rdkit-esm 0.1.0

package/dist/index.d.ts

@@ -0,0 +1,1578 @@
+//#region src/types/rdkit-minimalib-typings.d.ts
+// Type definitons for RDKit.js
+// Project: https://github.com/rdkit/rdkit-js
+// Definitions by: adam-of-barot <https://github.com/adam-of-barot>
+
+type JSONString = string;
+
+/**
+ * Represents a molecule object generated by RDKit.js
+ *
+ * @remarks
+ * JSMol's are created using the {@link RDKitModule.get_mol | RDKitModule.get_mol()} methods.
+ */
+interface JSMol {
+  /** Delete C++ mol objects manually from memory
+   *
+   * See {@link https://emscripten.org/docs/porting/connecting_cpp_and_javascript/embind.html#memory-management | Emscripten docs} for more details
+   */
+  delete(): void;
+
+  // string representations
+
+  /** Returns the SMILES string */
+  get_smiles(details_json?: JSONString): string;
+
+  /** Returns the Chemaxon Extended SMILES string */
+  get_cxsmiles(details_json?: JSONString): string;
+
+  /** Returns the SMARTS string */
+  get_smarts(details_json?: JSONString): string;
+
+  /** Returns the Chemaxon Extended SMARTS string */
+  get_cxsmarts(details_json?: JSONString): string;
+
+  /**
+   * Returns the V2000 Molfile string, unless the molecule contains V3000 features,
+   * in which case it returns a V3000 Molfile string
+   * @param RDKitGetMolBlockOpt as a stringifyed JSON
+   */
+  get_molblock(): string;
+  get_molblock(options: JSONString): string;
+
+  /** Returns the V3000 Molfile string
+   * @param RDKitGetMolBlockOpt as a stringifyed JSON
+   */
+  get_v2Kmolblock(): string;
+  get_v2Kmolblock(options: JSONString): string;
+
+  /** Returns the V3000 Molfile string
+   * @param RDKitGetMolBlockOpt as a stringifyed JSON
+   */
+  get_v3Kmolblock(): string;
+  get_v3Kmolblock(options: JSONString): string;
+
+  /** Return the InChI string */
+  get_inchi(): string;
+  /**
+   * @param args InchI CLI arguments
+   * @example mol.get_inchi("-FixedH -RecMet -SaveOpt -SUU -SLUUD")
+   */
+  get_inchi(args: string): string;
+
+  /** Returns the JSON representation */
+  get_json(): string;
+
+  // array representation
+
+  /** Returns an unsigned integer array representation */
+  get_as_uint8array(): Uint8Array;
+
+  // SVG representations
+
+  /** Returns an SVG of the molecule */
+  get_svg(): string;
+
+  /**
+   * Returns an SVG of the molcule, with atoms highlighted
+   *
+   * @param details A stringified JSON object containing any of the following options https://www.rdkitjs.com/#drawing-molecules-all-options
+   */
+  get_svg_with_highlights(details: string): string;
+
+  // substructure match methods
+
+  /**
+   * Returns a substructure match string
+   *
+   * @param q query molecule
+   * @returns A stringified JSON object containing the matched atoms and bonds of the parent molecule
+   */
+  get_substruct_match(q: JSMol): string;
+
+  /**
+   * Returns all substructure matches
+   *
+   * @param q query molecule
+   * @returns A stringified JSON object containing the matched atoms and bonds of the parent molecule
+   */
+  get_substruct_matches(q: JSMol): string;
+
+  // molecular descriptors
+
+  /** Returns a stringified JSON object of molecular descriptors */
+  get_descriptors(): string;
+
+  // fingerprint methods
+
+  /**
+   * Returns the Morgan fingerprint as string
+   */
+  get_morgan_fp(): string;
+
+  /**
+   * Returns the Morgan fingerprint as string.
+   *
+   * You can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} radius fingerprint radius
+   * @param {number} len fingerprint length
+   */
+  get_morgan_fp(options: JSONString): string;
+
+  /**
+   * Returns the Morgan fingerprint as an unsigned integer array
+   */
+  get_morgan_fp_as_uint8array(): Uint8Array;
+
+  /**
+   * Returns the Morgan fingerprint as an unsigned integer array
+   *
+   * You can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} radius fingerprint radius
+   * @param {number} fplen fingerprint length
+   */
+  get_morgan_fp_as_uint8array(options: JSONString): Uint8Array;
+
+  /**
+   * Returns the pattern fingerprint as string
+   */
+  get_pattern_fp(): string;
+
+  /**
+   * Returns the pattern fingerprint as string
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} len fingerprint length
+   */
+  get_pattern_fp(options: JSONString): string;
+
+  /**
+   * Returns the pattern fingerprint as an unsigned integer array
+   */
+  get_pattern_fp_as_uint8array(): Uint8Array;
+
+  /**
+   * Returns the pattern fingerprint as an unsigned integer array
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} fplen fingerprint length
+   */
+  get_pattern_fp_as_uint8array(options: JSONString): Uint8Array;
+
+  /**
+   * Returns the topological torsion fingerprint as string
+   */
+  get_topological_torsion_fp(): string;
+
+  /**
+   * Returns the topological torsion fingerprint as string
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} len fingerprint length
+   */
+  get_topological_torsion_fp(options: JSONString): string;
+
+  /**
+   * Returns the topological torsion fingerprint as an unsigned integer array
+   */
+  get_topological_torsion_fp_as_uint8array(): Uint8Array;
+
+  /**
+   * Returns the topological torsion fingerprint as an unsigned integer array
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} fplen fingerprint length
+   */
+  get_topological_torsion_fp_as_uint8array(options: JSONString): Uint8Array;
+
+  /**
+   * Returns the rdkit fingerprint as string
+   */
+  get_rdkit_fp(): string;
+
+  /**
+   * Returns the rdkit fingerprint as string
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} len fingerprint length
+   */
+  get_rdkit_fp(options: JSONString): string;
+
+  /**
+   * Returns the rdkit fingerprint as an unsigned integer array
+   */
+  get_rdkit_fp_as_uint8array(): Uint8Array;
+
+  /**
+   * Returns the rdkit fingerprint as an unsigned integer array
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} fplen fingerprint length
+   */
+  get_rdkit_fp_as_uint8array(options: JSONString): Uint8Array;
+
+  /**
+   * Returns the atom pair fingerprint as string
+   */
+  get_atom_pair_fp(): string;
+
+  /**
+   * Returns the atom pair fingerprint as string
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} len fingerprint length
+   */
+  get_atom_pair_fp(options: JSONString): string;
+
+  /**
+   * Returns the atom pair fingerprint as an unsigned integer array
+   */
+  get_atom_pair_fp_as_uint8array(): Uint8Array;
+
+  /**
+   * Returns the atom pair fingerprint as an unsigned integer array
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} fplen fingerprint length
+   */
+  get_atom_pair_fp_as_uint8array(options: JSONString): Uint8Array;
+
+  /**
+   * Returns the maccs fingerprint as string
+   */
+  get_maccs_fp(): string;
+
+  /**
+   * Returns the maccs fingerprint as string
+   *
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {number} len fingerprint length
+   */
+  get_maccs_fp(options: JSONString): string;
+
+  /**
+   * Returns the maccs fingerprint as an unsigned integer array
+   */
+  get_maccs_fp_as_uint8array(): Uint8Array;
+
+  // abbreviation methods
+
+  condense_abbreviations(): string;
+  condense_abbreviations(maxCoverage: number, useLinkers: boolean): string;
+
+  // coord generation
+
+  /**
+   * Aligns molecule with the template.
+   * you can also specify the following options
+   * (passed as a stringified JSON object)
+   * @param {boolean} useCoordGen
+   * @param {boolean} allowOptionalAttachements
+   * @param {boolean} acceptFailure
+   */
+  generate_aligned_coords(templateMol: JSMol, options: JSONString): string;
+
+  /** Returns true if the molecule's structure is valid */
+  is_valid(): boolean;
+  get_num_atoms(): number;
+  get_num_bonds(): number;
+
+  /** Check is the molecule has any 2D coordinates generated */
+  has_coords(): 0 | 2 | 3;
+
+  /** Returns a stringified JSON object containing the atoms and bonds of stereo centers */
+  get_stereo_tags(): string;
+
+  /** Returns the V2000 Molfile representation of the aromatic form of the molecule */
+  get_aromatic_form(): string;
+
+  /** Returns the V2000 Molfile representation of the kekule form of the molecule */
+  get_kekule_form(): string;
+
+  /** Returns the disconnected fragments of the molecule */
+  get_frags(): {
+    mappings: JSONString;
+    molList: MolList;
+  };
+
+  /** Generate new 2D coordinates */
+  set_new_coords(): boolean;
+
+  /**
+   * Generate new 2D coordinates
+   *
+   * @param useCoordGen use the CoordGen algorithm
+   */
+  set_new_coords(useCoordGen: boolean): boolean;
+
+  /** Return a V2000 Molfile string with newly generated coordinates */
+  get_new_coords(): string;
+
+  /**
+   * Return a V2000 Molfile string with newly generated coordinates
+   *
+   * @param useCoordGen use the CoordGen algorithm
+   */
+  get_new_coords(useCoordGen: boolean): string;
+
+  // property methods
+
+  /**
+   * Check whether the molecule has a certain property
+   *
+   * @param key property name
+   */
+  has_prop(key: string): boolean;
+
+  /** Returns the list of property names */
+  get_prop_list(): StringList;
+  get_prop_list(includePrivate: boolean): StringList;
+  get_prop_list(includePrivate: boolean, includeComputed: boolean): StringList;
+
+  /**
+   * Sets a property on the molecule
+   *
+   * @param key property name
+   * @param val property value
+   */
+  set_prop(key: string, val: string): boolean;
+
+  /**
+   * Sets a property on the molecule
+   *
+   * @param key property name
+   * @param val property value
+   * @param computed set true to flag the value as computed
+   */
+  set_prop(key: string, val: string, computed: boolean): boolean;
+
+  /**
+   * Get a property on the molecule
+   *
+   * @param key property name
+   */
+  get_prop(key: string): string;
+
+  /**
+   * Clears a property from the molecule
+   *
+   * @param key property name
+   */
+  clear_prop(key: string): boolean;
+
+  // hydrogen methods
+
+  /**
+   * Remove explicit hydrogens
+   *
+   * @returns V2000 Molfile string without explicit hydrogens
+   */
+  remove_hs(): string;
+  remove_hs(options: JSONString): string;
+
+  /** Remove explicit hydrogens from the molecule */
+  remove_hs_in_place(): boolean;
+  remove_hs_in_place(options: JSONString): boolean;
+
+  /**
+   * Add explicit hydrogens
+   *
+   * @returns V2000 Molfile string with explicit hydrogens
+   */
+  add_hs(): string;
+
+  /** Add explicit hydrogens on the molecule */
+  add_hs_in_place(): boolean;
+
+  // aromaticity methods
+
+  convert_to_aromatic_form(): void;
+  convert_to_kekule_form(): void;
+
+  /** Add component to the molecule object
+   * @param options stringified JSON object with { offset: [number, number, number] }
+   */
+  combine_with(other: JSMol, options?: string): void;
+
+  /** Returns a copy of the molecule */
+  copy(): JSMol;
+
+  // depiction methods
+
+  normalize_depiction(): number;
+  normalize_depiction(canonicalize: number): number;
+  normalize_depiction(canonicalize: number, scaleFactor: number): number;
+  straighten_depiction(smallRotation?: boolean): void;
+
+  // canvas methods
+
+  /**
+   * Draw the molecule to an HTML5 canvas
+   *
+   * @param canvas canvas ID
+   * @param width width in pixels
+   * @param height height in pixels
+   */
+  draw_to_canvas(canvas: HTMLCanvasElement, width: number, height: number): void;
+
+  /**
+   * Draw the molecule to an HTML5 canvas, with atom highlights
+   *
+   * @param canvas canvas ID
+   * @param details A stringified JSON object containing any of the following options https://www.rdkitjs.com/#drawing-molecules-all-options
+   */
+  draw_to_canvas_with_highlights(canvas: HTMLCanvasElement, details: string): void;
+
+  /**
+   * Draw the molecule to an HTML5 canvas with an offset
+   *
+   * @param canvas canvas ID
+   * @param offsetx offset X in pixels
+   * @param offsety offset Y in pixels
+   * @param width width in pixels
+   * @param height height in pixels
+   */
+  draw_to_canvas_with_offset(canvas: HTMLCanvasElement, offsetx: number, offsety: number, width: number, height: number): void;
+}
+interface JSReaction extends Pick<JSMol, 'delete' | 'draw_to_canvas' | 'draw_to_canvas_with_highlights' | 'get_svg' | 'get_svg_with_highlights'> {
+  is_Deleted(): boolean;
+  clone(): JSReaction;
+  run_reactants(reactants: MolList, maxProducts: number): EmscriptenVector<MolList>;
+}
+/**
+ * An object containing a collection of structures. Used for efficient substructure searching.
+ *
+ * @remarks
+ * Add molecules to the library with the {@link add_mol}, {@link add_smiles} or {@link add_trusted_smiles} methods.
+ *
+ * Perform substructure searches with the {@link get_matches} method.
+ */
+interface SubstructLibrary {
+  /**
+   * Add a molecule to the library
+   *
+   * @param m molecule
+   */
+  add_mol(m: JSMol): number;
+
+  /**
+   * Add a molecule to the library
+   *
+   * @param smi SMILES string
+   */
+  add_smiles(smi: string): number;
+
+  /**
+   * Add a molecule to the library.
+   *
+   * Molecule validity will not be checked!
+   *
+   * @param smi SMILES string (trusted to be valid)
+   */
+  add_trusted_smiles(smi: string): number;
+
+  /**
+   * Get a molecule from the library
+   *
+   * @param i index of the molecule
+   */
+  get_mol(i: number): JSMol;
+
+  /**
+   * Get all molecules from the library matching the substructure query
+   *
+   * @param q query molecule
+   */
+  get_matches(q: JSMol): string;
+
+  /**
+   * Get all molecules from the library matching the substructure query
+   *
+   * @param q query molecule
+   * @param maxResults maximum number of results
+   */
+  get_matches(q: JSMol, maxResults: number): string;
+
+  /**
+   * Get all molecules from the library matching the substructure query
+   *
+   * @param q query molecule
+   * @param useChirality set to true to enable chiral substructure searching
+   * @param numThreads number of threads to use
+   * @param maxResults maximum number of results
+   */
+  get_matches(q: JSMol, useChirality: boolean, numThreads: number, maxResults: number): string;
+
+  /**
+   * Return the number of substructure matches
+   *
+   * @param q query molecule
+   */
+  count_matches(q: JSMol): number;
+
+  /**
+   * Return the number of substructure matches
+   *
+   * @param q query molecule
+   * @param useChirality set to true to enable chiral substructure searching
+   * @param numThreads number of threads to use
+   */
+  count_matches(q: JSMol, useChirality: boolean, numThreads: number): number;
+}
+interface MolList {
+  /**
+   * push back a molecule to the list and return the new size of the list
+   * @param m molecule
+   */
+  append(m: JSMol): number;
+
+  /**
+   * return the molecule at index i, or null if i is out of bounds
+   * @param i position in the list (0-based index)
+   */
+  at(i: number): JSMol | null;
+
+  /**
+   * returns true if the current index for iteration is at the end of the list
+   * @returns boolean
+   */
+  at_end: () => boolean;
+  clone: () => MolList;
+  delete: () => void;
+  isDeleted: () => boolean;
+
+  /**
+   * Insert a molecule at the specified index
+   * @param i index at which to insert the molecule
+   * @param m molecule to insert
+   * @returns new size of the list
+   */
+  insert(i: number, m: JSMol): number;
+
+  /**
+   * Return the next molecule in the list, or null if at the end of the list. Advances the internal index by 1.
+   * @returns next molecule or null
+   */
+  next: () => JSMol | null;
+
+  /**
+   * Returns the molecule at index i and removes it and all subsequent molecules from the list. Returns null if i is out of bounds.
+   * @param i index at which to pop the molecule
+   */
+  pop(i: number): JSMol | null;
+
+  /**
+   * Reset the internal index for iteration to the beginning of the list
+   * @returns void
+   */
+  reset: () => void;
+
+  /**
+   * Return the current size of the list
+   * @returns size of the list
+   */
+  size: () => number;
+}
+/** Emscripten vector<T> wrapper — raw std::vector binding with get/size/delete */
+interface EmscriptenVector<T> {
+  size(): number;
+  get(i: number): T;
+  delete(): void;
+}
+/** Emscripten vector<string> wrapper */
+interface StringList extends EmscriptenVector<string> {}
+// constructor interfaces
+
+/** Returns a new SubstructLibrary instance */
+interface SubstructLibraryConstructor {
+  new (): SubstructLibrary;
+}
+interface MolListConstructor {
+  new (): MolList;
+}
+interface RGroupDecomposition {
+  add(mol: JSMol): number;
+  process(): boolean;
+  get_rgroups_as_columns(): {
+    [key: 'Core' | `R${number}`]: MolList;
+  };
+  get_rgroups_as_rows(): {
+    [key: 'Core' | `R${number}`]: JSMol;
+  }[];
+  delete(): void;
+}
+
+/** The main RDKit module */
+interface RDKitModule {
+  SubstructLibrary: SubstructLibraryConstructor;
+  MolList: MolListConstructor;
+
+  /**
+   * Create a molecule from a variety of input strings.
+   * This will return null if the input is invalid.
+   *
+   * @param input SMILES / SMARTS / MolFile / JSON string
+   * @param details_json @type {RDKitGetMolOpt}
+   */
+  get_mol(input: string, details_json?: string): JSMol | null;
+
+  /**
+   * Create a molecule from an integer array
+   *
+   * @param pklAsUInt8Array unsigned integer array
+   */
+  get_mol_from_uint8array(pklAsUInt8Array: Uint8Array): JSMol;
+
+  /**
+   * Create a copy of a molecule
+   *
+   * @param other molecule to copy
+   */
+  get_mol_copy(other: JSMol): JSMol;
+
+  /**
+   * Create a query molecule
+   * This will return null if the input is invalid.
+   *
+   * @param input SMARTS string
+   */
+  get_qmol(input: string): JSMol | null;
+  get_qmol(input: string, details_json?: string): JSMol | null;
+
+  /**
+   * Create a reaction instance
+   * @param input
+   * @param details_json RDKitRxnDetails in JSON string format
+   */
+  get_rxn(input: string, details_json?: JSONString): JSReaction;
+
+  /**
+   * Get the InChI key for an InChI string
+   *
+   * @param inchi InChI string
+   */
+  get_inchikey_for_inchi(inchi: string): string;
+  get_mcs_as_json(list: MolList, details_json?: string): string;
+  get_mcs_as_mol(list: MolList, details_json?: string): JSMol;
+  get_mcs_as_smarts(list: MolList, details_json?: string): string;
+
+  /**
+   * Zip two molecules together using dummy attachments by default,
+   * or specified labels in the details_json argument
+   * @param mol1
+   * @param mol2
+   * @param details_json
+   * @example
+   * const mol1 = RDKitModule.get_mol("F/C=C/[*:1]");
+   * const mol2 = RDKitModule.get_mol("[*:1]F");
+   * const mol = RDKitModule.molzip(mol1, mol2); // returns the molecule represented by "F/C=C/F"
+   */
+  molzip(mol1: JSMol, mol2: JSMol, details_json?: string): JSMol;
+  get_rgd(core: JSMol | MolList, details_json?: string): RGroupDecomposition;
+
+  /**
+   * Get the version number of the RDKit module
+   */
+  version(): string;
+
+  /**
+   * Set whether to prefer the CoordGen library's algorithm for coordinate generation
+   *
+   * @param prefer
+   */
+  prefer_coordgen(prefer: boolean): void;
+
+  /**
+   * Set whether to use legacy stereo perception
+   *
+   * @param value
+   */
+  use_legacy_stereo_perception(value: boolean): void;
+  enable_logging(): void;
+  disable_logging(): void;
+  /**
+   * Create a JSLog handle object and log messages to its buffer and the browser console
+   *
+   * @example const logHandle = rdkit.set_log_tee('rdApp.*')
+   * const logBuffer = logHandle.get_buffer()
+   * logHandle.clear_buffer()
+   * logHandle.delete()
+   */
+  set_log_tee(logLevel: LogLevel): RDKitJSLog;
+  /**
+   * Create a JSLog handle object and log messages to its buffer
+   *
+   * @example const logHandle = rdkit.set_log_tee('rdApp.*')
+   * const logBuffer = logHandle.get_buffer()
+   * logHandle.clear_buffer()
+   * logHandle.delete()
+   */
+
+  set_log_capture(logLevel: LogLevel): RDKitJSLog;
+}
+type LogLevel = 'rdApp.debug' | 'rdApp.info' | 'rdApp.warning' | 'rdApp.error' | 'rdApp.*';
+type RDKitJSLog = {
+  get_buffer(): string;
+  clear_buffer(): void;
+  delete(): void;
+  isDeleted(): boolean;
+};
+type RDKitLoaderOptions = {
+  /**
+   * Optional path to the RDKit module .wasm file on your server.
+   */
+  locateFile?: () => string;
+};
+
+/**
+ * Loads the RDKit module asynchronously.
+ * In order to use the RDKit module, calling this function is necessary.
+ */
+type RDKitLoader = (options?: RDKitLoaderOptions) => Promise<RDKitModule>;
+declare global {
+  interface Window {
+    initRDKitModule: RDKitLoader;
+  }
+}
+//#endregion
+//#region src/types/rdkit-minimalib-json-typings.d.ts
+/**
+ * Manually generated typings for the RDKit module functions responses and parameters
+ */
+
+type RDKitDescriptorNames = 'exactmw' | 'amw' | 'lipinskiHBA' | 'lipinskiHBD' | 'NumRotatableBonds' | 'NumHBD' | 'NumHBA' | 'NumHeavyAtoms' | 'NumAtoms' | 'NumHeteroatoms' | 'NumAmideBonds' | 'FractionCSP3' | 'NumRings' | 'NumAromaticRings' | 'NumAliphaticRings' | 'NumSaturatedRings' | 'NumHeterocycles' | 'NumAromaticHeterocycles' | 'NumSaturatedHeterocycles' | 'NumAliphaticHeterocycles' | 'NumSpiroAtoms' | 'NumBridgeheadAtoms' | 'NumAtomStereoCenters' | 'NumUnspecifiedAtomStereoCenters' | 'labuteASA' | 'tpsa' | 'CrippenClogP' | 'CrippenMR' | 'chi0v' | 'chi1v' | 'chi2v' | 'chi3v' | 'chi4v' | 'chi0n' | 'chi1n' | 'chi2n' | 'chi3n' | 'chi4n' | 'hallKierAlpha' | 'kappa1' | 'kappa2' | 'kappa3' | 'Phi';
+type RDKitDescriptors = Record<RDKitDescriptorNames, number>;
+type RDKitAtom = {
+  chg: number;
+  /** Implicit Hydrogens count */
+  impHs: number;
+  isotope: number;
+  nRad: number;
+  stereo: 'unspecified' | 'cw' | 'ccw' | 'other';
+  z: number;
+};
+type RDKitBond = {
+  /** Bond order */
+  bo: number;
+  stereo: 'unspecified' | 'cis' | 'trans' | 'either';
+  stereoAtoms: [number, number];
+  atoms: [number, number];
+};
+type RDKitExtension = {
+  aromaticAtoms?: number[];
+  aromaticBonds?: number[];
+  atomRings?: number[][];
+  cipCodes: [number, 'R' | 'S'][];
+  cipRanks: number[];
+  formatVersion: number;
+  name: 'rdkitRepresentation';
+  toolkitVersion: string;
+};
+type RDKitConformer2D = {
+  dim: 2;
+  coords: [number, number][];
+};
+type RDKitConformer3D = {
+  dim: 3;
+  coords: [number, number, number][];
+};
+type RDKitMolecule = {
+  atoms: Partial<RDKitAtom>[];
+  bonds: (Partial<RDKitBond> & Pick<RDKitBond, 'atoms'>)[];
+  conformers?: RDKitConformer2D[] | RDKitConformer3D[];
+  extensions: RDKitExtension[];
+  name: string;
+};
+type RDKitJson = {
+  defaults: {
+    atom: RDKitAtom;
+    bond: RDKitBond;
+  };
+  molecules: RDKitMolecule[];
+};
+type DrawColour = [number, number, number, number?];
+type ColourPalette = {
+  [k: number]: DrawColour;
+};
+type RDKitDepictionDetails = {
+  width: number;
+  height: number;
+  offsetx: number;
+  offsety: number;
+  atomLabelDeuteriumTritium: boolean;
+  dummiesAreAttachments: boolean;
+  circleAtoms: boolean;
+  splitBonds: boolean;
+  highlightColour: DrawColour;
+  continuousHighlight: boolean;
+  fillHighlights: boolean;
+  highlightRadius: number;
+  flagCloseContactsDist: number;
+  includeAtomTags: boolean;
+  clearBackground: boolean;
+  backgroundColour: DrawColour;
+  legendFontSize: number;
+  legendFraction: number;
+  maxFontSize: number;
+  minFontSize: number;
+  fixedFontSize: number;
+  annotationFontScale: number;
+  fontFile: string;
+  legendColour: DrawColour;
+  multipleBondOffset: number;
+  padding: number;
+  additionalAtomLabelPadding: number;
+  atomLabels: Record<number, string>;
+  noAtomLabels: boolean;
+  atomRegions: number[][];
+  symbolColour: DrawColour;
+  annotationColour: DrawColour;
+  bondLineWidth: number;
+  scaleBondWidth: number;
+  scaleHighlightBondWidth: boolean;
+  highlightBondWidthMultiplier: number;
+  prepareMolsBeforeDrawing: boolean;
+  highlightColourPalette: DrawColour[];
+  atomColourPalette: ColourPalette;
+  fixedScale: number;
+  fixedBondLength: number;
+  rotate: number;
+  addAtomIndices: boolean;
+  addBondIndices: boolean;
+  isotopeLabels: boolean;
+  dummyIsotopeLabels: boolean;
+  addStereoAnnotation: boolean;
+  atomHighlightsAreCircles: boolean;
+  centreMoleculesBeforeDrawing: boolean;
+  explicitMethyl: boolean;
+  includeRadicals: boolean;
+  includeMetadata: boolean;
+  comicMode: boolean;
+  variableBondWidthMultiplier: number;
+  variableAtomRadius: number;
+  variableAttachmentColour: DrawColour;
+  includeChiralFlagLabel: boolean;
+  simplifiedStereoGroupLabel: boolean;
+  unspecifiedStereoIsUnknown: boolean;
+  singleColourWedgeBonds: boolean;
+  useMolBlockWedging: boolean;
+  scalingFactor: number;
+  baseFontSize: number;
+  drawMolsSameScale: boolean;
+  atoms: number[];
+  bonds: number[];
+  highlightAtomColors: Record<number, DrawColour>;
+  highlightBondColors: Record<number, DrawColour>;
+  standardColoursForHighlightedAtoms: boolean;
+};
+type RDKitRxnDepictionDetails = RDKitDepictionDetails & {
+  highlightByReactant: boolean;
+  highlightColorsReactants: DrawColour[];
+};
+type RDKitStereoTags = {
+  CIP_atoms: [number, '(S)' | '(R)' | '(?)'][];
+  CIP_bonds: [number, number, string][];
+};
+type RDKitRxnDetails = {
+  sanitize: boolean;
+  useSmiles: boolean;
+  removeHs: boolean;
+  strictParsing: boolean;
+  adjustReactants: boolean;
+  mergeQueryHs: boolean;
+};
+type RDKitSubstructMatch = {
+  atoms: number[];
+  bonds: number[];
+};
+type RDKitGetMolOpt = {
+  kekulize: boolean;
+  setAromaticity: boolean;
+  fastFindRings: boolean;
+  mappedDummiesAreRGroups: boolean;
+  sanitize: boolean;
+  removeHs: boolean;
+  assignStereo: boolean;
+  mergeQueryHs: boolean;
+};
+type RDKitGetMolBlockOptions = {
+  /** @default true */
+  includeStereo: boolean;
+  /** @default true */
+  kekulize: boolean;
+  /** @default false */
+  useMolBlockWedging: boolean;
+  /** @default false */
+  addChiralHs: boolean;
+  /** @default 'AUTO' */
+  forceMDLVersion: 'AUTO' | 'V2000' | 'V3000';
+};
+type RDKitGetSmilesOptions = {
+  /** Include stereochemistry and isotope information @default true */
+  doIsomericSmiles: boolean;
+  /**
+   * Kekulize the molecule before generating the SMILES and output
+   * single/double bonds. NOTE that the output is not canonical and that this
+   * will throw an exception if the molecule cannot be kekulized.
+   * @default false
+   */
+  doKekule: boolean;
+  /**
+   * Make sure the SMILES starts at the specified atom. The resulting SMILES
+   * is not canonical and the value of the canonical parameter will be ignored.
+   * @default -1
+   */
+  rootedAtAtom: number;
+  /** Generate canonical SMILES @default true */
+  canonical: boolean;
+  /** Include symbols for all bonds @default false */
+  allBondsExplicit: boolean;
+  /** Provide hydrogen counts for every atom @default false */
+  allHsExplicit: boolean;
+  /**
+   * Randomize the output order. The resulting SMILES is not canonical and
+   * the value of the canonical parameter will be ignored.
+   * @default false
+   */
+  doRandom: boolean;
+};
+/** CX extension field names (without the `CX_` prefix) */
+type CxSmilesField = 'NONE' | 'ATOM_LABELS' | 'MOLFILE_VALUES' | 'COORDS' | 'RADICALS' | 'ATOM_PROPS' | 'LINKNODES' | 'ENHANCEDSTEREO' | 'SGROUPS' | 'POLYMER' | 'BOND_CFG' | 'BOND_ATROPISOMER' | 'COORDINATE_BONDS' | 'HYDROGEN_BONDS' | 'ZERO_BONDS' | 'ALL' | 'ALL_BUT_COORDS';
+type RDKitGetMCSOptions = {
+  MaximizeBonds: boolean;
+  Threshold: number;
+  Timeout: number;
+  InitialSeed: string;
+  MatchValences: boolean;
+  MatchChiralTag: boolean;
+  MatchFormalCharge: boolean;
+  /**
+   * @alias BondRingMatchesRingOnly
+   */
+  RingMatchesRingOnly: boolean;
+  AtomRingMatchesRingOnly: boolean;
+  BondRingMatchesRingOnly: boolean;
+  MaxDistance: number;
+  /**
+   * @alias BondCompleteRingsOnly
+   */
+  CompleteRingsOnly: boolean;
+  AtomCompleteRingsOnly: boolean;
+  BondCompleteRingsOnly: boolean;
+  /**
+   * @alias BondCompleteRingsOnly
+   */
+  CompleteRingsOnly: boolean;
+  MatchFusedRings: boolean;
+  MatchFusedRingsStrict: boolean;
+  MatchStereo: boolean;
+  StoreAll: boolean;
+  AtomCompare: 'Elements' | 'Any' | 'Isotopes' | 'AnyHeavy';
+  BondCompare: 'Order' | 'Any' | 'OrderExact';
+};
+type RDKitMCSResult = {
+  numAtoms: number;
+  numBonds: number;
+  canceled: boolean;
+  /**
+   * Can be an array iff option `StoreAll` is set to true
+   */
+  smarts: string | string[];
+};
+type RDKitMorganFPOptions = {
+  /** @default 2 */
+  radius: number;
+  /** @default 2048 */
+  nBits: number;
+  /** @default false */
+  useCountSimulation: boolean;
+  /** @default false */
+  useChirality: boolean;
+  /** @default true */
+  useBondTypes: boolean;
+  /** @default false */
+  includeRedundantEnvironments: boolean;
+  /** @default false */
+  onlyNonzeroInvariants: boolean;
+};
+type RDKitPatternFPOptions = {
+  /** @default 2048 */
+  nBits: number;
+  /** @default false */
+  tautomericFingerprint: boolean;
+};
+type RDKitTopologicalTorsionFPOptions = {
+  /** @default 2048 */
+  nBits: number;
+  /** @default false */
+  useChirality: boolean;
+  /** @default 4 */
+  torsionAtomCount: number;
+  /** @default true */
+  useCountSimulation: boolean;
+};
+type RDKitRdkitFpOptions = {
+  /** @default 2048 */
+  nBits: number;
+  /** @default 2 */
+  nBitsPerHash: number;
+  /** @default 1 */
+  minPath: number;
+  /** @default 7 */
+  maxPath: number;
+  /** @default true */
+  useBondOrder: boolean;
+  /** @default true */
+  branchedPaths: boolean;
+  /** @default false */
+  useCountSimulation: boolean;
+  /** @default true */
+  useHs: boolean;
+};
+type RDKitAtomPairFPOptions = {
+  /** @default 2048 */
+  nBits: number;
+  /** @default false */
+  useChirality: boolean;
+  /** @default 1 */
+  minLength: number;
+  /** @default 30 */
+  maxLength: number;
+  /** @default true */
+  useCountSimulation: boolean;
+  /** @default true */
+  use2D: boolean;
+};
+type RDKitRemoveHsOptions = {
+  /** @default false — hydrogens that have no bonds */
+  removeDegreeZero: boolean;
+  /** @default false — hydrogens with two (or more) bonds */
+  removeHigherDegrees: boolean;
+  /** @default false — hydrogens with bonds only to other hydrogens */
+  removeOnlyHNeighbors: boolean;
+  /** @default false — hydrogens with non-default isotopes */
+  removeIsotopes: boolean;
+  /** @default false — removes isotopic Hs, tracks them via _isotopicHs property */
+  removeAndTrackIsotopes: boolean;
+  /** @default false — hydrogens with at least one dummy-atom neighbor */
+  removeDummyNeighbors: boolean;
+  /** @default false — hydrogens defining bond stereochemistry */
+  removeDefiningBondStereo: boolean;
+  /** @default true — hydrogens with wedged bonds */
+  removeWithWedgedBond: boolean;
+  /** @default false — hydrogens with queries defined */
+  removeWithQuery: boolean;
+  /** @default true — mapped hydrogens */
+  removeMapped: boolean;
+  /** @default true — hydrogens in SubstanceGroups */
+  removeInSGroups: boolean;
+  /** @default true — display warnings for Hs that are not removed */
+  showWarnings: boolean;
+  /** @default true @deprecated — equivalent of !implicitOnly */
+  removeNonimplicit: boolean;
+  /** @default false @deprecated */
+  updateExplicitCount: boolean;
+  /** @default false — remove hydrides */
+  removeHydrides: boolean;
+  /** @default false — remove Hs bonded to atoms with non-tetrahedral stereochemistry */
+  removeNontetrahedralNeighbors: boolean;
+};
+type RDKitAlignedCoordsOptions = {
+  useCoordGen: boolean;
+  referenceSmarts: string;
+  allowRGroups: boolean;
+  acceptFailure: boolean;
+  alignOnly: boolean;
+};
+type RDKitMolZipOptions = {
+  Label: string;
+  AtomSymbols: string[];
+  AtomProperty: string;
+  EnforceValenceRules: boolean;
+  GenerateCoordinates: boolean;
+  AlignCoordinates: boolean;
+};
+type RDKitGetRgdOptions = {
+  labels: 'IsotopeLabels' | 'AtomMapLabels' | 'MDLRGroupLabels' | 'DummyAtomLabels' | 'AtomIndexLabels' | 'AutoDetect' | 'RelabelDuplicateLabels';
+  /**
+   * choose where the rlabels are stored on the decomposition
+   * @default "AtomMap | MDLRGroup"
+   * */
+  rgroupLabelling: 'AtomMap' | 'Isotope' | 'MDLRGroup';
+  alignment: 'None' | 'NoAlignment' | 'MCS';
+  scoreMethod: 'Match' | 'FingerprintVariance';
+  matchingStrategy: 'Greedy' | 'GreedyChunks' | 'Exhaustive' | 'NoSymmetrization' | 'GA';
+  /**
+   * only allow rgroup decomposition at the specified rgroups
+   */
+  onlyMatchAtRGroups: boolean;
+  removeAllHydrogenRGroupsAndLabels: boolean;
+  removeHydrogensPostMatch: boolean;
+  allowNonTerminalRGroups: boolean;
+  doTautomers: boolean;
+  doEnumeration: boolean;
+  allowMultipleRGroupsOnUnlabelled: boolean;
+  allowMultipleCoresInSameMol: boolean;
+  includeTargetMolInResults: boolean;
+  timeout: number;
+  chunkSize: number;
+};
+//#endregion
+//#region src/mol-array.d.ts
+/**
+ * An array of {@link Mol} instances with batch lifecycle management.
+ *
+ * Extends the native `Array` so all standard array methods (indexing,
+ * iteration, `map`, `filter`, …) work out of the box.
+ *
+ * Call {@link delete} (or use the `using` keyword) to delete every `Mol`
+ * in the array at once.
+ */
+declare class MolArray extends Array<Mol> implements Disposable {
+  /** Deletes every Mol in this array */
+  delete(): void;
+  /** Disposable support — allows use with the `using` keyword */
+  [Symbol.dispose](): void;
+}
+//#endregion
+//#region src/types/inchi.d.ts
+type InChI_Flags = 'DoNotAddH' | 'SNon' | 'SRel' | 'SRac' | 'SUCF' | 'ChiralFlagON' | 'ChiralFlagOff' | 'SUU' | 'SLUUD' | 'FixedH' | 'RecMet' | 'KET' | '15T' | 'AuxNone';
+//#endregion
+//#region src/types/rdkit-esm.typings.d.ts
+/** Wrapper-level CX SMILES options with ergonomic `fields` array */
+type RDKitGetCxSmilesOptions = RDKitGetSmilesOptions & {
+  /** CX extension fields to include. Omit for all fields (default). Empty array for none. */
+  fields: CxSmilesField[];
+  /** Restore bond direction option. Accepts `true`, `'true'`, or `'clear'`. */
+  restoreBondDirOption: true | 'true' | 'clear';
+};
+//#endregion
+//#region src/mol.d.ts
+/**
+ * A wrapper around RDKit's JSMol object providing a typed, camelCase API.
+ *
+ * @remarks
+ * Mol instances are created via RDKit.getMol or RDKit.getQMol,
+ * not directly by consumers. The underlying `jsMol` is accessible for advanced use cases.
+ *
+ * Implements `Disposable` for use with the `using` keyword:
+ * ```ts
+ * using mol = rdkit.getMol('c1ccccc1')!;
+ * const svg = mol.getSvg();
+ * // mol is automatically deleted when the scope exits
+ * ```
+ */
+declare class Mol implements Disposable {
+  #private;
+  constructor(jsMol: JSMol, module: RDKitModule);
+  /**
+   * The underlying JSMol object for direct access to the raw API.
+   * @throws If the molecule has been deleted.
+   */
+  get jsMol(): JSMol;
+  /**
+   * Resolves a substructure query argument to a JSMol.
+   * If the query is a string, creates a temporary query molecule.
+   * @returns A tuple of [jsMol, shouldDelete] where shouldDelete indicates
+   *          whether the caller is responsible for deleting the JSMol.
+   */
+  private resolveQuery;
+  /** Returns the canonical SMILES string */
+  getSmiles(options?: RDKitGetSmilesOptions): string;
+  /** Returns the Chemaxon Extended SMILES string */
+  getCxSmiles(options?: Partial<RDKitGetCxSmilesOptions>): string;
+  /** Returns the SMARTS string */
+  getSmarts(options?: RDKitGetSmilesOptions): string;
+  /** Returns the Chemaxon Extended SMARTS string */
+  getCxSmarts(options?: Partial<RDKitGetCxSmilesOptions>): string;
+  /**
+   * Returns the V2000 Molfile string
+   * @param options - Molblock generation options
+   */
+  getMolblock(options?: Partial<RDKitGetMolBlockOptions>): string;
+  /**
+   * Returns the V3000 Molfile string
+   * @param options - Molblock generation options
+   */
+  getV2KMolblock(options?: Partial<RDKitGetMolBlockOptions>): string;
+  /**
+   * Returns the V3000 Molfile string
+   * @param options - Molblock generation options
+   */
+  getV3KMolblock(options?: Partial<RDKitGetMolBlockOptions>): string;
+  /**
+   * Returns the InChI string
+   * @param args - Optional InChI CLI arguments
+   * @example mol.getInchi(["FixedH", "RecMet", "SaveOpt", "SUU", "SLUUD"])
+   */
+  getInchi(args?: InChI_Flags[]): string;
+  /**
+   * Returns the InChIKey string
+   * @param args - Optional InChI CLI arguments
+   * @example mol.getInchi(["FixedH", "RecMet", "SaveOpt", "SUU", "SLUUD"])
+   */
+  getInchikey(args?: InChI_Flags[]): string;
+  /** Returns the parsed JSON representation of the molecule */
+  getJson(): RDKitJson;
+  /** Returns an unsigned integer array representation of the molecule */
+  getAsUint8Array(): Uint8Array;
+  /**
+   * Returns an SVG depiction of the molecule
+   *
+   * @param options - Drawing options including dimensions and highlighting.
+   *   When omitted, uses RDKit defaults (250×200).
+   *
+   * @example
+   * // Default SVG
+   * const svg = mol.getSvg();
+   *
+   * // Custom size with atom indices
+   * const svg = mol.getSvg({ width: 400, height: 300, addAtomIndices: true });
+   *
+   * // With atom highlighting
+   * const svg = mol.getSvg({ atoms: [0, 1, 2], highlightColour: [1, 0, 0, 1] });
+   */
+  getSvg(options?: Partial<RDKitDepictionDetails>): string;
+  /**
+   * Returns the first substructure match
+   *
+   * @param query - A Mol instance or a SMARTS string to use as query
+   * @returns The matched atom and bond indices
+   */
+  getSubstructMatch(query: Mol | string): RDKitSubstructMatch;
+  /**
+   * Returns all substructure matches
+   *
+   * @param query - A Mol instance or a SMARTS string to use as query
+   * @returns An array of matched atom and bond indices
+   */
+  getSubstructMatches(query: Mol | string): RDKitSubstructMatch[];
+  /** Returns molecular descriptors as a typed object */
+  getDescriptors(): RDKitDescriptors | null;
+  /**
+   * Returns the Morgan fingerprint as a bit string
+   * @param options - Fingerprint options
+   */
+  getMorganFp(options?: Partial<RDKitMorganFPOptions>): string;
+  /** Returns the pattern fingerprint as a bit string */
+  getPatternFp(options?: Partial<RDKitPatternFPOptions>): string;
+  /** Returns the topological torsion fingerprint as a bit string */
+  getTopologicalTorsionFp(options?: Partial<RDKitTopologicalTorsionFPOptions>): string;
+  /** Returns the RDKit fingerprint as a bit string */
+  getRdkitFp(options?: Partial<RDKitRdkitFpOptions>): string;
+  /** Returns the atom pair fingerprint as a bit string */
+  getAtomPairFp(options?: Partial<RDKitAtomPairFPOptions>): string;
+  /** Returns the MACCS fingerprint as a bit string (fixed 167-bit) */
+  getMaccsFp(): string;
+  /** Returns the Morgan fingerprint as a Uint8Array */
+  getMorganFpAsUint8Array(options?: Partial<RDKitMorganFPOptions>): Uint8Array;
+  /** Returns the pattern fingerprint as a Uint8Array */
+  getPatternFpAsUint8Array(options?: Partial<RDKitPatternFPOptions>): Uint8Array;
+  /** Returns the topological torsion fingerprint as a Uint8Array */
+  getTopologicalTorsionFpAsUint8Array(options?: Partial<RDKitTopologicalTorsionFPOptions>): Uint8Array;
+  /** Returns the RDKit fingerprint as a Uint8Array */
+  getRdkitFpAsUint8Array(options?: Partial<RDKitRdkitFpOptions>): Uint8Array;
+  /** Returns the atom pair fingerprint as a Uint8Array */
+  getAtomPairFpAsUint8Array(options?: Partial<RDKitAtomPairFPOptions>): Uint8Array;
+  /** Returns the MACCS fingerprint as a Uint8Array */
+  getMaccsFpAsUint8Array(): Uint8Array;
+  /**
+   * Checks whether the molecule has a given property
+   * @param key - Property name
+   */
+  hasProp(key: string): boolean;
+  /**
+   * Gets a property value from the molecule
+   * @param key - Property name
+   */
+  getProp(key: string): string;
+  /**
+   * Sets a property on the molecule
+   * @param key - Property name
+   * @param val - Property value
+   */
+  setProp(key: string, val: string): boolean;
+  /**
+   * Clears a property from the molecule
+   * @param key - Property name
+   */
+  clearProp(key: string): boolean;
+  /**
+   * Returns the list of property names
+   * @param options - Filter options
+   */
+  getPropList(options?: {
+    includePrivate?: boolean;
+    includeComputed?: boolean;
+  }): string[];
+  /** Returns true if the molecule's structure is valid */
+  isValid(): boolean;
+  /** Returns the number of atoms in the molecule */
+  getNumAtoms(): number;
+  /** Returns the number of bonds in the molecule */
+  getNumBonds(): number;
+  /** Returns 0 if no coords, 2 for 2D, 3 for 3D */
+  hasCoords(): 0 | 2 | 3;
+  /** Returns stereo tags (CIP codes) for the molecule */
+  getStereoTags(): RDKitStereoTags;
+  /** Returns the V2000 Molfile representation of the aromatic form */
+  getAromaticForm(): string;
+  /** Returns the V2000 Molfile representation of the Kekule form */
+  getKekuleForm(): string;
+  /** Converts the molecule to aromatic form in place */
+  convertToAromaticForm(): void;
+  /** Converts the molecule to Kekule form in place */
+  convertToKekuleForm(): void;
+  /**
+   * Returns a V2000 Molfile string with explicit hydrogens removed
+   * @param options - Options controlling which hydrogens to remove
+   */
+  removeHs(options?: Partial<RDKitRemoveHsOptions>): string;
+  /**
+   * Removes explicit hydrogens from the molecule in place
+   * @param options - Options controlling which hydrogens to remove
+   */
+  removeHsInPlace(options?: Partial<RDKitRemoveHsOptions>): boolean;
+  /** Returns a V2000 Molfile string with explicit hydrogens added */
+  addHs(): string;
+  /** Adds explicit hydrogens to the molecule in place */
+  addHsInPlace(): boolean;
+  combineWith(other: Mol, options?: {
+    offset: [number, number, number];
+  }): void;
+  zipWith(other: Mol, options?: RDKitMolZipOptions): void;
+  /**
+   * Generates new 2D coordinates for the molecule
+   * @param useCoordGen - Use the CoordGen algorithm
+   */
+  setNewCoords(useCoordGen?: boolean): boolean;
+  /**
+   * Returns a V2000 Molfile string with newly generated coordinates
+   * @param useCoordGen - Use the CoordGen algorithm
+   */
+  getNewCoords(useCoordGen?: boolean): string;
+  /**
+   * Aligns molecule coordinates with a template molecule
+   * @param template - Template molecule to align to
+   * @param options - Alignment options
+   */
+  generateAlignedCoords(template: Mol, options?: Partial<RDKitAlignedCoordsOptions>): string;
+  /**
+   * Normalizes the depiction of the molecule
+   * @param options - Normalization options
+   */
+  normalizeDepiction(options?: {
+    canonicalize?: number;
+    scaleFactor?: number;
+  }): number;
+  /**
+   * Straightens the depiction of the molecule
+   * @param smallRotation - Only apply small rotations
+   */
+  straightenDepiction(smallRotation?: boolean): void;
+  /**
+   * Condenses functional group abbreviations in the molecule
+   * @param options - Abbreviation options
+   */
+  condenseAbbreviations(options?: {
+    maxCoverage?: number;
+    useLinkers?: boolean;
+  }): string;
+  drawToCanvas(canvas: HTMLCanvasElement, options?: Partial<RDKitDepictionDetails>): void;
+  /**
+   * Returns the disconnected fragments of the molecule
+   * @warning The `mols` array contains new `Mol` instances that must be
+   * manually deleted by the caller to avoid memory leaks.
+   * @returns An object with atom/fragment mappings and a `MolArray` of fragments
+   */
+  getFrags(): {
+    mappings: {
+      atomToFrag: number[];
+      fragToAtoms: number[][];
+    };
+    mols: MolArray;
+  };
+  /** Returns a copy of the molecule */
+  copy(): Mol;
+  /**
+   * Deletes the underlying C++ molecule object from memory.
+   *
+   * @see {@link https://emscripten.org/docs/porting/connecting_cpp_and_javascript/embind.html#memory-management | Emscripten docs}
+   */
+  delete(): void;
+  /** Disposable support — allows use with the `using` keyword */
+  [Symbol.dispose](): void;
+}
+//#endregion
+//#region src/reaction.d.ts
+/**
+ * A wrapper around RDKit's JSReaction object providing a typed, camelCase API.
+ *
+ * @remarks
+ * Reaction instances are created via {@link RDKit.getRxn}, not directly by consumers.
+ *
+ * Implements `Disposable` for use with the `using` keyword:
+ * ```ts
+ * using rxn = rdkit.getRxn('[CH3:1][OH:2]>>[CH2:1]=[OH0:2]')!;
+ * const products = rxn.runReactants(['CO']);
+ * ```
+ */
+declare class Reaction implements Disposable {
+  #private;
+  constructor(jsReaction: JSReaction, module: RDKitModule);
+  /**
+   * The underlying JSReaction object for direct access to the raw API.
+   * @throws If the reaction has been deleted.
+   */
+  get jsReaction(): JSReaction;
+  /**
+   * Runs the reaction on a set of reactants.
+   *
+   * Returns an array of product sets. Each product set is an array of `Mol`
+   * instances corresponding to one match between the reactants and the
+   * reaction definition.
+   *
+   * **WARNING:** The caller is responsible for deleting each returned `Mol`
+   * (via `.delete()` or `using`) to avoid memory leaks.
+   *
+   * @param reactants - An array of Mol instances or molecule strings
+   *   (SMILES, MolBlocks, etc.)
+   * @param maxProducts - Maximum number of product sets to return (default: 1000)
+   * @returns An array of product sets, where each set is an array of Mol instances
+   */
+  runReactants(reactants: Mol[] | string[], maxProducts?: number): MolArray[];
+  /**
+   * Returns an SVG depiction of the reaction
+   *
+   * @param options - Drawing options including highlighting.
+   *   When omitted, uses RDKit defaults.
+   */
+  getSvg(options?: Partial<RDKitRxnDepictionDetails>): string;
+  /**
+   * Draws the reaction to an HTML5 canvas with highlighting options
+   * @param canvas - Target canvas element
+   * @param options - Drawing options including dimensions and highlighting
+   */
+  drawToCanvas(canvas: HTMLCanvasElement, options: Partial<RDKitRxnDepictionDetails>): void;
+  /**
+   * Deletes the underlying C++ reaction object from memory.
+   *
+   * @see {@link https://emscripten.org/docs/porting/connecting_cpp_and_javascript/embind.html#memory-management | Emscripten docs}
+   */
+  delete(): void;
+  /** Disposable support — allows use with the `using` keyword */
+  [Symbol.dispose](): void;
+}
+//#endregion
+//#region src/rgd.d.ts
+/**
+ * A row from R-Group Decomposition, mapping labels like `Core`, `R1`, `R2`, …
+ * to Mol instances.
+ */
+type RGDRow = Record<string, Mol>;
+//#endregion
+//#region src/init.d.ts
+/** Options for initializing the RDKit module */
+interface InitRDKitOptions {
+  /**
+   * Custom function to locate the WASM file.
+   * By default, the WASM file is resolved relative to the bundled JS output
+   * using the Vite/Rolldown `?url` import.
+   */
+  locateFile?: () => string;
+}
+/** The main RDKit wrapper interface returned by {@link initRDKit} */
+interface RDKit {
+  /**
+   * Creates a molecule from a variety of input formats.
+   *
+   * @param input - SMILES, SMARTS, MolFile, or JSON string
+   * @param options - Molecule parsing options
+   * @returns A Mol instance, or null if the input is invalid
+   */
+  getMol(input: string, options?: Partial<RDKitGetMolOpt>): Mol | null;
+  /**
+   * Creates a query molecule from a SMARTS string.
+   *
+   * @param input - SMARTS string
+   * @returns A Mol instance, or null if the input is invalid
+   */
+  getQMol(input: string): Mol | null;
+  /**
+   * Computes the Maximum Common Substructure (MCS) of a set of molecules.
+   *
+   * @param mols - An array of Mol instances or SMILES strings
+   * @param options - MCS algorithm options
+   * @returns An MCSResult with match info and a lazy `qmol` getter
+   */
+  getMCS(mols: Mol[] | string[], options?: Partial<RDKitGetMCSOptions>): MCSResult;
+  /**
+   * Creates a Reaction from a reaction SMARTS, SMILES, or RXN block.
+   *
+   * @param input - Reaction SMARTS, SMILES, or RXN block string
+   * @param options - Reaction parsing options
+   * @returns A Reaction instance, or null if the input is invalid
+   */
+  getRxn(input: string, options?: Partial<RDKitRxnDetails>): Reaction | null;
+  /**
+   * Performs R-Group Decomposition on a set of molecules against one or more cores.
+   *
+   * **WARNING:** The caller is responsible for deleting each `Mol` in the
+   * returned rows (via `.delete()` or `using`) to avoid memory leaks.
+   *
+   * @param core - Core structure(s): a SMARTS string, an array of SMARTS strings,
+   *   a Mol instance, or an array of Mol instances
+   * @param molecules - Molecules to decompose: an array of SMILES strings or Mol instances
+   * @param options - R-Group decomposition options
+   * @returns An array of rows, one per molecule. Each row maps R-group labels
+   *   (`Core`, `R1`, `R2`, …) to Mol instances.
+   */
+  getRGD(core: string | string[] | Mol | Mol[], molecules: string[] | Mol[], options?: Partial<RDKitGetRgdOptions>): RGDRow[] | null;
+  molzip(mol1: Mol, mol2: Mol): Mol | null;
+  /** Returns the RDKit version string */
+  version: string;
+  /** The underlying RDKitModule for direct access to the raw API */
+  readonly module: RDKitModule;
+}
+/** Result of a Maximum Common Substructure (MCS) computation */
+interface MCSResult {
+  numAtoms: number;
+  numBonds: number;
+  canceled: boolean;
+  /** SMARTS string(s) — an array when the `StoreAll` option is used */
+  smarts: string | string[];
+  /**
+   * Lazily creates a query Mol from the first SMARTS.
+   * Returns null if SMARTS is empty.
+   *
+   * **WARNING:** The caller is responsible for explicitly deleting this
+   * object (via `.delete()` or `using`) to avoid memory leaks.
+   */
+  get qmol(): Mol | null;
+}
+/**
+ * Initializes the RDKit WASM module and returns a typed wrapper.
+ *
+ * @param options - Initialization options
+ * @returns A promise that resolves to the RDKit wrapper
+ *
+ * @example
+ * ```ts
+ * const rdkit = await initRDKit();
+ * const mol = rdkit.getMol('c1ccccc1');
+ * ```
+ */
+declare function initRDKit(options?: InitRDKitOptions): Promise<RDKit>;
+//#endregion
+export { type InitRDKitOptions, type JSMol, type JSReaction, type MCSResult, Mol, MolArray, type MolList, type RDKit, type RDKitAlignedCoordsOptions, type RDKitAtomPairFPOptions, type RDKitDepictionDetails, type RDKitDescriptors, type RDKitGetMCSOptions, type RDKitGetMolBlockOptions, type RDKitGetMolOpt, type RDKitGetRgdOptions, type RDKitGetSmilesOptions, type RDKitJson, type RDKitMCSResult, type RDKitModule, type RDKitMorganFPOptions, type RDKitPatternFPOptions, type RDKitRdkitFpOptions, type RDKitRemoveHsOptions, type RDKitRxnDetails, type RDKitStereoTags, type RDKitSubstructMatch, type RDKitTopologicalTorsionFPOptions, type RGDRow, Reaction, initRDKit };