingerprint¶

Molecule.fractionCsp3() → number¶

Molecule.fragments() → Molecule[]¶

Sanitized components in source order, including conformers; self is unchanged.

Molecule.free() → void¶

Molecule.hallKierAlpha() → number¶

Molecule.hallKierAlphaWithContributions() → [number, Float64Array<ArrayBufferLike>]¶

Molecule.has2dCoordinates() → boolean¶

Molecule.hasSubstructMatch(query: QueryGraph, params: SubstructMatchOptions | SubstructMatchParams) → boolean¶

Molecule.hasSubstructMatchWithParams(query: QueryGraph, params: SubstructMatchParams) → boolean¶

Molecule.hasValenceViolation(atom_id: number) → boolean¶

Molecule.kappa1() → number¶

Molecule.kappa2() → number¶

Molecule.kappa3() → number¶

Molecule.kekulizeBonds(params: KekulizeParamsOptions | KekulizeParams) → void¶

Molecule.kekulizeBondsWithParams(params: KekulizeParams) → void¶

Molecule.labuteAsa() → number¶

Molecule.labuteAsaContributions() → LabuteAsaContributions¶

Molecule.labuteAsaContributionsWithParams(include_hydrogens: boolean, force: boolean) → LabuteAsaContributions¶

Molecule.labuteAsaWithParams(include_hydrogens: boolean, force: boolean) → number¶

Molecule.largestFragment() → Molecule¶

Most atoms, last on ties. Empty input throws OperationError.

Molecule.lipinskiHba() → number¶

Molecule.lipinskiHbd() → number¶

Molecule.mmffEnergyGradient(params: MmffEvaluationParamsOptions | MmffEvaluationParams) → MmffEnergyGradient | null¶

Molecule.mmffEnergyGradientWithParams(params: MmffEvaluationParams) → MmffEnergyGradient | null¶

Molecule.mmffForceField(params: MmffForceFieldParamsOptions | MmffForceFieldParams) → MolecularForceField¶

Molecule.mmffForceFieldWithParams(params: MmffForceFieldParams) → MolecularForceField¶

Molecule.mmffHasAllMoleculeParams() → boolean¶

Molecule.mmffProperties(params: MmffPropertiesParamsOptions | MmffPropertiesParams) → MmffProperties¶

Molecule.mmffPropertiesWithParams(params: MmffPropertiesParams) → MmffProperties¶

Molecule.molecularFormula() → string¶

Molecule.molecularFormulaWithParams(separate_isotopes: boolean, abbreviate_h_isotopes: boolean) → string¶

Molecule.molecularHash() → bigint¶

Molecule.molecularHashWithRanks(ranks: number[] | Uint32Array<ArrayBufferLike>) → bigint¶

Molecule.molecularWeight() → number¶

Molecule.molecularWeightWithParams(only_heavy: boolean) → number¶

Molecule.mqns(force: boolean) → Uint32Array¶

Molecule.murckoDecompose() → Molecule¶

ChemTransforms MurckoDecompose; retains ring-exocyclic double bonds.

Molecule.murckoScaffold() → Molecule¶

MolHash MurckoScaffold; returns a new molecule.

Molecule.nameOrEmpty() → string¶

Returns the molecule name, or an empty string when no name is stored.

Molecule.netScaffold() → Molecule¶

MolHash ExtendedMurcko; neighboring substituents become dummy atoms.

Molecule.num3dConformers() → number¶

Molecule.numAliphaticCarbocycles() → number¶

Molecule.numAliphaticHeterocycles() → number¶

Molecule.numAliphaticRings() → number¶

Molecule.numAmideBonds() → number¶

Molecule.numAromaticCarbocycles() → number¶

Molecule.numAromaticHeterocycles() → number¶

Molecule.numAromaticRings() → number¶

Molecule.numAtomStereoCenters() → number¶

Molecule.numAtoms() → number¶

Number of atoms in the molecular graph.

Molecule.numBonds() → number¶

Number of bonds in the molecular graph.

Molecule.numBridgeheadAtoms() → number¶

Molecule.numConformers3d() → number¶

Returns the number of 3D conformers.

Molecule.numHba() → number¶

Molecule.numHbd() → number¶

Molecule.numHeavyAtoms() → number¶

Molecule.numHeteroatoms() → number¶

Molecule.numHeterocycles() → number¶

Molecule.numRings() → number¶

Molecule.numRotatableBonds() → number¶

Molecule.numRotatableBondsWithParams(params: RotatableBondsOptions) → number¶

Molecule.numSaturatedCarbocycles() → number¶

Molecule.numSaturatedHeterocycles() → number¶

Molecule.numSaturatedRings() → number¶

Molecule.numSpiroAtoms() → number¶

Molecule.numUnspecifiedAtomStereoCenters() → number¶

Molecule.perceiveStereochemistry() → void¶

Molecule.phi() → number¶

Molecule.potentialStereo(params: PotentialStereoParamsOptions | PotentialStereoParams) → PotentialStereoResult¶

Molecule.potentialStereoWithParams(params: PotentialStereoParams) → PotentialStereoResult¶

Molecule.properties() → MoleculeProperties¶

Molecule.property(key: string) → PropertyValue | null¶

Molecule.propertyKeys() → string[]¶

Returns user/computed property names in stable source insertion order.

Molecule.propertyOrEmpty(key: string) → string¶

Returns a String-tag property, or an empty string when it is absent. Wrong value kinds and invalid UTF-8 propagate as binding errors.

Molecule.qed() → number¶

Molecule.reactionProducts(reaction: Reaction, reactant_template: number, params: ReactionSingleRunParamsOptions | ReactionSingleRunParams) → Molecule[][]¶

Molecule.reactionProductsFromInputs(reaction: Reaction, reactants: Molecule[], params: ReactionRunParams) → Molecule[][]¶

Molecule.reactionProductsWithParams(reaction: Reaction, reactant_template: number, params: ReactionSingleRunParams) → Molecule[][]¶

Molecule.removeHydrogens(params: RemoveHsParamsOptions | RemoveHsParams) → void¶

Molecule.removeHydrogensWithParams(params: RemoveHsParams) → void¶

Molecule.sanitize(params: SanitizeParamsOptions | SanitizeParams) → Molecule¶

Molecule.sanitizeWithParams(params: SanitizeParams) → Molecule¶

Molecule.sanitizeWithParams_(params: SanitizeParams) → void¶

Molecule.sanitize_(params: SanitizeParamsOptions | SanitizeParams) → void¶

Molecule.sdfDataFieldNames() → string[]¶

Returns SDF data-field names in their source order, including duplicates.

Molecule.sdfDataFieldOrEmpty(name: string) → string¶

Returns the first SDF data-field value with name, or an empty string.

Molecule.set2dCoordinates(coordinates: number[][], params: Coordinate2DInputParamsOptions | Coordinate2DInputParams) → void¶

Molecule.set2dCoordinatesWithParams(coordinates: number[][], params: Coordinate2DInputParams) → void¶

Molecule.set3dCoordinates(coordinates: number[][], params: Replace3DCoordinatesParamsOptions | Replace3DCoordinatesParams) → void¶

Molecule.set3dCoordinatesWithParams(coordinates: number[][], params: Replace3DCoordinatesParams) → void¶

Molecule.setAtomPosition(atom: number, position: [number, number, number], params: AtomPositionParamsOptions | AtomPositionParams) → void¶

Molecule.setAtomPositionWithParams(atom: number, position: [number, number, number], params: AtomPositionParams) → void¶

Molecule.setAtomProperty(atom: number, key: string, value: string | number | boolean | string[] | number[]) → void¶

Set metadata in place; COW keeps other molecule copies unchanged.

Molecule.setOnly3dConformer(coordinates: number[][], params: Coordinate3DInputParamsOptions | Coordinate3DInputParams) → number¶

Molecule.setOnly3dConformerWithParams(coordinates: number[][], params: Coordinate3DInputParams) → number¶

Molecule.slogpVsa() → Float64Array¶

Molecule.slogpVsa1() → number¶

Molecule.slogpVsa10() → number¶

Molecule.slogpVsa11() → number¶

Molecule.slogpVsa12() → number¶

Molecule.slogpVsa2() → number¶

Molecule.slogpVsa3() → number¶

Molecule.slogpVsa4() → number¶

Molecule.slogpVsa5() → number¶

Molecule.slogpVsa6() → number¶

Molecule.slogpVsa7() → number¶

Molecule.slogpVsa8() → number¶

Molecule.slogpVsa9() → number¶

Molecule.slogpVsaWithParams(bins: number[] | Float64Array<ArrayBufferLike> | null, force: boolean) → Float64Array¶

Molecule.smrVsa() → Float64Array¶

Molecule.smrVsa1() → number¶

Molecule.smrVsa10() → number¶

Molecule.smrVsa2() → number¶

Molecule.smrVsa3() → number¶

Molecule.smrVsa4() → number¶

Molecule.smrVsa5() → number¶

Molecule.smrVsa6() → number¶

Molecule.smrVsa7() → number¶

Molecule.smrVsa8() → number¶

Molecule.smrVsa9() → number¶

Molecule.smrVsaWithParams(bins: number[] | Float64Array<ArrayBufferLike> | null, force: boolean) → Float64Array¶

Molecule.stereoisomerCount(options: StereoisomerOptionsConfiguration | StereoisomerOptions) → bigint¶

Molecule.stereoisomerCountWithOptions(options: StereoisomerOptions) → bigint¶

Molecule.substructMatch(query: QueryGraph, params: SubstructMatchOptions | SubstructMatchParams) → MatchResult | null¶

Molecule.substructMatchWithParams(query: QueryGraph, params: SubstructMatchParams) → MatchResult | null¶

Molecule.substructMatches(query: QueryGraph, params: SubstructMatchOptions | SubstructMatchParams) → MatchResult[]¶

Molecule.substructMatchesCompiled(query: CompiledQuery) → MatchResult[]¶

Molecule.substructMatchesWithParams(query: QueryGraph, params: SubstructMatchParams) → MatchResult[]¶

Molecule.tautomerScore(params: TautomerScoreParams | TautomerScoreParamsOptions) → TautomerScore¶

Molecule.tautomerScoreWithParams(params: TautomerScoreParams) → TautomerScore¶

Molecule.tetrahedralStereo() → TetrahedralStereo[]¶

Molecule.toBuilder() → MoleculeBuilder¶

Molecule.toCxSmarts(params: SmartsWriteParamsOptions | SmartsWriteParams) → string¶

Molecule.toCxSmartsWithParams(params: SmartsWriteParams) → string¶

Molecule.toCxSmiles(params: CxSmilesWriteParamsOptions | CxSmilesWriteParams) → string¶

Molecule.toCxSmilesWithParams(params: CxSmilesWriteParams) → string¶

Molecule.toFragmentCxSmiles(atoms: number[], params: FragmentCxSmilesWriteParamsOptions | FragmentCxSmilesWriteParams) → string¶

Molecule.toFragmentCxSmilesWithParams(params: FragmentCxSmilesWriteParams) → string¶

Molecule.toFragmentSmiles(atoms: number[], params: FragmentSmilesWriteParamsOptions | FragmentSmilesWriteParams) → string¶

Molecule.toFragmentSmilesWithParams(params: FragmentSmilesWriteParams) → string¶

Molecule.toInchi(params: InchiWriteParamsOptions | InchiWriteParams) → string¶

Molecule.toInchiKey(params: InchiWriteParamsOptions | InchiWriteParams) → string¶

Molecule.toInchiKeyWithParams(params: InchiWriteParams) → string¶

Molecule.toInchiWithParams(params: InchiWriteParams) → string¶

Molecule.toMol(params: MolBlockWriteParamsOptions | MolBlockWriteParams) → string¶

Molecule.toMolWithParams(params: MolBlockWriteParams) → string¶

Molecule.toPng(width: number, height: number) → Uint8Array¶

Molecule.toRandomSmiles(count: number, seed: number, params: RandomSmilesWriteParamsOptions | RandomSmilesWriteParams) → string[]¶

Molecule.toRandomSmilesWithParams(count: number, seed: number, params: RandomSmilesWriteParams) → string[]¶

Molecule.toSdf(params: MolBlockWriteParamsOptions | MolBlockWriteParams) → string¶

Molecule.toSdf2d(params: MolBlockWriteParamsOptions | MolBlockWriteParams) → string¶

Molecule.toSdf2dWithParams(params: MolBlockWriteParams) → string¶

Molecule.toSdf3d(params: MolBlockWriteParamsOptions | MolBlockWriteParams) → string¶

Molecule.toSdf3dWithParams(params: MolBlockWriteParams) → string¶

Molecule.toSdfWithParams(params: MolBlockWriteParams) → string¶

Molecule.toSmarts(params: SmartsWriteParamsOptions | SmartsWriteParams) → string¶

Molecule.toSmartsWithParams(params: SmartsWriteParams) → string¶

Molecule.toSmiles(params: SmilesWriteParams | SmilesWriteParamsOptions) → string¶

Molecule.toSmilesWithParams(params: SmilesWriteParams) → string¶

Molecule.toSvg(width: number, height: number) → string¶

Molecule.toXyz(params: XyzWriteParamsOptions | XyzWriteParams) → string¶

Molecule.toXyzWithParams(params: XyzWriteParams) → string¶

Molecule.topologicalTorsionIds() → bigint[]¶

Molecule.topologicalTorsionIdsWithParams(torsion_atom_count: number) → bigint[]¶

Molecule.topologicalTorsionPathScore(path: number[] | Uint32Array<ArrayBufferLike>, size: number, atom_codes: number[] | Uint32Array<ArrayBufferLike> | null) → bigint¶

Molecule.topology() → TopologyBlock¶

Molecule.totalAtomCount() → number¶

Molecule.tpsa() → number¶

Molecule.tpsaWithParams(include_sulfur_phosphorus: boolean, force: boolean) → number¶

Molecule.uffEnergyGradient(params: UffEvaluationParamsOptions | UffEvaluationParams) → UffEnergyGradient¶

Molecule.uffEnergyGradientWithParams(params: UffEvaluationParams) → UffEnergyGradient¶

Molecule.uffForceField(params: UffForceFieldParamsOptions | UffForceFieldParams) → MolecularForceField¶

Molecule.uffForceFieldWithParams(params: UffForceFieldParams) → MolecularForceField¶

Molecule.uffHasAllMoleculeParams() → boolean¶

Molecule.with2dCoordinateBlock(coordinates: number[][], params: Coordinate2DInputParamsOptions | Coordinate2DInputParams) → Molecule¶

Molecule.with2dCoordinateBlockWithParams(coordinates: number[][], params: Coordinate2DInputParams) → Molecule¶

Molecule.with2dCoordinates(params: Coordinate2DParamsOptions | Coordinate2DParams) → Molecule¶

Molecule.with2dCoordinatesWithParams(params: Coordinate2DParams) → Molecule¶

Molecule.with3dConformer(params: EmbedParamsOptions | EmbedParams) → Molecule¶

Molecule.with3dConformerResult(params: EmbedParamsOptions | EmbedParams) → EmbedMoleculeResult¶

Molecule.with3dConformerResultWithParams(params: EmbedParams) → EmbedMoleculeResult¶

Molecule.with3dConformerWithParams(params: EmbedParams) → Molecule¶

Molecule.with3dConformers(num_confs: number, params: EmbedParamsOptions | EmbedParams) → Molecule¶

Molecule.with3dConformersResult(num_confs: number, params: EmbedParamsOptions | EmbedParams) → EmbedMultipleConfsResult¶

Molecule.with3dConformersResultWithParams(num_confs: number, params: EmbedParams) → EmbedMultipleConfsResult¶

Molecule.with3dConformersWithParams(num_confs: number, params: EmbedParams) → Molecule¶

Molecule.with3dCoordinates(coordinates: number[][], params: Replace3DCoordinatesParamsOptions | Replace3DCoordinatesParams) → Molecule¶

Molecule.with3dCoordinatesWithParams(coordinates: number[][], params: Replace3DCoordinatesParams) → Molecule¶

Molecule.withAdded3dConformer(coordinates: number[][], params: Coordinate3DInputParamsOptions | Coordinate3DInputParams) → Molecule¶

Molecule.withAdded3dConformerWithParams(coordinates: number[][], params: Coordinate3DInputParams) → Molecule¶

Molecule.withAlignedConformers(params: ConformerAlignmentParametersOptions | ConformerAlignmentParameters) → [Molecule, ConformerAlignmentReport]¶

Molecule.withAlignedConformersWithParams(params: ConformerAlignmentParameters) → [Molecule, ConformerAlignmentReport]¶

Molecule.withAlignmentTo(reference: Molecule, params: AlignmentParametersOptions | AlignmentParameters) → [Molecule, AlignmentResult]¶

Molecule.withAlignmentToWithParams(reference: Molecule, params: AlignmentParameters) → [Molecule, AlignmentResult]¶

Molecule.withAssignedAromaticity(params: AromaticityParamsOptions | AromaticityParams) → Molecule¶

Molecule.withAssignedAromaticityWithParams(params: AromaticityParams) → Molecule¶

Molecule.withAssignedRadicals() → Molecule¶

Molecule.withAssignedRingFamilies(params: RingSearchParamsOptions | RingSearchParams) → Molecule¶

Molecule.withAssignedRingFamiliesWithParams(params: RingSearchParams) → Molecule¶

Molecule.withAssignedRings() → Molecule¶

Molecule.withAssignedValence(params: ValenceParamsOptions | ValenceParams) → Molecule¶

Molecule.withAssignedValenceWithParams(params: ValenceParams) → Molecule¶

Molecule.withAtomPairAtomCode(atom_id: number, branch_subtract: number, include_chirality: boolean, use_legacy_stereo_perception: boolean) → AtomPairAtomCodeResult¶

Molecule.withAtomPosition(atom: number, position: [number, number, number], params: AtomPositionParamsOptions | AtomPositionParams) → Molecule¶

Molecule.withAtomPositionWithParams(atom: number, position: [number, number, number], params: AtomPositionParams) → Molecule¶

Molecule.withAtomProperty(atom: number, key: string, value: string | number | boolean | string[] | number[]) → Molecule¶

Return a new molecule; the receiver and its shared copies are unchanged.

Molecule.withChiralTagsFromStructure(params: StructureTagParamsOptions | StructureTagParams) → Molecule¶

Molecule.withChiralTagsFromStructureWithParams(params: StructureTagParams) → Molecule¶

Molecule.withCipLabels(options: CipLabelOptionsOptions | CipLabelOptions) → Molecule¶

Molecule.withCipLabelsWithOptions(options: CipLabelOptions) → Molecule¶

Molecule.withCleared3dConformers() → Molecule¶

Molecule.withHydrogens(params: AddHsParamsOptions | AddHsParams) → Molecule¶

Molecule.withHydrogensWithParams(params: AddHsParams) → Molecule¶

Molecule.withKekulizedBonds(params: KekulizeParamsOptions | KekulizeParams) → Molecule¶

Molecule.withKekulizedBondsWithParams(params: KekulizeParams) → Molecule¶

Molecule.withMmffOptimized(params: MmffOptimizationParamsOptions | MmffOptimizationParams) → MmffOptimizeMoleculeResult¶

Molecule.withMmffOptimizedConformers(params: MmffConformerOptimizationParamsOptions | MmffConformerOptimizationParams) → MmffOptimizeMoleculeConfsResult¶

Molecule.withMmffOptimizedConformersWithParams(params: MmffConformerOptimizationParams) → MmffOptimizeMoleculeConfsResult¶

Molecule.withMmffOptimizedWithParams(params: MmffOptimizationParams) → MmffOptimizeMoleculeResult¶

Molecule.withName(name: string) → Molecule¶

Returns a molecule with its name replaced.

Molecule.withOnly3dConformer(coordinates: number[][], params: Coordinate3DInputParamsOptions | Coordinate3DInputParams) → Molecule¶

Molecule.withOnly3dConformerWithParams(coordinates: number[][], params: Coordinate3DInputParams) → Molecule¶

Molecule.withProperty(key: string, value: string) → Molecule¶

Returns a molecule with a string property replaced or inserted.

Molecule.withSdfDataField(key: string, value: string) → Molecule¶

Returns a molecule with an SDF data field appended.

Molecule.withUffOptimized(params: UffOptimizationParamsOptions | UffOptimizationParams) → UffOptimizationResult¶

Molecule.withUffOptimizedConformers(params: UffConformerOptimizationParamsOptions | UffConformerOptimizationParams) → UffConformerOptimizationResult¶

Molecule.withUffOptimizedConformersWithParams(params: UffConformerOptimizationParams) → UffConformerOptimizationResult¶

Molecule.withUffOptimizedWithParams(params: UffOptimizationParams) → UffOptimizationResult¶

Molecule.withoutHydrogens(params: RemoveHsParamsOptions | RemoveHsParams) → Molecule¶

Molecule.withoutHydrogensWithParams(params: RemoveHsParams) → Molecule¶

Molecule.writeMol(path: string, params: MolBlockWriteParamsOptions | MolBlockWriteParams) → void¶

Molecule.writeMolWithParams(path: string, params: MolBlockWriteParams) → void¶

Molecule.writePng(path: string, width: number, height: number) → void¶

Molecule.writeSdf(path: string, params: MolBlockWriteParamsOptions | MolBlockWriteParams) → void¶

Molecule.writeSdfFiles(directory: string, file_name: string | null, params: MolBlockWriteParamsOptions | MolBlockWriteParams) → string¶

Molecule.writeSdfFilesWithParams(directory: string, file_name: string | null, params: MolBlockWriteParams) → string¶

Molecule.writeSdfWithParams(path: string, params: MolBlockWriteParams) → void¶

Molecule.writeSvg(path: string, width: number, height: number) → void¶

Molecule.writeXyz(path: string, params: XyzWriteParamsOptions | XyzWriteParams) → void¶

Molecule.writeXyzWithParams(path: string, params: XyzWriteParams) → void¶

static Molecule.fromInchi(text: string, params: InchiReadParamsOptions | InchiReadParams) → Molecule¶

static Molecule.fromInchiWithParams(text: string, params: InchiReadParams) → Molecule¶

static Molecule.fromMol(text: string, params: SdfReadParamsOptions | SdfReadParams) → Molecule¶

static Molecule.fromMol2(text: string, params: Mol2ReadParamsOptions | Mol2ReadParams) → Molecule¶

static Molecule.fromMol2WithParams(text: string, params: Mol2ReadParams) → Molecule¶

static Molecule.fromMolWithParams(text: string, params: SdfReadParams) → Molecule¶

static Molecule.fromParts(topology: TopologyBlock, coordinates: CoordinateBlock, properties: MoleculeProperties) → Molecule¶

static Molecule.fromSdf(text: string, params: SdfReadParamsOptions | SdfReadParams) → Molecule¶

static Molecule.fromSdfWithParams(text: string, params: SdfReadParams) → Molecule¶

static Molecule.fromSmiles(smiles: string, params: SmilesParseParamsOptions | SmilesParseParams) → Molecule¶

static Molecule.fromSmilesWithParams(smiles: string, params: SmilesParseParams) → Molecule¶

static Molecule.fromSmilesWithSanitize(smiles: string, sanitize: boolean) → Molecule¶

static Molecule.fromXyzBlock(text: string) → Molecule¶

static Molecule.new() → Molecule¶

Creates an empty molecule.

static Molecule.readMol(text: string, params: SdfReadParamsOptions | SdfReadParams) → Molecule¶

static Molecule.readMol2(text: string, params: Mol2ReadParamsOptions | Mol2ReadParams) → Molecule¶

static Molecule.readMol2WithParams(text: string, params: Mol2ReadParams) → Molecule¶

static Molecule.readMolWithParams(text: string, params: SdfReadParams) → Molecule¶

static Molecule.readSdf(text: string, params: SdfReadParamsOptions | SdfReadParams) → Molecule¶

static Molecule.readSdfWithParams(text: string, params: SdfReadParams) → Molecule¶

static Molecule.readXyz(text: string) → Molecule¶